From 585bceb8eb8d2c451a8075691c6e39fdb8b09066 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 9 Jul 2024 12:03:00 -0500 Subject: [PATCH 01/23] Add three CRISPR assays --- src/ontology/modules/assays.owl | 143 ++++++++++++++++++++++++++++++ src/ontology/templates/assays.tsv | 3 + 2 files changed, 146 insertions(+) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index d7454e09..a9ec11ca 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -21909,6 +21909,12 @@ + + + + + + @@ -26567,6 +26573,143 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screening assay + An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screening assay + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screen using single RNA-Seq + An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screen using single RNA-Seq + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR perturbation screen using FISH and flow cytometry + An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR perturbation screen using FISH and flow cytometry + + + + diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 8679701b..56a4b328 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -656,6 +656,9 @@ OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay +OBI:0003659 in vitro CRISPR screening assay in vitro CRISPR screening assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell +OBI:0003660 in vitro CRISPR screen using single RNA-Seq in vitro CRISPR screen using single RNA-Seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay +OBI:0003661 in vitro CRISPR perturbation screen using FISH and flow cytometry in vitro CRISPR perturbation screen using FISH and flow cytometry An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay flow cytometry assay|fluorescence in-situ hybridization assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course From cea0b79081b5b5316799f530ae4285111f1a25ea Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 16 Jul 2024 12:26:15 -0500 Subject: [PATCH 02/23] Add snmCT-seq assay --- src/ontology/modules/assays.owl | 2239 +++++++++++++++-------------- src/ontology/templates/assays.tsv | 1 + 2 files changed, 1170 insertions(+), 1070 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index d7454e09..19b5a372 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -664,7 +664,7 @@ - Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. + Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. FM fluorescence imaging fluorescence microscopic imaging @@ -678,7 +678,7 @@ - Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. + Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. CLSM LSCM confocal fluorescence imaging @@ -698,7 +698,7 @@ - Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. + Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. OM light microscopy optical microscopy @@ -718,7 +718,7 @@ - A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. + A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. LC-MS-MS LC-MS/MS LC-MS2 @@ -1441,7 +1441,7 @@ - An assay where the output data is a datum with one of two values denoting success and failure. + An assay where the output data is a datum with one of two values denoting success and failure. PlanAndPlannedProcess Branch OBI branch derived Bernoulli trial @@ -1498,7 +1498,7 @@ Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). - A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. + A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. IEDB PlanAndPlannedProcess Branch IEDB @@ -1518,7 +1518,7 @@ - An assay that produces a picture of an entity. + An assay that produces a picture of an entity. PlanAndPlannedProcess Branch OBI branch derived imaging assay @@ -1576,7 +1576,7 @@ Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. - An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. + An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. IEDB PlanAndPlannedProcess Branch IEDB @@ -1602,7 +1602,7 @@ - An assay that determines interactions between proteins, such as protein-protein binding. + An assay that determines interactions between proteins, such as protein-protein binding. protein-protein interaction detection assay @@ -1631,7 +1631,7 @@ Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. - An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors + An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors Philippe Rocca-Serra TF binding OBI @@ -1659,7 +1659,7 @@ Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 - An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism + An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism Philippe Rocca-Serra metabolite assay metabolomic assay @@ -1745,7 +1745,7 @@ Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319. - An assay that determines the concentration of glucose molecules in a blood serum sample + An assay that determines the concentration of glucose molecules in a blood serum sample Bjoern Peters OBI measuring glucose concentration in blood serum assay @@ -1850,7 +1850,7 @@ Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 - An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. + An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. Philippe Rocca-Serra gene expression profiling @@ -1913,7 +1913,7 @@ genotyping using an Affymetrix chip - An assay with the objective to determine a sequence feature of DNA + An assay with the objective to determine a sequence feature of DNA Bjoern Peters Philippe Rocca-Serra OBI @@ -1990,7 +1990,7 @@ High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 - An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra SNP analysis genotype profiling @@ -2030,7 +2030,7 @@ Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 - An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. + An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. Philippe Rocca-Serra OBI Biomaterial DNA sequence variation detection assay @@ -2062,7 +2062,7 @@ example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output - An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. + An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Alan Ruttenberg Bjoern Peters Helen Parkinson @@ -2123,7 +2123,7 @@ The patients was weighed and mass was determined to be 47 kilograms - An assay that determines the mass of an evaluant + An assay that determines the mass of an evaluant Helen Parkinson OBI mass measurement assay @@ -2153,7 +2153,7 @@ - An electrophysiology assay where the recording location of the electrode is intracellular. + An electrophysiology assay where the recording location of the electrode is intracellular. Frank Gibson Frank Gibson intracellular electrophysiology recording assay @@ -2184,7 +2184,7 @@ The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron - An electrophysiology assay where the recording location of the electrode is extracellular. + An electrophysiology assay where the recording location of the electrode is extracellular. Frank Gibson Helen Parkinson Frank Gibson @@ -2226,7 +2226,7 @@ Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. - An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. + An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. Philippe Rocca-Serra Philippe Rocca-Serra mass spectrometry assay @@ -2298,7 +2298,7 @@ Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. - An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. + An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. Philippe Rocca-Serra chemical pathology detection of analyte in blood sample @@ -2331,7 +2331,7 @@ Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 - An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping + An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping Philippe Rocca-Serra CNV analysis copy number variation profiling assay @@ -2421,7 +2421,7 @@ Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203 - An assay that determines protein expression and translation activity using protein extracts collected from a material entity. + An assay that determines protein expression and translation activity using protein extracts collected from a material entity. Phlippe Rocca-Serra proteomic analysis OBI branch derived @@ -2436,7 +2436,7 @@ Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 - An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. + An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. Philippe Rocca-Serra Nuclear magnetic resonance spectroscopy url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy @@ -2524,7 +2524,7 @@ Illumina (Solexa) sequencing is an example of DNA sequencing - A sequencing assay which determines information on the sequence of a DNA molecule. + A sequencing assay which determines information on the sequence of a DNA molecule. Philippe Rocca-Serra nucleotide sequencing url:https://en.wikipedia.org/wiki/DNA_sequencing @@ -2555,7 +2555,7 @@ Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments + An assay that studies blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology @@ -2644,7 +2644,7 @@ Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 - An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. + An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. Philippe Rocca-Serra DNA methylation profiling OBI branch derived @@ -2694,7 +2694,7 @@ 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. - An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. + An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB ELISA IEDB @@ -2732,7 +2732,7 @@ The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. - A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. + A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. IEDB IEDB BrdU incorporation assay @@ -2782,7 +2782,7 @@ The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. - A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. + A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. IEDB IEDB tritiated thymidine incorporation assay @@ -2968,7 +2968,7 @@ PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. - A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. + A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. Philippe Rocca-Serra Methylated DNA immunoprecipitation sequencing assay url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation @@ -3027,7 +3027,7 @@ PMID: 271968. DNA sequencing with chain-terminating inhibitors. - A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position + A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position Philippe Rocca-Serra Sanger sequencing dye terminator sequencing @@ -3073,7 +3073,7 @@ PMID: 18388294. Single-molecule DNA sequencing of a viral genome. - A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. + A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. Philippe Rocca-Serra true single molecule sequencing url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing @@ -3110,7 +3110,7 @@ - An assay that measures the occurrence of death events in one or more organisms over time + An assay that measures the occurrence of death events in one or more organisms over time survival assessment assay @@ -3174,7 +3174,7 @@ Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. - A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. + A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. IEDB IEDB Edman degradation @@ -3226,7 +3226,7 @@ PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. - A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. + A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing SOLiD sequencing assay @@ -3291,7 +3291,7 @@ PMID: 19275939 - An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin Bjoern Peters Philippe Rocca-Serra chromatin immunoprecipitation sequencing assay @@ -3383,7 +3383,7 @@ PMID: 19527607 - An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. + An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. Philippe Rocca-Serra NuGO OBI plan branch glucose tolerance test @@ -3409,7 +3409,7 @@ ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing). - A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase + A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/Sequencing_by_ligation DNA sequencing by ligation assay @@ -3460,7 +3460,7 @@ PMID: 18987734 - A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. + A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. Philippe Rocca-Serra reversible terminator sequencing Solexa web site (SS_DNAsequencing.pdf document available on july 2009) @@ -3513,7 +3513,7 @@ Pyrosequencing sheds light on DNA sequencing. PMID:1115661 - A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. + A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. Philippe Rocca-Serra url:http://en.wikipedia.org/wiki/Pyrosequencing pyrosequencing assay @@ -3539,7 +3539,7 @@ Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing - A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. + A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. Philippe Rocca-Serra url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html DNA sequencing by synthesis assay @@ -3576,7 +3576,7 @@ Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. - An assay that determines information about an immune response + An assay that determines information about an immune response Bjoern Peters Randi Vita IEDB @@ -3698,7 +3698,7 @@ PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. - A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. + A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. Philippe Rocca-Serra Sagar Jain url:https://en.wikipedia.org/wiki/Bisulfite_sequencing @@ -3774,7 +3774,7 @@ PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. - An assay that measures the amount of antithrombin III in blood. + An assay that measures the amount of antithrombin III in blood. Alan Ruttenberg AT-III assay url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 @@ -3818,7 +3818,7 @@ PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). - An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. + An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. Alan Ruttenberg url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 prothrombin time assay @@ -3849,7 +3849,7 @@ - An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard + An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard AT-III assay url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 antithrombin-III berichrome assay @@ -3880,7 +3880,7 @@ PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). - An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. + An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. Alan Ruttenberg url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 spectrolyse heparin antifactor-Xa assay @@ -3906,7 +3906,7 @@ An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus - An assay that measures neural activity in the caudate nucleus + An assay that measures neural activity in the caudate nucleus Helen Parkinson Dirk Derom, OBI Jessica Turner, NIF @@ -3996,7 +3996,7 @@ The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) - An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. + An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). Alan Ruttenberg OBI call @@ -4030,7 +4030,7 @@ PMID:19696660#The thrombin time was determined using thromboclotin assay kit. - An assay that measures the time between the addition of the thrombin and the clot formation in plasma. + An assay that measures the time between the addition of the thrombin and the clot formation in plasma. Alan Ruttenberg url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 thrombin time assay @@ -4079,7 +4079,7 @@ Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. - An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. + An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. IEDB Philippe Rocca-Serra IEDB @@ -4131,7 +4131,7 @@ The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay. - An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. + An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. Philippe Rocca-Serra Richard Scheuermann northern blot @@ -4169,7 +4169,7 @@ - A serum neutralization of viral infectivity assay which is performed in a 96-well plate. + A serum neutralization of viral infectivity assay which is performed in a 96-well plate. Bjoern Peters Melanie Courtot microneutralization assay @@ -4204,7 +4204,7 @@ - An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. + An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. Philippe Rocca-Serra RNAO single-nucleotide-resolution nucleic acid structure mapping assay @@ -4230,7 +4230,7 @@ Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells. - An assay that quantifies viruses by their hemagglutination activity. + An assay that quantifies viruses by their hemagglutination activity. Bjoern Peters Melanie Courtot Randi Vita @@ -4317,7 +4317,7 @@ - An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. + An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. Bjoern Peters Melanie Courtot influenza neutralization assay @@ -4402,7 +4402,7 @@ Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. - An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. + An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. IEDB IEDB detection of specific nucleic acid polymers with complementary probes @@ -4445,7 +4445,7 @@ Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. - An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors. + An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors. Bjoern Peters Melanie Courtot Randi Vita @@ -4490,7 +4490,7 @@ Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - A cytometry assay that monitors a cell population to track how many are killed by other cells. + A cytometry assay that monitors a cell population to track how many are killed by other cells. IEDB IEDB cell-cell killing assay @@ -4541,7 +4541,7 @@ Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells. - A cell killing assay that measures if and how many target cells are killed within an organism. + A cell killing assay that measures if and how many target cells are killed within an organism. IEDB IEDB in vivo cell killing assay @@ -4575,7 +4575,7 @@ Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. - A cytometry assay which measures the degreee to which input cells are replicating. + A cytometry assay which measures the degreee to which input cells are replicating. IEDB IEDB cell proliferation assay @@ -4683,7 +4683,7 @@ PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. - An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. + An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. Marcus Chibucos Philippe Rocca-Serra Southern blot @@ -4704,7 +4704,7 @@ - An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. + An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. Bjoern Peters Melanie Courtot Q-PCR @@ -4759,7 +4759,7 @@ PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. - A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe Philippe Rocca-Serra RNA ontology DEPC structure mapping assay @@ -4810,7 +4810,7 @@ Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. + A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. IEDB IEDB in vitro cell killing assay @@ -4853,7 +4853,7 @@ CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. - An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. + An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. IEDB IEDB reporter cell line analyte detection bioassay @@ -4916,7 +4916,7 @@ To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. - An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. + An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. IEDB IEDB radio immuno assay @@ -4965,7 +4965,7 @@ - An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. + An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. Bjoern Peters Melanie Courtot RRT-PCR @@ -5005,7 +5005,7 @@ Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. - A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. + A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. IEDB IEDB X-ray crystallography 3D molecular structure determination assay @@ -5035,7 +5035,7 @@ A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. - An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. + An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. IEDB IEDB promoter activity detection by reporter gene assay @@ -5087,7 +5087,7 @@ Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. - A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. + A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. IEDB FACS IEDB @@ -5140,7 +5140,7 @@ Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. - An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest. + An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest. IEDB Luminex assay IEDB @@ -5178,7 +5178,7 @@ Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow. - A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. + A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. IEDB IEDB surface plasmon resonance binding assay @@ -5227,7 +5227,7 @@ The Edinburgh handedness assay is a specific method of determing handedness - An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. + An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. Helen Parkinson handedness test url:http://en.wikipedia.org/wiki/Handedness @@ -5258,7 +5258,7 @@ - An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. + An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. self reported handedness assessment @@ -5269,7 +5269,7 @@ - An assay in which a measurement is made by observing entities located in a live cell. + An assay in which a measurement is made by observing entities located in a live cell. in live cell assay @@ -5307,7 +5307,7 @@ Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. - An assay in which a measurement is made by observing entities located in an organism. + An assay in which a measurement is made by observing entities located in an organism. Bjoern Peters in vivo assay in live organism assay @@ -5352,7 +5352,7 @@ Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. - A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. + A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. IEDB IEDB cell-cell binding detection by flow cytometry assay @@ -5365,7 +5365,7 @@ - An assay in which a measurement is made by observing entities located in a container. + An assay in which a measurement is made by observing entities located in a container. in container assay @@ -5447,7 +5447,7 @@ Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)" - An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. + An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. Alan Ruttenberg Gully Burns (orcid:0000-0003-1493-865X) Jessica Turner @@ -5533,7 +5533,7 @@ PMID:16453415 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse CL3 RNA ontology @@ -5578,7 +5578,7 @@ PMID:2422386 and PMID:2446263 - A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure + A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Philippe Rocca-Serra single nucleotide resolution mapping assay using CMCT probe RNA ontology @@ -5616,7 +5616,7 @@ PMID:6209709 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Fe-MP probe RNA ontology @@ -5667,7 +5667,7 @@ PMID:7002606 and PMID:2446263 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using ENU probe RNA ontology @@ -5746,7 +5746,7 @@ PMID:7031604 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse V1 RNA ontology @@ -5791,7 +5791,7 @@ single nucleotide resolution mapping assay using Kethoxal probe - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe Philippe Rocca-Serra RNA ontology kethoxal structure mapping assay @@ -5841,7 +5841,7 @@ - A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. Philippe Rocca-Serra RNAO and OBI https://github.com/obi-ontology/obi/issues/808 @@ -5886,7 +5886,7 @@ PMID:6159633 and PMID:2446263 - A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using DMS probe RNA Ontology @@ -5970,7 +5970,7 @@ PMID:3773731 - A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Philippe Rocca-Serra DNAse footprinting assay single nucleotide resolution mapping assay using DNAse I @@ -6040,7 +6040,7 @@ - A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. Philippe Rocca-Serra RNAO and OBI single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing @@ -6084,7 +6084,7 @@ PMID:2843807 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Rhodium probe RNA ontology @@ -6168,7 +6168,7 @@ PMID:7527340 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using RNA adenosine deaminase I RNA ontology @@ -6213,7 +6213,7 @@ PMID:2686708 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using Lead probe RNA ontology @@ -6297,7 +6297,7 @@ PMID:6207483 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse T2 RNA ontology @@ -6311,7 +6311,7 @@ - An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. + An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. Bjoern Peters David Osumi Sutherland gene dosage assay @@ -6348,7 +6348,7 @@ PMID: 7862644 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Fe-BABE probe RNA ontology @@ -6432,7 +6432,7 @@ PMID:409999 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse U2 RNA ontology @@ -6453,7 +6453,7 @@ Determination of KD value for an antibody binding a protein using a BIACORE assay. - A binding assay where the specified output is a binding constant + A binding assay where the specified output is a binding constant Bjoern Peters Jason Greenbaum Randi Vita @@ -6492,7 +6492,7 @@ PMID: 15796531 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe Philippe Rocca-Serra SHAPE mapping assay single nucleotide resolution mapping assay using NMIA probe @@ -6531,7 +6531,7 @@ PMID:10772868 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using Terbium probe RNA ontology @@ -6576,7 +6576,7 @@ PMID:2501870 - A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe Philippe Rocca-Serra MOHCA assay OH footprinting assay @@ -6662,7 +6662,7 @@ PMID:114514 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse T1 RNA ontology @@ -6746,7 +6746,7 @@ PMID:363143 - A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Nuclease S1 RNA ontology @@ -6791,7 +6791,7 @@ PMID:3016894 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe Philippe Rocca-Serra RNA Ontology Ruthenium structure mapping assay @@ -6828,7 +6828,7 @@ PMID:10573122 and PMID: 18369975 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity Philippe Rocca-Serra RNA ontology inline probing RNA structure mapping assay @@ -6932,7 +6932,7 @@ Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. - A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. + A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. IEDB IEDB 3D structure determination of bound molecular complex assay @@ -6962,7 +6962,7 @@ Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. - An assay with the objective to characterize the disposition of two or more material entities to form a complex. + An assay with the objective to characterize the disposition of two or more material entities to form a complex. Bjoern Peters Jason Greenbaum Randi Vita @@ -7028,7 +7028,7 @@ - An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). + An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. Alan Ruttenberg age measurement assay @@ -7112,7 +7112,7 @@ - An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. + An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. Chris Stoeckert Jie Zheng Penn Group @@ -7207,7 +7207,7 @@ - An assay that determines the sequence of an RNA molecule. + An assay that determines the sequence of an RNA molecule. Bjoern Peters Bjoern Peters RNA sequencing assay @@ -7220,7 +7220,7 @@ - An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism. + An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism. Bjoern Peters efficacy of in vivo intervention efficacy of epitope intervention experiment @@ -7233,7 +7233,7 @@ - An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. + An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. Bjoern Peters protection from infectious challenge epitope protection from infectious challenge experiment @@ -7252,7 +7252,7 @@ - An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. + An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. Bjoern Peters protection from tumor challenge epitope protection from tumor challenge experiment @@ -7265,7 +7265,7 @@ - An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. + An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. Bjoern Peters protection from challenge epitope protection experiment @@ -7278,7 +7278,7 @@ - An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. + An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. Bjoern Peters burden after infectious challenge epitope protection from infectious challenge experiment based on pathogen burden @@ -7303,7 +7303,7 @@ Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus. - An assay that measures the presence or amount of an infectious agent in an evaluant + An assay that measures the presence or amount of an infectious agent in an evaluant Bjoern Peters Jason Greenbaum Randi Vita @@ -7318,7 +7318,7 @@ - An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. + An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. Bjoern Peters exacerbation assay epitope disease exacerbation experiment @@ -7331,7 +7331,7 @@ - An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. + An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. Bjoern Peters host survival after challenge epitope protection experiment based on survival @@ -7344,7 +7344,7 @@ - An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. + An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. Bjoern Peters decreased disease symptoms after treatment epitope treatment experiment @@ -7387,7 +7387,7 @@ - A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin ArrayExpress production team EFO:0002764 ChIP-chip by SNP array assay @@ -7430,7 +7430,7 @@ - A transcription profiling by array assay that uses a tiling path array. + A transcription profiling by array assay that uses a tiling path array. James Malone EFO:0002769 transcription profiling by tiling array assay @@ -7467,7 +7467,7 @@ - A genotyping assay that uses a high througput sequencer + A genotyping assay that uses a high througput sequencer James Malone EFO:0002771 genotyping by high throughput sequencing assay @@ -7519,7 +7519,7 @@ - An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin Bjoern Petesr James Malone ChIP-on-chip assay @@ -7558,7 +7558,7 @@ - A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology ArrayExpress production team Helen Parkinson James Malone @@ -7584,7 +7584,7 @@ - An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. + An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. James Malone transcription profiling by high throughput sequencing EFO:0002770 @@ -7622,7 +7622,7 @@ - A genotyping assay that uses an array + A genotyping assay that uses an array ArrayExpress production team EFO:0002767 genotyping by array assay @@ -7641,7 +7641,7 @@ - An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. + An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. James Malone EFO:0001033 translation profiling assay @@ -7714,7 +7714,7 @@ - An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. + An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. James Malone EFO:0001030 RNAi profiling by array assay @@ -7809,7 +7809,7 @@ - An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. + An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. James Malone EFO:0002765 proteomic profiling by array assay @@ -7852,7 +7852,7 @@ - A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology James Malone EFO:0002759 DNA methylation profiling by array assay @@ -7952,7 +7952,7 @@ - An assay that analyses the microRNA component of the transcriptome using a microRNA array. + An assay that analyses the microRNA component of the transcriptome using a microRNA array. James Malone EFO:0000753 microRNA profiling by array assay @@ -7995,7 +7995,7 @@ - A transcription profiling assay that uses reverse transcription PCR (RT-PCR). + A transcription profiling assay that uses reverse transcription PCR (RT-PCR). Anna Farne EFO:0002943 transcription profiling by RT-PCR assay @@ -8084,7 +8084,7 @@ - An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. + An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. James Malone array CGH EFO:0000749 @@ -8134,7 +8134,7 @@ - A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin ArrayExpress production team EFO:0002762 ChIP-chip by tiling array assay @@ -8171,7 +8171,7 @@ - A transcription profiling assay that uses array technology. + A transcription profiling assay that uses array technology. James Malone RNA profiling by array assay EFO:0002768 @@ -8211,7 +8211,7 @@ Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated. - A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. + A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. IEDB IEDB phage display binding assay @@ -8236,7 +8236,7 @@ - An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response + An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response IEDB tolerance induction IEDB @@ -8267,7 +8267,7 @@ - A binding assay that uses radioactivity detection as an indicator of binding. + A binding assay that uses radioactivity detection as an indicator of binding. Bjoern Peters Randi Vita IEDB @@ -8298,7 +8298,7 @@ - A binding assay that uses fluorescence detection as an indicator of binding. + A binding assay that uses fluorescence detection as an indicator of binding. Bjoern Peters Randi Vita IEDB @@ -8332,7 +8332,7 @@ Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. - An assay in which a material's fluorescence is determined. + An assay in which a material's fluorescence is determined. IEDB IEDB fluorescence detection assay @@ -8358,7 +8358,7 @@ Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._ - A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. + A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. Bjoern Peters Randi Vita IEDB @@ -8388,7 +8388,7 @@ Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._ - A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. + A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. IEDB IEDB competitive inhibition of binding assay @@ -8417,7 +8417,7 @@ - An organism detection assay that identifies the organism species in a specimen. + An organism detection assay that identifies the organism species in a specimen. Chris Stoeckert Jie Zheng organism identification assay @@ -8482,7 +8482,7 @@ Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column. - An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. + An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. IEDB IEDB analytical chromatography @@ -8523,7 +8523,7 @@ Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure. - An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. + An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. IEDB IEDB electron microscopy imaging assay @@ -8560,7 +8560,7 @@ Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye. - A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. + A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. IEDB IEDB immuno staining assay @@ -8601,7 +8601,7 @@ A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell ._ - A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. + A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. IEDB IEDB calorimetric binding assay @@ -8672,7 +8672,7 @@ The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). - A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). + A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). IEDB IEDB antibody binding detection by fluorescence quenching @@ -8715,7 +8715,7 @@ Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. PMID:17513562 - A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. + A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. Marcus Chibucos Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/Two-hybrid_screening @@ -8766,7 +8766,7 @@ Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457 - An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. + An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. Marcus Chibucos Philippe Rocca-Serra PMID:18079728 @@ -8804,7 +8804,7 @@ Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. PMID:11518275 - An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. + An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. Marcus Chibucos Philippe Rocca-Serra RNAse protection assay @@ -8844,7 +8844,7 @@ Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. PMID:21918373 - An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. + An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. Marcus Chibucos Philippe Rocca-Serra EMSA @@ -8893,7 +8893,7 @@ - An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. + An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. Marcus Chibucos Philippe Rocca-Serra PMID:17430206 @@ -8937,7 +8937,7 @@ Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846 - A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). + A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). Marcus Chibucos Philippe Rocca-Serra nano-CAGE @@ -9012,7 +9012,7 @@ 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160 - A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome + A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome Marcus Chibucos Philippe Rocca-Serra CAGE @@ -9057,7 +9057,7 @@ Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. PMID:10627486 - An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. + An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. Marcus Chibucos Philippe Rocca-Serra Y2H @@ -9102,7 +9102,7 @@ The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. PMID:20300944 - A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. + A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. Marcus Chibucos Philippe Rocca-Serra SRS @@ -9141,7 +9141,7 @@ Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 - An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. + An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. Marcus Chibucos Philippe Rocca-Serra Y1H @@ -9186,7 +9186,7 @@ A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 - An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence + An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence Marcus Chibucos Philippe Rocca-Serra B1H @@ -9273,7 +9273,7 @@ Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 - An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity + An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity Marcus Chibucos Philippe Rocca-Serra https://github.com/obi-ontology/obi/issues/788| @@ -9305,7 +9305,7 @@ Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 - An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. + An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. Marcus Chibucos Philippe Rocca-Serra MSP @@ -9350,7 +9350,7 @@ Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 - An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. + An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. Marcus Chibucos Philippe Rocca-Serra AIMS assay @@ -9402,7 +9402,7 @@ Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 - An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. + An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. Marcus Chibucos Philippe Rocca-Serra ISH @@ -9447,7 +9447,7 @@ - An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). + An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). Marcus Chibucos Philippe Rocca-Serra cytochalasin-induced inhibition of actin polymerization assay @@ -9510,7 +9510,7 @@ Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. - A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. + A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. IEDB antibody inhibition of antibody binding IEDB @@ -9556,7 +9556,7 @@ Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. - An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. + An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. IEDB IEDB immunoprecipitation assay @@ -9672,7 +9672,7 @@ Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] - An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. + An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. Chris Stoeckert Jie Zheng Venkat Malladi @@ -9690,7 +9690,7 @@ Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] - An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. + An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. Chris Stoeckert Jie Zheng Venkat Malladi @@ -9797,7 +9797,7 @@ Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] - A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. + A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. Chris Stoeckert Jie Zheng Venkat Malladi @@ -9922,7 +9922,7 @@ Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] - An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. + An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10069,7 +10069,7 @@ Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] - An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). + An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi @@ -10188,7 +10188,7 @@ Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] - An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. + An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10289,7 +10289,7 @@ Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] - An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. + An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10413,7 +10413,7 @@ Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] - An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. + An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10443,7 +10443,7 @@ Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] - A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. + A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10492,7 +10492,7 @@ Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. - A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. + A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10608,7 +10608,7 @@ Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] - An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. + An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10760,7 +10760,7 @@ Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] - An assay which quantifies the timing of DNA replication as a function of genome position using array technology. + An assay which quantifies the timing of DNA replication as a function of genome position using array technology. Chris Stoeckert Jie Zheng Venkat Malladi @@ -10872,7 +10872,7 @@ Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] - An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). + An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi @@ -10997,7 +10997,7 @@ van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] - An assay that measures the organization of chromosomes at the genome-wide scale. + An assay that measures the organization of chromosomes at the genome-wide scale. Chris Stoeckert Jie Zheng Venkat Malladi @@ -11145,7 +11145,7 @@ Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139_�_144. [PMID:19966280] - An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. + An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. Chris Stoeckert Jie Zheng Venkat Malladi @@ -11187,7 +11187,7 @@ Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] - An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). + An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi @@ -11297,7 +11297,7 @@ Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767 - A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. + A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. Chris Stoeckert Jie Zheng Venkat Malladi @@ -11387,7 +11387,7 @@ Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] - A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. + A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. Chris Stoeckert Jie Zheng Venkat Malladi @@ -11485,7 +11485,7 @@ Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] - An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease + An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease Chris Stoeckert Jie Zheng Venkat Malladi @@ -11545,7 +11545,7 @@ Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] - A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site + A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site Bjoern Peters Chris Stoeckert Jie Zheng @@ -11613,7 +11613,7 @@ - A transcription profiling assay that quantifies the microRNA species within a biological sample. + A transcription profiling assay that quantifies the microRNA species within a biological sample. Chris Stoeckert Jie Zheng Venkat Malladi @@ -11698,7 +11698,7 @@ PMID: 6379641 - An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed + An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed Bjoern Peters Philippe Rocca-Serra chromatin immunoprecipitation assay @@ -11739,7 +11739,7 @@ http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html - An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation + An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation Philippe Rocca-Serra http://sourceforge.net/p/obi/obi-terms/707/ assay using chromatin immunoprecipitation @@ -11773,7 +11773,7 @@ PMID:20679230 PMID:25367129 - An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. + An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. Philippe Rocca-Serra environmental gene survey targeted gene survey @@ -11819,7 +11819,7 @@ Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. - A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. + A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. IEDB IEDB hydrogen/deuterium exchange footprinting assay @@ -11870,7 +11870,7 @@ An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. - An assay that counts and/or measures characteristics of cells. + An assay that counts and/or measures characteristics of cells. IEDB IEDB cytometry assay @@ -11936,7 +11936,7 @@ - An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. + An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. IEDB IEDB immunoblot assay @@ -11961,7 +11961,7 @@ - A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. + A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. IEDB IEDB fluorescence quenching binding assay @@ -12008,7 +12008,7 @@ Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival. - An assay in which the effect of a targeted process (the intervention) on an organism is tested. + An assay in which the effect of a targeted process (the intervention) on an organism is tested. The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay. IEDB IEDB @@ -12022,7 +12022,7 @@ Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide. - An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. + An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. Should have data about disease severity as readout; could just use disease for now IEDB IEDB @@ -12036,7 +12036,7 @@ Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide. - An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. + An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. should have challenge as intervention IEDB IEDB @@ -12050,7 +12050,7 @@ Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide. - An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. + An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. should have tolerance induction as intervention IEDB IEDB @@ -12064,7 +12064,7 @@ Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. - An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. + An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. should have treatment as intervention IEDB IEDB @@ -12106,7 +12106,7 @@ Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. - An analyte assay where binding of the analyte to immobilized matrix is measured. + An analyte assay where binding of the analyte to immobilized matrix is measured. IEDB IEDB microarray assay @@ -12179,7 +12179,7 @@ Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. - An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. + An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. IEDB IEDB immunohistochemistry @@ -12282,7 +12282,7 @@ - An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. + An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. Chris Stoeckert Jie Zheng DNA methylation ChIP-chip @@ -12339,7 +12339,7 @@ - A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). + A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). Chris Stoeckert Jie Zheng expression MPSS @@ -12461,7 +12461,7 @@ - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. Chris Stoeckert Jie Zheng histone modification ChIP-chip @@ -12583,7 +12583,7 @@ - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Chris Stoeckert Jie Zheng histone modification ChIP-Seq @@ -12705,7 +12705,7 @@ - A transcription factor binding site assay that utilizes ChIP-chip technology. + A transcription factor binding site assay that utilizes ChIP-chip technology. Chris Stoeckert Jie Zheng TF Binding ChIP-chip @@ -12827,7 +12827,7 @@ - A transcription factor binding site assay that utilizes ChIP-seq technology. + A transcription factor binding site assay that utilizes ChIP-seq technology. Chris Stoeckert Jie Zheng TF Binding ChIP-Seq @@ -12851,7 +12851,7 @@ - An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. + An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. Chris Stoeckert Jie Zheng Penn group @@ -12915,7 +12915,7 @@ PMID:15905473 - A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. + A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. Chris Stoeckert Janos Demeter Jie Zheng @@ -12957,7 +12957,7 @@ PMID:19521816 - A genotyping by array assay that uses tiling array technology. + A genotyping by array assay that uses tiling array technology. Chris Stoeckert Janos Demeter Jie Zheng @@ -12999,7 +12999,7 @@ PMID:20080586 - A genotyping by array assay that uses SNP array technology. + A genotyping by array assay that uses SNP array technology. Chris Stoeckert Janos Demeter Jie Zheng @@ -13074,7 +13074,7 @@ pmid:20811459 - A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes + A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes Chris Stoeckert Janos Demeter PARS @@ -13090,7 +13090,7 @@ pmid:23580730 - An RNA-seq assay that combines TL-seq with polysome fractionation + An RNA-seq assay that combines TL-seq with polysome fractionation Chris Stoeckert Janos Demeter TATL-seq @@ -13106,7 +13106,7 @@ pmid:23580730 - An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. + An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. Chris Stoeckert Janos Demeter TL-seq @@ -13121,7 +13121,7 @@ - A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. + A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. Chris Stoeckert Janos Demeter PMF @@ -13139,7 +13139,7 @@ pmid:23580730 - An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. + An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. Chris Stoeckert Janos Demeter OBI:0000870 @@ -13154,7 +13154,7 @@ pmid:17873876 - An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays + An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays Chris Stoeckert Janos Demeter https://sourceforge.net/p/obi/obi-terms/725/ @@ -13168,7 +13168,7 @@ Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 - A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. + A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. Chris Stoeckert Jie Zheng Venkat Malladi @@ -13186,7 +13186,7 @@ Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. - An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. + An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. Chris Stoeckert Jie Zheng Venkat Malladi @@ -13216,7 +13216,7 @@ Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111. - A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. + A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. Chris Stoeckert Jie Zheng Venkat Malladi @@ -13234,7 +13234,7 @@ Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. - An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. + An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. Chris Stoeckert Jie Zheng Venkat Malladi @@ -13252,7 +13252,7 @@ Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. - A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. + A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. Chris Stoeckert Jie Zheng Venkat Malladi @@ -13270,7 +13270,7 @@ Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 - A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. + A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. Chris Stoeckert Jie Zheng Venkat Malladi @@ -13287,7 +13287,7 @@ - An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). + An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi @@ -13305,7 +13305,7 @@ Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. - A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. + A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. Chris Stoeckert Jie Zheng Venkat Malladi @@ -13324,7 +13324,7 @@ - An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. + An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. Chris Stoeckert Paul D. Thomas reporter gene detection assay @@ -13341,7 +13341,7 @@ PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules" - A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. + A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. Paul D. Thomas Yang Chai enhancer reporter gene assay @@ -13358,7 +13358,7 @@ PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue" - A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. + A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. Paul D. Thomas Yang Chai chromatin modifier binding site identification by ChIP-Seq assay @@ -13375,7 +13375,7 @@ PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" - An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. + An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. Paul D. Thomas Yang Chai transcript expression location detection by fluorescent HCR. @@ -13391,7 +13391,7 @@ - A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. + A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. Bjoern Peters Chris Stoeckert Jason Hilton @@ -13411,7 +13411,7 @@ MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants. - A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. + A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. Chris Stoeckert David Bujold Capture Methylome @@ -13438,7 +13438,7 @@ Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. - An assay using carboxyfluorescein succinimidyl ester staining. + An assay using carboxyfluorescein succinimidyl ester staining. IEDB CFSE assay IEDB @@ -13452,7 +13452,7 @@ Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds. - A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. + A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. IEDB biolayer interferometry, BLI IEDB @@ -13466,7 +13466,7 @@ Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein - A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. + A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. IEDB SAXS IEDB @@ -13480,7 +13480,7 @@ - An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. + An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. Chris Stoeckert Jason Hilton eCLIP @@ -13495,7 +13495,7 @@ - An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. + An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. Chris Stoeckert Jason Hilton Mark A. Miller @@ -13514,7 +13514,7 @@ - An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. + An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. Chris Stoeckert Jason Hilton Bru-seq @@ -13529,7 +13529,7 @@ - An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. + An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. Chris Stoeckert Jason Hilton BruChase-seq @@ -13581,7 +13581,7 @@ Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining reflective of the level of expression of those surface receptors. - A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. + A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. ImmPort CyTOF mass cytometry assay @@ -13624,7 +13624,7 @@ On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. - An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. + An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. ImmPort HPLC PMID:9491555 @@ -13638,7 +13638,7 @@ WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. - A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. ImmPort WGS @@ -13654,7 +13654,7 @@ DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified. - A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). + A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). ImmPort WES PMID:25827230 @@ -13696,7 +13696,7 @@ Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy. - An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. + An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. ImmPort PMID:21685355 microscopy assay @@ -13733,7 +13733,7 @@ T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells. - A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). + A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). ImmPort MLR PMID:14969764 @@ -13747,7 +13747,7 @@ DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself. - A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. + A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. ImmPort KIR typing @@ -13762,7 +13762,7 @@ Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both_ according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size_ were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. - A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. + A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. IEDB MHC typing, HLA typing @@ -13777,7 +13777,7 @@ - An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. + An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. Rob Nash dynamic SILAC pulse SILAC @@ -13822,7 +13822,7 @@ - An assay to determine the temperature of an evaluant. + An assay to determine the temperature of an evaluant. Bjoern Peters Chris Stoeckert OBI @@ -13852,7 +13852,7 @@ - An assay to determine the volume of an evaluant. + An assay to determine the volume of an evaluant. Bjoern Peters Chris Stoeckert OBI @@ -13866,7 +13866,7 @@ - A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. + A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. Chris Stoeckert Jason Hilton microRNA counts @@ -13884,7 +13884,7 @@ - An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. + An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. Chris Stoeckert Jason Hilton BruUV-seq @@ -13901,7 +13901,7 @@ - An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. + An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. Chris Stoeckert Jason Hilton circulome-seq @@ -13919,7 +13919,7 @@ Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens - An analyte assay that measures the presence or amount of antibodies to a specified antigen. + An analyte assay that measures the presence or amount of antibodies to a specified antigen. Bjoern Peters Chris Stoeckert James Overton @@ -13994,7 +13994,7 @@ - An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36) Bjoern Peters Chris Stoeckert @@ -14073,7 +14073,7 @@ - An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. https://www.cdc.gov/mmwr/preview/mmwrhtml/00042810.htm Bjoern Peters Chris Stoeckert @@ -14136,7 +14136,7 @@ - An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14198,7 +14198,7 @@ - An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14260,7 +14260,7 @@ - An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. + An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14322,7 +14322,7 @@ - An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. + An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14384,7 +14384,7 @@ - An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. + An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14446,7 +14446,7 @@ - An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. + An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14508,7 +14508,7 @@ - An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. + An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14550,7 +14550,7 @@ - An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. + An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. Bjoern Peters Chris Stoeckert James Overton @@ -14592,7 +14592,7 @@ - An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. + An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. Bjoern Peters Chris Stoeckert James Overton @@ -14634,7 +14634,7 @@ - An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. + An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. Bjoern Peters Chris Stoeckert James Overton @@ -14696,7 +14696,7 @@ - An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. + An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. Bjoern Peters Chris Stoeckert James Overton @@ -14758,7 +14758,7 @@ - An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. + An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. Bjoern Peters Chris Stoeckert James Overton @@ -14777,7 +14777,7 @@ - A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. + A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. Chris Stoeckert Jason Hilton Mint-ChIP @@ -14794,7 +14794,7 @@ - A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ + A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ Rebecca Jackson SELEX PMID:21720957 @@ -14807,7 +14807,7 @@ - An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. + An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. Bjoern Peters doi:10.1002/3527600906.mcb.200300025 footprinting assay @@ -14819,7 +14819,7 @@ - An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis + An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis Rebecca Jackson OBI development call DNAse footprinting assay @@ -14831,7 +14831,7 @@ - A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. + A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. Rebecca Jackson ECO:0001095 PMID:9043710 @@ -14844,7 +14844,7 @@ - An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. + An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. Rebecca Jackson OBI development call protein localization assay @@ -14856,7 +14856,7 @@ - A protein localization assay that determines the specific location of a protein in a living tissue sample. + A protein localization assay that determines the specific location of a protein in a living tissue sample. Rebecca Jackson PMID:14686950 tissue-based protein localization assay @@ -14892,7 +14892,7 @@ - A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. + A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. Rebecca Jackson ECO subcellular protein localization assay @@ -14904,7 +14904,7 @@ - An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. + An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. Rebecca Jackson ECO subcellular protein immunohistochemistry assay @@ -14929,7 +14929,7 @@ - A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. + A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. Chris Stoeckert PMID:18388953 ChIP-qPCR assay @@ -14941,7 +14941,7 @@ - A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. + A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. Chris Stoeckert PMID:20541015 genomic SELEX @@ -14953,7 +14953,7 @@ - An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. + An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. Bjoern Peters dot blot analysis PMID:10473518 @@ -14966,7 +14966,7 @@ - A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. + A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. Bjoern Peters Northwestern analysis Northwestern assay @@ -14980,7 +14980,7 @@ - A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. + A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. Bjoern Peters PMID:26404144 Southwestern blot assay @@ -15026,7 +15026,7 @@ - An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed + An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed Bjoern Peters immunocytochemistry @@ -15061,7 +15061,7 @@ - An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. + An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. Rebecca Jackson ATP quantitation assay cell viability ATP quantitation assay @@ -15075,7 +15075,7 @@ - An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). + An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues. Gully Burns url:https://en.wikipedia.org/wiki/Electrophysiology @@ -15112,7 +15112,7 @@ - An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. + An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. Gully Burns ECO:0006012 url:http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 @@ -15150,7 +15150,7 @@ - A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. + A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. Gully Burns ECO:0006015 url:https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch @@ -15187,7 +15187,7 @@ - A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. + A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. Gully Burns url:https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch cell-attached patch clamp assay @@ -15223,7 +15223,7 @@ - A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. + A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. Gully Burns url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ url:https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch @@ -15260,7 +15260,7 @@ - A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. + A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. Gully Burns url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ url:https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch @@ -15297,7 +15297,7 @@ - An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. + An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. Gully Burns url:https://en.wikipedia.org/wiki/Voltage_clamp voltage clamp assay @@ -15333,7 +15333,7 @@ - The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. + The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. Gully Burns TEVC url:https://en.wikipedia.org/wiki/Voltage_clamp#Two-electrode_voltage_clamp_using_microelectrodes @@ -15370,7 +15370,7 @@ - The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. + The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. Gully Burns COVG PMID:9711615 @@ -15383,7 +15383,7 @@ - The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. + The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. Gully Burns url:https://en.wikipedia.org/wiki/Electrophysiology#Current_clamp current clamp assay @@ -15395,7 +15395,7 @@ - An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. + An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. Gully Burns EEG electroencephalography @@ -15476,7 +15476,7 @@ - An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. + An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. Can be used on any cell, not just neurons. Gully Burns url:http://www.thieme.com/media/samples/pubid-80418214.pdf @@ -15489,7 +15489,7 @@ - An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. + An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. Gully Burns multi-unit recording @@ -15587,7 +15587,7 @@ - An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. + An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. Gully Burns doi:10.1007/978-1-4614-7320-6_723-1 local field potential recording @@ -15612,7 +15612,7 @@ - An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. + An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. Rebecca Jackson PMID:26463381 RNA interactome capture @@ -15624,7 +15624,7 @@ - A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. + A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. Jie Zheng WFM url:http://bitesizebio.com/19409/the-many-flavors-of-widefield-microscopy/ @@ -15650,7 +15650,7 @@ - An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. + An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. Chris S PMID:8327891 nuclear ligation assay @@ -15668,7 +15668,7 @@ - A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. + A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. Chris S 3C assay PMID:11847345 @@ -15695,7 +15695,7 @@ - A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. + A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. Chris S PMID:20461051 Hi-C assay @@ -15707,7 +15707,7 @@ - An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques. + An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques. physical examination of an organism @@ -15775,7 +15775,7 @@ - A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. + A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. Jie Zheng PMID:21770468 hydroxyl-radical footprinting assay @@ -15851,7 +15851,7 @@ - A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. + A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. Jie Zheng MPE-Fe(II) footprinting PMID:6225070 @@ -15900,7 +15900,7 @@ - A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. + A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. Rebecca Jackson PMID:23378648 url:https://en.wikipedia.org/wiki/Primer_extension @@ -15919,7 +15919,7 @@ - An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. + An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. Rebecca Jackson PRO-Seq precision nuclear run-on and sequencing assay @@ -15940,7 +15940,7 @@ - A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. + A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Rebecca Jackson 4C assay circularized chromosome conformation capture assay @@ -15968,7 +15968,7 @@ - A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. + A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. Rebecca Jackson haplotype reconstruction by Hi-C assay PMID:19815776 @@ -15983,7 +15983,7 @@ - A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. + A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. Dan Berrios Junhyong Kim Stephen A. Fisher @@ -16044,7 +16044,7 @@ - An organism detection assay that uses a differential medium to achieve its objective. + An organism detection assay that uses a differential medium to achieve its objective. John Judkins EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm differential medium assay @@ -16104,7 +16104,7 @@ - A histological assay that is intended to check for the presence or level of a specific disease. + A histological assay that is intended to check for the presence or level of a specific disease. OBI histopathology assay @@ -16121,7 +16121,7 @@ - An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. + An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. Jason Hilton Mark A. Miller mRNA-seq @@ -16142,7 +16142,7 @@ - An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. + An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. Jason Hilton Mark A. Miller polyA-depleted RNA-seq @@ -16165,7 +16165,7 @@ Novel transcript forms were assessed by isoform sequencing. - A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. + A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. ISO-seq url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/ isoform sequencing @@ -16258,7 +16258,7 @@ - A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. + A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. Rebecca Jackson 3C-seq assay PMID:23411633 @@ -16321,7 +16321,7 @@ "In an attempt to define the mechanism of insulin-regulated glucose transporter 4 (Glut4) translocation, we have developed an in vitro reconstitution assay... insulin-induced Glut4 translocation can be reconstituted in vitro to a limited extent by using isolated membranes." (PMID:10611313) - An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. + An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. Rebecca Jackson reconstitution experiment url:https://jcs.biologists.org/content/132/4/jcs227488 @@ -16348,7 +16348,7 @@ An in vitro reconstituted mouse transcription system helped identify an NF-Y interacting promoter as essential for high-level expression from the R2 promoter. (PMID:11502214) - A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. + A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. Rebecca Jackson PMID:9237163 https://github.com/obi-ontology/obi/issues/1059 @@ -16362,7 +16362,7 @@ - A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). Rebecca Jackson WMS @@ -16404,7 +16404,7 @@ "Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid Acyrthosiphon pisum. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed Ap-crt genes encoding a calreticulin and the gut specific Ap-cath-L gene encoding a cathepsin-L." (PMID:17903251) - A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. + A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. Rebecca Jackson RNA interference knockdown assay RNAi gene knockdown assay @@ -16420,7 +16420,7 @@ - An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. + An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. Dan Berrios DRS direct RNA-seq @@ -16438,7 +16438,7 @@ Single-cell RNA sequencing (scRNA-seq) assays provide the expression profiles of individual cells. - An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. + An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. Dan Berrios scRNA-seq Anna Maria Masci @@ -16524,7 +16524,7 @@ Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs - An assay that uses a Giemsa stain to characterize cells. + An assay that uses a Giemsa stain to characterize cells. Chris Stoeckert Jie Zheng https://github.com/obi-ontology/obi/issues/1093 @@ -16619,7 +16619,7 @@ - An organism detection assay that detects microorganisms in a blood specimen. + An organism detection assay that detects microorganisms in a blood specimen. John Judkins https://github.com/obi-ontology/obi/issues/1064 blood microbiology assay @@ -16632,7 +16632,7 @@ - An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. + An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. Damion Dooley MPRA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364389/ @@ -16647,7 +16647,7 @@ “Inhibition of MERS-CoV-spike-mediated pseudovirus entry by the HKU4 S1 domain “ (from https://doi.org/10.1073/pnas.1405889111); “protease treatment did not enhance pseudotype entry in the absence of host receptor “; “bat-derived cell lines derived from other species were infected with VSV-reporter particles pseudotyped with chimeric spikes and luciferase was measured as readout for cell entry” (from https://doi.org/10.1038/s41564-020-0688-y) ; “teicoplanin could inhibit the entry of HIV-1-2019-nCoV-S pseudoviruses with the IC50 value of 1.66 uM” (from https://doi.org/10.1101/2020.02.05.935387) - An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. + An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. Thomas Lemberger pseudotype cell entry pseudotype entry @@ -16722,7 +16722,7 @@ - An assay that uses polymerase chain reaction technique to amplify DNA. + An assay that uses polymerase chain reaction technique to amplify DNA. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 @@ -16825,7 +16825,7 @@ - An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. + An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. VEuPathDB RFLP restriction fragment length polymorphism @@ -16877,7 +16877,7 @@ - An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. + An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. VEuPathDB DNA finger printing DNA fingerprint @@ -16906,7 +16906,7 @@ - An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. + An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. VEuPathDB resistance identification/monitoring MIRO:20000001 @@ -16928,7 +16928,7 @@ - An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. + An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. VEuPathDB monitoring known mutations MIRO:20000096 @@ -16961,7 +16961,7 @@ - An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. + An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. VEuPathDB metabolic resistance assay MIRO:20000003 @@ -16983,7 +16983,7 @@ - An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. + An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. VEuPathDB bioassay MIRO:20000058 @@ -17016,7 +17016,7 @@ - An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. + An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. VEuPathDB alpha esterase activity assay IRO:0000149 @@ -17049,7 +17049,7 @@ - An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. + An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. VEuPathDB beta esterase activity assay IRO:0000150 @@ -17082,7 +17082,7 @@ - An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. + An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. VEuPathDB AChE activity assay AChE assay @@ -17119,7 +17119,7 @@ - An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). + An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). VEuPathDB GST related assay MIRO:20000083 @@ -17152,7 +17152,7 @@ - An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. + An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. VEuPathDB pNPA assay MIRO:20000019 @@ -17174,7 +17174,7 @@ - An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. + An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. VEuPathDB mixed-function oxidase assay MIRO:20000062 @@ -17196,7 +17196,7 @@ - An insecticide resistance bioassay without the use of any synergist. + An insecticide resistance bioassay without the use of any synergist. VEuPathDB direct bioassay MIRO:20000044 @@ -17218,7 +17218,7 @@ - An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. + An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. VEuPathDB topical application assay IRO:0000155 @@ -17240,7 +17240,7 @@ - A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. + A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. VEuPathDB diagnostic test MIRO:20000075 @@ -17262,7 +17262,7 @@ - A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. + A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. VEuPathDB dose response test MIRO:20000076 @@ -17284,7 +17284,7 @@ - A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. + A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. VEuPathDB time response test MIRO:20000013 @@ -17330,7 +17330,7 @@ - A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. + A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. VEuPathDB CDC bottle bioassay MIRO:20000009 @@ -17352,7 +17352,7 @@ - A direct insecticide resistance diagnostic assay uses WHO cone kit. + A direct insecticide resistance diagnostic assay uses WHO cone kit. VEuPathDB cone DT MIRO:20000039 @@ -17374,7 +17374,7 @@ - A direct insecticide resistance diagnostic assay uses WHO paper kit. + A direct insecticide resistance diagnostic assay uses WHO paper kit. VEuPathDB WHO paper kit DT MIRO:20000041 @@ -17396,7 +17396,7 @@ - A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. + A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. VEuPathDB WHO larvicide DT MIRO:20000049 @@ -17442,7 +17442,7 @@ - An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. + An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. VEuPathDB bottle bioassay DR test MIRO:20000011 @@ -17464,7 +17464,7 @@ - An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. + An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. VEuPathDB WHO larvicide DR test MIRO:20000050 @@ -17486,7 +17486,7 @@ - An insecticide resistance dose response assay using WHO paper kit. + An insecticide resistance dose response assay using WHO paper kit. VEuPathDB WHO paper kit DR test MIRO:20000048 @@ -17532,7 +17532,7 @@ - An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. + An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. VEuPathDB bottle bioassay TR test MIRO:20000030 @@ -17554,7 +17554,7 @@ - An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. + An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. VEuPathDB WHO paper kit TR test MIRO:20000036 @@ -17616,7 +17616,7 @@ - An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. + An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. VEuPathDB ARMS Amplification Refractory Mutation System @@ -17686,7 +17686,7 @@ - An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. + An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. VEuPathDB PIRA-PCR Primer Introduced Restriction Analysis PCR @@ -17751,7 +17751,7 @@ - An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. + An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. VEuPathDB gene mutation detection by nested PCR IRO:0000127 @@ -17813,7 +17813,7 @@ - An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. + An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. VEuPathDB MIRO:20000103 https://github.com/obi-ontology/obi/issues/1117 @@ -17874,7 +17874,7 @@ - An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. + An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. VEuPathDB gene mutation detection by LDR-FMA ligase detection reaction-fluorescent microsphere assay @@ -17937,7 +17937,7 @@ - An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. VEuPathDB PASA PCR amplification of specific alleles @@ -18001,7 +18001,7 @@ - An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. + An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. VEuPathDB MIRO:20000102 https://github.com/obi-ontology/obi/issues/1117 @@ -18075,7 +18075,7 @@ - An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. + An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. VEuPathDB PCR-RFLP MIRO:20000113 @@ -18137,7 +18137,7 @@ - An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). VEuPathDB Short Interspersed Elements PCR IRO:0000013 @@ -18172,7 +18172,7 @@ - An organism detection assay that detects pathogens. + An organism detection assay that detects pathogens. VEuPathDB pathogen detection method IRO:0000137 @@ -18205,7 +18205,7 @@ - A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. + A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. VEuPathDB VectorTest IRO:0000138 @@ -18238,7 +18238,7 @@ - A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. + A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. VEuPathDB Rapid Analyte Measurement Platform IRO:0000164 @@ -18277,7 +18277,7 @@ - A pathogen detection assay that is based on loop-mediated isothermal amplification. + A pathogen detection assay that is based on loop-mediated isothermal amplification. VEuPathDB Loop-mediated isothermal amplification IRO:0000165 @@ -18303,7 +18303,7 @@ - An assay that analyzes the specimen taken from blood meal fed organism, such as insect. + An assay that analyzes the specimen taken from blood meal fed organism, such as insect. VEuPathDB blood meal analysis IRO:0000135 @@ -18331,7 +18331,7 @@ - A blood meal assay that uses a counter current immunoelectrophoresis technique. + A blood meal assay that uses a counter current immunoelectrophoresis technique. VEuPathDB CIE countercurrent immunoelectrophoresis @@ -18388,7 +18388,7 @@ - A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. + A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. VEuPathDB DNA based blood meal finger printing VEuPathDB @@ -18405,7 +18405,7 @@ - An organism detection assay that is based on the size of organism. + An organism detection assay that is based on the size of organism. VEuPathDB by size IRO:0000145 @@ -18421,7 +18421,7 @@ - An organism detection assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. + An organism detection assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. VEuPathDB cross mating experiment MIRO:30000036 @@ -18437,7 +18437,7 @@ - An organism detection assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. + An organism detection assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. VEuPathDB cytological chromosome examination MIRO:30000037 @@ -18459,7 +18459,7 @@ - An organism detection assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. + An organism detection assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. VEuPathDB isoenzyme electrophoresis MIRO:30000038 @@ -18475,7 +18475,7 @@ - An organism detection assay that is based on examination of morphology and the use of specific taxonomic keys to determine the species of the specimen. + An organism detection assay that is based on examination of morphology and the use of specific taxonomic keys to determine the species of the specimen. VEuPathDB morphological examination MIRO:30000039 @@ -18497,7 +18497,7 @@ - An organism detection assay that is based on PCR. + An organism detection assay that is based on PCR. VEuPathDB PCR-based species identification MIRO:30000040 @@ -18519,7 +18519,7 @@ - An organism detection assay that is based on DNA hybrdization. + An organism detection assay that is based on DNA hybrdization. VEuPathDB species specific DNA hybridization MIRO:30000041 @@ -18535,7 +18535,7 @@ - An organism detection assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. + An organism detection assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. VEuPathDB salinity tolerance tests MIRO:30000042 @@ -18574,7 +18574,7 @@ - Precision nuclear run-on and sequencing to detect Pol II initiation sites + Precision nuclear run-on and sequencing to detect Pol II initiation sites Bonita Lam PRO-CAP https://github.com/obi-ontology/obi/issues/1102 @@ -18599,7 +18599,7 @@ - An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. + An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18621,7 +18621,7 @@ - An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. + An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18636,7 +18636,7 @@ - An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. + An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18653,7 +18653,7 @@ snATAC-seq can be used to dissect heterogeneity and delineate gene regulatory sequences in complex tissues, and uncover both the cell types and the regulatory elements in each cell type without prior knowledge. - An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. + An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. Mark Andrew Miller, ORCID:0000-0001-9076-6066 snATAC-seq http://www.biorxiv.org/content/early/2017/07/06/159137 @@ -18685,7 +18685,7 @@ - An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18701,7 +18701,7 @@ - An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. + An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. Mark Andrew Miller, ORCID:0000-0001-9076-6066 scATAC-seq http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html @@ -18768,7 +18768,7 @@ - A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. + A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18784,7 +18784,7 @@ - An analyte assay to study presence, concentration, or amount of cytokines. + An analyte assay to study presence, concentration, or amount of cytokines. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18857,7 +18857,7 @@ - A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. + A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18873,7 +18873,7 @@ - A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18889,7 +18889,7 @@ Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2. - An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest + An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA) Mark Andrew Miller, ORCID:0000-0001-9076-6066 IA @@ -18924,7 +18924,7 @@ - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18953,7 +18953,7 @@ - A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. + A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -18983,7 +18983,7 @@ - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19012,7 +19012,7 @@ - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19041,7 +19041,7 @@ - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19070,7 +19070,7 @@ - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19101,7 +19101,7 @@ - A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. + A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19117,7 +19117,7 @@ - A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. + A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19148,7 +19148,7 @@ - A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. + A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19177,7 +19177,7 @@ - A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. + A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19195,7 +19195,7 @@ - A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. + A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19213,7 +19213,7 @@ - A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. + A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19246,7 +19246,7 @@ - A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. + A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19263,7 +19263,7 @@ - A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. + A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19292,7 +19292,7 @@ - A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. + A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19329,7 +19329,7 @@ - A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. + A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19348,7 +19348,7 @@ - A type of assay that identifies compounds that inhibit the activity of kinases. + A type of assay that identifies compounds that inhibit the activity of kinases. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19366,7 +19366,7 @@ - A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. + A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19382,7 +19382,7 @@ - A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. + A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19398,7 +19398,7 @@ - A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. + A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19415,7 +19415,7 @@ - A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. + A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19432,7 +19432,7 @@ - A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. + A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19461,7 +19461,7 @@ - A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. + A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19478,7 +19478,7 @@ - A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. + A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19495,7 +19495,7 @@ - A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. + A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -19518,7 +19518,7 @@ PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. - A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. + A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. Bonita Lam cHi-C PMID:29979818 @@ -19578,7 +19578,7 @@ - An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. + An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. Alexander D. Bartnik, ORCID:0000-0001-9676-7377 Alexander D. Diehl, ORCID:0000-0001-9990-8331 Lauren M. Wishnie, ORCID:0000-0002-7245-3450 @@ -19622,7 +19622,7 @@ - An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. + An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. Rebecca Jackson CAT scan CT scan @@ -19662,7 +19662,7 @@ - An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. + An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. Rebecca Jackson PET scan positron emission tomography scan @@ -19677,7 +19677,7 @@ - A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. + A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. Rebecca Jackson TCR repertoire sequencing assay bulk TCR assay @@ -19692,7 +19692,7 @@ - A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. + A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. Rebecca Jackson Antibody repertoire sequencing assay BCR repertoire sequencing assay @@ -19723,7 +19723,7 @@ - An assay that measures ferritin + An assay that measures ferritin James A. Overton, ORCID:0000-0001-5139-5557 OBI ferritin assay @@ -19750,7 +19750,7 @@ - An assay that measures fibrinogen + An assay that measures fibrinogen James A. Overton, ORCID:0000-0001-5139-5558 OBI fibrinogen assay @@ -19790,7 +19790,7 @@ - An analyte assay that measures the abundance of iron + An analyte assay that measures the abundance of iron James A. Overton, ORCID:0000-0001-5139-5559 OBI iron assay @@ -19830,7 +19830,7 @@ - An analyte assay that measures the abundance of ionized calcium + An analyte assay that measures the abundance of ionized calcium James A. Overton, ORCID:0000-0001-5139-5561 OBI ionized calcium assay @@ -19870,7 +19870,7 @@ - An analyte assay that measures the abundance of transferrin + An analyte assay that measures the abundance of transferrin James A. Overton, ORCID:0000-0001-5139-5562 OBI transferrin assay @@ -19910,7 +19910,7 @@ - An analyte assay that measures the abundance of uric acid + An analyte assay that measures the abundance of uric acid James A. Overton, ORCID:0000-0001-5139-5563 OBI uric acid assay @@ -19950,7 +19950,7 @@ - An analyte assay that measures the abundance of globulin + An analyte assay that measures the abundance of globulin James A. Overton, ORCID:0000-0001-5139-5564 OBI globulin assay @@ -19977,7 +19977,7 @@ - A cytometry assay that measures the abundance and/or characteristics of myelocytes + A cytometry assay that measures the abundance and/or characteristics of myelocytes James A. Overton, ORCID:0000-0001-5139-5565 OBI myelocyte assay @@ -20004,7 +20004,7 @@ - A cytometry assay that measures the abundance and/or characteristics of metamyelocytes + A cytometry assay that measures the abundance and/or characteristics of metamyelocytes James A. Overton, ORCID:0000-0001-5139-5566 OBI metamyelocyte assay @@ -20031,7 +20031,7 @@ - A cytometry assay that measures the proportion of red blood cells + A cytometry assay that measures the proportion of red blood cells James A. Overton, ORCID:0000-0001-5139-5567 OBI hematocrit assay @@ -20058,7 +20058,7 @@ - A cytometry assay that measures the abundance and/or characteristics of promyelocytes + A cytometry assay that measures the abundance and/or characteristics of promyelocytes James A. Overton, ORCID:0000-0001-5139-5568 OBI promyelocyte assay @@ -20085,7 +20085,7 @@ - A cytometry assay that measures the abundance and/or characteristics of basophils + A cytometry assay that measures the abundance and/or characteristics of basophils James A. Overton, ORCID:0000-0001-5139-5569 OBI basophil assay @@ -20112,7 +20112,7 @@ - A cytometry assay that measures the abundance and/or characteristics of neutrophils + A cytometry assay that measures the abundance and/or characteristics of neutrophils James A. Overton, ORCID:0000-0001-5139-5570 OBI neutrophil assay @@ -20139,7 +20139,7 @@ - A cytometry assay that measures the abundance and/or characteristics of eosinophils + A cytometry assay that measures the abundance and/or characteristics of eosinophils James A. Overton, ORCID:0000-0001-5139-5571 OBI eosinophil assay @@ -20166,7 +20166,7 @@ - A cytometry assay that measures the abundance and/or characteristics of lymphocytes + A cytometry assay that measures the abundance and/or characteristics of lymphocytes James A. Overton, ORCID:0000-0001-5139-5572 OBI lymphocyte assay @@ -20193,7 +20193,7 @@ - A cytometry assay that measures the abundance and/or characteristics of monocytes + A cytometry assay that measures the abundance and/or characteristics of monocytes James A. Overton, ORCID:0000-0001-5139-5573 OBI monocyte assay @@ -20220,7 +20220,7 @@ - A cytometry assay that measures the abundance and/or characteristics of reticulocytes + A cytometry assay that measures the abundance and/or characteristics of reticulocytes James A. Overton, ORCID:0000-0001-5139-5574 OBI reticulocyte assay @@ -20247,7 +20247,7 @@ - A cytometry assay that measures the abundance and/or characteristics of macrophages + A cytometry assay that measures the abundance and/or characteristics of macrophages James A. Overton, ORCID:0000-0001-5139-5577 OBI macrophage assay @@ -20274,7 +20274,7 @@ - A cytometry assay that measures the abundance and/or characteristics of platelets + A cytometry assay that measures the abundance and/or characteristics of platelets James A. Overton, ORCID:0000-0001-5139-5578 OBI platelet assay @@ -20286,7 +20286,7 @@ - A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. + A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. John Judkins TaqMan MIRO:20000102 @@ -20307,7 +20307,7 @@ genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. - A genotyping assay that uses polymerase chain reaction. + A genotyping assay that uses polymerase chain reaction. Chris Stoeckert, ORCID:0000-0002-5714-991X Jie Zheng, ORCID:0000-0002-2999-0103 VEuPathDB @@ -20322,7 +20322,7 @@ - A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. + A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -20339,7 +20339,7 @@ - A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. + A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -20357,7 +20357,7 @@ Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. - A physical examination of an organism that has the objective to determine the severity of coma in a patient. + A physical examination of an organism that has the objective to determine the severity of coma in a patient. John Judkins https://github.com/obi-ontology/obi/issues/1357 John Judkins @@ -20428,7 +20428,7 @@ - An assay that detects Plasmodium gametocytes in a specimen. + An assay that detects Plasmodium gametocytes in a specimen. Chris Stoeckert Jie Zheng John Judkins @@ -20501,7 +20501,7 @@ - An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. + An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. Chris Stoeckert Jie Zheng malaria rapid diagnosis test @@ -20574,7 +20574,7 @@ - An assay that detects parasite in a specimen. + An assay that detects parasite in a specimen. Chris Stoeckert Jie Zheng VEuPathDB @@ -20646,7 +20646,7 @@ - An organism detection assay that detects microorganisms in a feces specimen. + An organism detection assay that detects microorganisms in a feces specimen. John Judkins stool test for microorganisms VEuPathDB @@ -20698,7 +20698,7 @@ - An assay that has a blood specimen as evaulant. + An assay that has a blood specimen as evaulant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 @@ -20745,7 +20745,7 @@ - A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. + A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 @@ -20792,7 +20792,7 @@ - A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. + A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 @@ -20843,7 +20843,7 @@ - An assay that has a urine specimen as evaluant. + An assay that has a urine specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 @@ -20869,7 +20869,7 @@ - A parasite detection by PCR assay that identifies the species of parasite. + A parasite detection by PCR assay that identifies the species of parasite. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 @@ -20901,7 +20901,7 @@ - A parasite detection assay that uses PCR. + A parasite detection assay that uses PCR. Chris Stoeckert Jie Zheng VEuPathDB @@ -20949,7 +20949,7 @@ - An assay that detects body temperature of an organism. + An assay that detects body temperature of an organism. Chris Stoeckert Jie Zheng VEuPathDB @@ -20963,7 +20963,7 @@ - A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength. + A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21005,7 +21005,7 @@ - An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength. + An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21022,7 +21022,7 @@ - An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21039,7 +21039,7 @@ - An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21068,7 +21068,7 @@ - An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells. + An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21084,7 +21084,7 @@ - A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section. + A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21101,7 +21101,7 @@ - A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels. + A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21131,7 +21131,7 @@ - An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. + An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21245,7 +21245,7 @@ - A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. + A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21264,7 +21264,7 @@ - A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry. + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21292,7 +21292,7 @@ - A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. + A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21309,7 +21309,7 @@ - A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. + A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21325,7 +21325,7 @@ - A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses. + A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21342,7 +21342,7 @@ - A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry. + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21359,7 +21359,7 @@ - A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray. + A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21389,7 +21389,7 @@ - A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression. + A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21406,7 +21406,7 @@ - A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components. + A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21423,7 +21423,7 @@ - An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation. + An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21440,7 +21440,7 @@ - A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. + A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21457,7 +21457,7 @@ - A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. + A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21474,7 +21474,7 @@ - An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. + An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21490,7 +21490,7 @@ - A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. + A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21508,7 +21508,7 @@ - A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing. + A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21528,7 +21528,7 @@ - A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds. + A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds. Michelle Giglio Rebecca Jackson Suvarna Nadendla @@ -21545,7 +21545,7 @@ - An analyte assay that uses aptamers to detect protein analytes in serum. + An analyte assay that uses aptamers to detect protein analytes in serum. Bjoern Peters Randi Vita Rohloff JC, et al. Nucleic acid ligands with protein-like side chains: modified aptamers and their uses as diagnostic and therapeutic agents. Mol Ther Nucleic Acids. 2014;3:e201. @@ -21560,7 +21560,7 @@ - A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR. + A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR. Bjoern Peters Hector Guzman-Orozco Randi Vita @@ -21589,7 +21589,7 @@ - An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. + An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. Bjoern Peters Hector Guzman-Orozco Randi Vita @@ -21616,7 +21616,7 @@ - A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. + A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. CMI-PB CMI-PB https://github.com/obi-ontology/obi/issues/1399 @@ -21640,7 +21640,7 @@ - A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. + A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. CMI-PB CMI-PB https://github.com/obi-ontology/obi/issues/1399 @@ -21679,7 +21679,7 @@ - An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. + An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. Bjoern Peters Hector Guzman-Orozco IEDB @@ -21717,7 +21717,7 @@ - A 3D molecular structure determination assay that uses electron microscopy imaging. + A 3D molecular structure determination assay that uses electron microscopy imaging. Bjoern Peters Hector Guzman-Orozco IEDB @@ -21782,7 +21782,7 @@ - A 3D structure determination assay that determines the 3-dimensional configuration of a cell. + A 3D structure determination assay that determines the 3-dimensional configuration of a cell. Hector Guzman-Orozco Patrick Ray Hector Guzman-Orozco @@ -21816,7 +21816,7 @@ - A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. + A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. Hector Guzman-Orozco Patrick Ray Hector Guzman-Orozco @@ -21849,7 +21849,7 @@ - A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. + A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. Hector Guzman-Orozco Patrick Ray Patrick Ray @@ -21881,7 +21881,7 @@ - A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. + A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. Patrick Ray MORF genetic sparse labeling https://biccn.org/teams/u01-yang @@ -21897,7 +21897,7 @@ - A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). + A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). The representation of the morphology (3D structure) of a neuron can be a summary of various measurements relating to the dimensions of the neuron in question. Hector Guzman-Orozco Patrick Ray @@ -21913,7 +21913,7 @@ - An albumin assay that measures the concentration of albumin in a specimen. + An albumin assay that measures the concentration of albumin in a specimen. James A. Overton albumin concentration assay @@ -21924,7 +21924,7 @@ - A basophil assay that measures the percentage of basophils in a specimen. + A basophil assay that measures the percentage of basophils in a specimen. James A. Overton basophil percentage assay @@ -21935,7 +21935,7 @@ - A calcium cation assay that measures the concentration of calcium cations in a specimen. + A calcium cation assay that measures the concentration of calcium cations in a specimen. James A. Overton calcium cation concentration assay @@ -21946,7 +21946,7 @@ - A chloride assay that measures the concentration of chloride in a specimen. + A chloride assay that measures the concentration of chloride in a specimen. James A. Overton chloride concentration assay @@ -21957,7 +21957,7 @@ - A cholesterol assay that measures the concentration of cholesterol in a specimen. + A cholesterol assay that measures the concentration of cholesterol in a specimen. James A. Overton cholesterol concentration assay @@ -21968,7 +21968,7 @@ - A creatinine assay that measures the concentration of creatinine in a specimen. + A creatinine assay that measures the concentration of creatinine in a specimen. James A. Overton creatinine concentration assay @@ -21979,7 +21979,7 @@ - An eosinophil assay that measures the percentage of eosinophils in a specimen. + An eosinophil assay that measures the percentage of eosinophils in a specimen. James A. Overton eosinophil percentage assay @@ -21990,7 +21990,7 @@ - A globulin assay that measures the concentration of globulin in a specimen. + A globulin assay that measures the concentration of globulin in a specimen. James A. Overton globulin concentration assay @@ -22001,7 +22001,7 @@ - A hemoglobin assay that measures the amount of hemoglobin in a specimen. + A hemoglobin assay that measures the amount of hemoglobin in a specimen. James A. Overton hemoglobin concentration assay @@ -22012,7 +22012,7 @@ - A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen. + A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen. James A. Overton high-density lipoprotein cholesterol concentration assay @@ -22023,7 +22023,7 @@ - An iron assay that measures the concentration of iron cation in a specimen. + An iron assay that measures the concentration of iron cation in a specimen. James A. Overton iron concentration assay @@ -22034,7 +22034,7 @@ - A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen. + A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen. James A. Overton low-density lipoprotein cholesterol concentration assay @@ -22045,7 +22045,7 @@ - A lymphocyte assay that measures the percentage of lymphocytes in a specimen. + A lymphocyte assay that measures the percentage of lymphocytes in a specimen. James A. Overton lymphocyte percentage assay @@ -22056,7 +22056,7 @@ - A metamyelocyte assay that measures the number of metamyelocytes in a specimen. + A metamyelocyte assay that measures the number of metamyelocytes in a specimen. James A. Overton metamyelocyte count assay @@ -22067,7 +22067,7 @@ - A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen. + A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen. James A. Overton metamyelocyte percentage assay @@ -22078,7 +22078,7 @@ - A methemoglobin assay that measures the percentage of methemoglobin in a specimen. + A methemoglobin assay that measures the percentage of methemoglobin in a specimen. James A. Overton methemoglobin percentage assay @@ -22089,7 +22089,7 @@ - A monocyte assay that measures the percentage of monocytes in a specimen. + A monocyte assay that measures the percentage of monocytes in a specimen. James A. Overton monocyte percentage assay @@ -22100,7 +22100,7 @@ - A myelocyte assay that measures the number of myelocytes in a specimen. + A myelocyte assay that measures the number of myelocytes in a specimen. James A. Overton myelocyte count assay @@ -22111,7 +22111,7 @@ - A neutrophil assay that measures the percentage of neutrophils in a specimen. + A neutrophil assay that measures the percentage of neutrophils in a specimen. James A. Overton neutrophil percentage assay @@ -22122,7 +22122,7 @@ - A phosphate ion assay that measures the concentration of phosphate ions in a specimen. + A phosphate ion assay that measures the concentration of phosphate ions in a specimen. James A. Overton phosphate ion concentration assay @@ -22133,7 +22133,7 @@ - A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen. + A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen. James A. Overton potassium(1+) concentration assay @@ -22144,7 +22144,7 @@ - A reticulocyte assay that measures the percentage of reticulocytes in a specimen. + A reticulocyte assay that measures the percentage of reticulocytes in a specimen. James A. Overton reticulocyte percentage assay @@ -22155,7 +22155,7 @@ - A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen. + A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen. James A. Overton sodium(1+) concentration assay @@ -22166,7 +22166,7 @@ - A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen. + A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen. James A. Overton thyroid stimulating hormone concentration assay @@ -22177,7 +22177,7 @@ - A triglyceride assay that measures the concentration of triglycerides in a specimen. + A triglyceride assay that measures the concentration of triglycerides in a specimen. James A. Overton triglyceride concentration assay @@ -22188,7 +22188,7 @@ - A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen. + A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen. James A. Overton 3,3',5'-triiodothyronine concentration assay @@ -22199,7 +22199,7 @@ - A fibrinogen assay that measures the concentration of fibrinogen in a specimen. + A fibrinogen assay that measures the concentration of fibrinogen in a specimen. James A. Overton fibrinogen concentration assay @@ -22210,7 +22210,7 @@ - A thyroxine assay that measures the concentration of free thyroxine in a specimen. + A thyroxine assay that measures the concentration of free thyroxine in a specimen. James A. Overton free thyroxine concentration assay @@ -22221,7 +22221,7 @@ - A thyroxine assay that measures the concentration of total thyroxine in a specimen. + A thyroxine assay that measures the concentration of total thyroxine in a specimen. James A. Overton total thyroxine concentration assay @@ -22232,7 +22232,7 @@ - A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen. + A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen. James A. Overton direct bilirubin concentration assay @@ -22243,7 +22243,7 @@ - A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen. + A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen. James A. Overton indirect bilirubin concentration assay @@ -22254,7 +22254,7 @@ - A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen. + A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen. James A. Overton total bilirubin concentration assay @@ -22265,7 +22265,7 @@ - A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes. + A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes. James A. Overton mean cell hemoglobin assay @@ -22276,7 +22276,7 @@ - A hemoglobin assay that measures the concentration of hemoglobin in a specimen. + A hemoglobin assay that measures the concentration of hemoglobin in a specimen. James A. Overton mean cell hemoglobin concentration assay @@ -22287,7 +22287,7 @@ - A platelet assay that measures the average volume of platelets in a specimen. + A platelet assay that measures the average volume of platelets in a specimen. James A. Overton mean platelet volume assay @@ -22333,7 +22333,7 @@ - A neutrophil assay that measures the number of immature neutrophils in a specimen. + A neutrophil assay that measures the number of immature neutrophils in a specimen. James A. Overton immature neutrophil count assay @@ -22379,7 +22379,7 @@ - An neutrophil assay that measures the percentage of immature neutrophils in a specimen. + An neutrophil assay that measures the percentage of immature neutrophils in a specimen. James A. Overton immature neutrophil percentage assay @@ -22425,7 +22425,7 @@ - An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen. + An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen. James A. Overton nucleated erythrocyte percentage assay @@ -22436,7 +22436,7 @@ - An erythrocyte assay that measures the average volume of erythrocytes in a specimen. + An erythrocyte assay that measures the average volume of erythrocytes in a specimen. James A. Overton mean cell volume assay @@ -22482,7 +22482,7 @@ - A cytometry assay that measures the abundance and/or characteristics of erythrocytes. + A cytometry assay that measures the abundance and/or characteristics of erythrocytes. James A. Overton erythrocyte assay @@ -22528,7 +22528,7 @@ - A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes. + A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes. James A. Overton manual hematocrit assay @@ -22563,7 +22563,7 @@ - An analyte assay that measures the abundance of adiponectin + An analyte assay that measures the abundance of adiponectin James A. Overton adiponectin assay @@ -22598,7 +22598,7 @@ - An adiponectin assay that measures the concentration of adiponectin in a specimen. + An adiponectin assay that measures the concentration of adiponectin in a specimen. James A. Overton adiponectin concentration assay @@ -22633,7 +22633,7 @@ - An analyte assay that measures the abundance of creatine + An analyte assay that measures the abundance of creatine James A. Overton creatine assay @@ -22668,7 +22668,7 @@ - A creatine assay that measures the concentration of creatine in a specimen. + A creatine assay that measures the concentration of creatine in a specimen. James A. Overton creatine concentration assay @@ -22703,7 +22703,7 @@ - An analyte assay that measures the abundance of estradiol + An analyte assay that measures the abundance of estradiol James A. Overton estradiol assay @@ -22738,7 +22738,7 @@ - An estradiol assay that measures the concentration of estradiol in a specimen. + An estradiol assay that measures the concentration of estradiol in a specimen. James A. Overton estradiol concentration assay @@ -22773,7 +22773,7 @@ - An analyte assay that measures the abundance of leptin + An analyte assay that measures the abundance of leptin James A. Overton leptin assay @@ -22784,7 +22784,7 @@ - An leptin assay that measures the concentration of leptin in a specimen. + An leptin assay that measures the concentration of leptin in a specimen. James A. Overton leptin concentration assay @@ -22819,7 +22819,7 @@ - An analyte assay that measures the abundance of lipoprotein + An analyte assay that measures the abundance of lipoprotein James A. Overton lipoprotein concentration assay @@ -22854,7 +22854,7 @@ - A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen. + A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen. James A. Overton high-density lipoprotein concentration assay @@ -22889,7 +22889,7 @@ - A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen. + A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen. James A. Overton low-density lipoprotein concentration assay @@ -22924,7 +22924,7 @@ - A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen. + A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen. James A. Overton very-low-density lipoprotein concentration assay @@ -22959,7 +22959,7 @@ - An analyte assay that measures the abundance of luteinizing hormone + An analyte assay that measures the abundance of luteinizing hormone James A. Overton luteinizing hormone assay @@ -22970,7 +22970,7 @@ - A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen. + A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen. James A. Overton luteinizing hormone concentration assay @@ -23005,7 +23005,7 @@ - An analyte assay that measures the abundance of nitrite + An analyte assay that measures the abundance of nitrite James A. Overton nitrite assay @@ -23016,7 +23016,7 @@ - A nitrite assay that measures the concentration of nitrite in a specimen. + A nitrite assay that measures the concentration of nitrite in a specimen. James A. Overton nitrite concentration assay @@ -23051,7 +23051,7 @@ - An analyte assay that measures the abundance of phospholipid + An analyte assay that measures the abundance of phospholipid James A. Overton phospholipid assay @@ -23062,7 +23062,7 @@ - A phospholipid assay that measures the concentration of phospholipids in a specimen. + A phospholipid assay that measures the concentration of phospholipids in a specimen. James A. Overton phospholipid concentration assay @@ -23097,7 +23097,7 @@ - An analyte assay that measures the abundance of progesterone + An analyte assay that measures the abundance of progesterone James A. Overton progesterone assay @@ -23108,7 +23108,7 @@ - A progesterone assay that measures the concentration of progesterone in a specimen. + A progesterone assay that measures the concentration of progesterone in a specimen. James A. Overton progesterone concentration assay @@ -23143,7 +23143,7 @@ - An analyte assay that measures the abundance of testosterone + An analyte assay that measures the abundance of testosterone James A. Overton testosterone assay @@ -23154,7 +23154,7 @@ - A testosterone assay that measures the concentration of testosterone in a specimen. + A testosterone assay that measures the concentration of testosterone in a specimen. James A. Overton testosterone concentration assay @@ -23189,7 +23189,7 @@ - An analyte assay that measures the abundance of bile salt + An analyte assay that measures the abundance of bile salt James A. Overton bile salt assay @@ -23200,7 +23200,7 @@ - A bile salt assay that measures the concentration of bile salt in a specimen. + A bile salt assay that measures the concentration of bile salt in a specimen. James A. Overton bile salt concentration assay @@ -23235,7 +23235,7 @@ - An analyte assay that measures the abundance of fatty acid + An analyte assay that measures the abundance of fatty acid James A. Overton fatty acid assay @@ -23246,7 +23246,7 @@ - A fatty acid assay that measures the concentration of free fatty acids in a specimen. + A fatty acid assay that measures the concentration of free fatty acids in a specimen. James A. Overton free fatty acid concentration assay @@ -23281,7 +23281,7 @@ - An analyte assay that measures the abundance of insulin + An analyte assay that measures the abundance of insulin James A. Overton insulin assay @@ -23292,7 +23292,7 @@ - A insulin assay that measures the concentration of insulin in a specimen. + A insulin assay that measures the concentration of insulin in a specimen. James A. Overton insulin concentration assay @@ -23327,7 +23327,7 @@ - An analyte assay that measures the abundance of follicle stimulating hormone + An analyte assay that measures the abundance of follicle stimulating hormone James A. Overton follicle stimulating hormone assay @@ -23338,7 +23338,7 @@ - A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen. + A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen. James A. Overton follicle stimulating hormone concentration assay @@ -23349,7 +23349,7 @@ - A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen. + A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen. James A. Overton total lymphocyte count assay @@ -23360,7 +23360,7 @@ - A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen. + A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen. James A. Overton total lymphocyte percentage assay @@ -23384,7 +23384,7 @@ - A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies. + A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies. Hector Guzman-Orozco FLUOROSPOT https://en.wikipedia.org/wiki/ELISpot#Mechanism_of_FluoroSpot @@ -23405,7 +23405,7 @@ - A proteomics profiling assay that detects proteins in a blood plasma specimen. + A proteomics profiling assay that detects proteins in a blood plasma specimen. Hector Guzman-Orozco CMI-PB https://github.com/obi-ontology/obi/issues/1414 @@ -23419,7 +23419,7 @@ - A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers. + A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers. Hector Guzman-Orozco https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955771/ https://github.com/obi-ontology/obi/issues/1414 @@ -23471,7 +23471,7 @@ - An assay that has a cerebrospinal fluid specimen as evaluant. + An assay that has a cerebrospinal fluid specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23522,7 +23522,7 @@ - An assay that has an endotracheal aspirate specimen as evaluant. + An assay that has an endotracheal aspirate specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23573,7 +23573,7 @@ - An assay that has an induced sputum specimen as evaluant. + An assay that has an induced sputum specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23624,7 +23624,7 @@ - An assay that has a lung specimen as evaluant. + An assay that has a lung specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23675,7 +23675,7 @@ - An assay that has a milk specimen as evaluant. + An assay that has a milk specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23726,7 +23726,7 @@ - An assay that has a feces specimen as evaluant. + An assay that has a feces specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23777,7 +23777,7 @@ - An assay that has an umbilical cord blood specimen as evaluant. + An assay that has an umbilical cord blood specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23828,7 +23828,7 @@ - An assay that has a saliva specimen as evaluant. + An assay that has a saliva specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23875,7 +23875,7 @@ - An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen. + An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23922,7 +23922,7 @@ - An organism detection assay that detects microorganisms in an endotracheal aspirate specimen. + An organism detection assay that detects microorganisms in an endotracheal aspirate specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -23969,7 +23969,7 @@ - An organism detection assay that detects microorganisms in an induced sputum specimen. + An organism detection assay that detects microorganisms in an induced sputum specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -24016,7 +24016,7 @@ - An organism detection assay that detects microorganisms in a lung specimen. + An organism detection assay that detects microorganisms in a lung specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -24063,7 +24063,7 @@ - An organism detection assay that detects microorganisms in a pleural fluid specimen. + An organism detection assay that detects microorganisms in a pleural fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -24110,7 +24110,7 @@ - An organism detection assay that detects microorganisms in an umbilical cord blood specimen. + An organism detection assay that detects microorganisms in an umbilical cord blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -24169,7 +24169,7 @@ - An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen. + An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -24216,7 +24216,7 @@ - An organism detection assay that detects microorganisms in a urine specimen. + An organism detection assay that detects microorganisms in a urine specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 @@ -24229,7 +24229,7 @@ - A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. + A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. John Judkins multiplexed real time polymerase chain reaction assay VEuPathDB @@ -24243,7 +24243,7 @@ - A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. + A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. John Judkins multiplexed real time reverse-transcription polymerase chain reaction assay VEuPathDB @@ -24346,7 +24346,7 @@ Testing the effectiveness of drugs or antibodies against parasite transmission. - An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. + An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1439 @@ -24365,7 +24365,7 @@ - A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. + A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. John Judkins NCIT:C85736 https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html @@ -24438,7 +24438,7 @@ PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes. - An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. + An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. John Judkins ALS assay antibodies from lymphocyte supernatant assay @@ -24454,7 +24454,7 @@ - A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm. + A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm. Michelle Giglio Suvarna Nadendla TSA-seq @@ -24471,7 +24471,7 @@ - An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed. + An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed. Michelle Giglio Suvarna Nadendla DamID assay @@ -24501,7 +24501,7 @@ - A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site. + A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site. Michelle Giglio Suvarna Nadendla 4DN DCIC @@ -24516,7 +24516,7 @@ - A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains. + A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains. Michelle Giglio Suvarna Nadendla NAD-seq @@ -24533,7 +24533,7 @@ - A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts. + A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts. Michelle Giglio Suvarna Nadendla EFO:0009976 @@ -24549,7 +24549,7 @@ - A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step. + A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step. Michelle Giglio Suvarna Nadendla EFO:0008808 @@ -24565,7 +24565,7 @@ - A Hi-C assay performed on massively multiplexed single-cell samples. + A Hi-C assay performed on massively multiplexed single-cell samples. Michelle Giglio Suvarna Nadendla sci-Hi-C @@ -24582,7 +24582,7 @@ - A Hi-C assay performed on isolated nuclei. + A Hi-C assay performed on isolated nuclei. Michelle Giglio Suvarna Nadendla sn-Hi-C @@ -24599,7 +24599,7 @@ - A Hi-C assay performed on a single cell. + A Hi-C assay performed on a single cell. Michelle Giglio Suvarna Nadendla EFO:0009979 @@ -24614,7 +24614,7 @@ - A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. Michelle Giglio Suvarna Nadendla 4DN DCIC @@ -24629,7 +24629,7 @@ - A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer. + A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer. Michelle Giglio Suvarna Nadendla MC-3C @@ -24646,7 +24646,7 @@ - A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions. + A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions. Michelle Giglio Suvarna Nadendla TrAC-Loop @@ -24663,7 +24663,7 @@ - A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed. + A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed. Michelle Giglio Suvarna Nadendla SPRITE @@ -24680,7 +24680,7 @@ - A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA. + A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA. Michelle Giglio Suvarna Nadendla DNA SPRITE @@ -24697,7 +24697,7 @@ - A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions. + A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions. Michelle Giglio Suvarna Nadendla RNA-DNA SPRITE @@ -24714,7 +24714,7 @@ - A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions. + A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions. Michelle Giglio Suvarna Nadendla GAM @@ -24744,7 +24744,7 @@ - A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed. + A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed. Michelle Giglio Suvarna Nadendla MARGI @@ -24819,7 +24819,7 @@ - A blood microbiology assay that detects a microorganism in a venous blood specimen. + A blood microbiology assay that detects a microorganism in a venous blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1491 @@ -24851,7 +24851,7 @@ Using a radioactivity detection assay as part of a tritiated thymidine incorporation assay to determine the degree to which cells are replicating by detecting radioactivity of tritiated thymidine, where radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. - An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B. + An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B. Bjoern Peters Hector Guzman-Orozco OBI @@ -24905,7 +24905,7 @@ - A blood microbiology assay that detects microorganisms in a placental blood specimen. + A blood microbiology assay that detects microorganisms in a placental blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 @@ -24952,7 +24952,7 @@ - An antigen specific antibodies assay that has a blood specimen as evaluant. + An antigen specific antibodies assay that has a blood specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -25000,7 +25000,7 @@ - An antigen specific antibodies assay that has a milk specimen as evaluant. + An antigen specific antibodies assay that has a milk specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -25025,7 +25025,7 @@ - An assay in which the level of catalytic activity of an enzyme is determined. + An assay in which the level of catalytic activity of an enzyme is determined. James A. Overton enzymatic activity level assay @@ -25051,7 +25051,7 @@ - An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample. + An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample. James A. Overton 5'-nucleotidase activity level assay @@ -25077,7 +25077,7 @@ - An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample. + An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample. James A. Overton alanine aminotransferase activity level assay @@ -25103,7 +25103,7 @@ - An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample. + An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample. James A. Overton alkaline phosphatase activity level assay @@ -25129,7 +25129,7 @@ - An enzymatic activity level assay that measures the activity of amylase in a sample. + An enzymatic activity level assay that measures the activity of amylase in a sample. James A. Overton amylase activity level assay @@ -25155,7 +25155,7 @@ - An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample. + An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample. James A. Overton aspartate aminotransferase activity level assay @@ -25181,7 +25181,7 @@ - An enzymatic activity level assay that measures the activity of cholinesterase in a sample. + An enzymatic activity level assay that measures the activity of cholinesterase in a sample. James A. Overton cholinesterase activity level assay @@ -25207,7 +25207,7 @@ - An enzymatic activity level assay that measures the activity of creatine kinase in a sample. + An enzymatic activity level assay that measures the activity of creatine kinase in a sample. James A. Overton creatine kinase activity level assay @@ -25233,7 +25233,7 @@ - An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample. + An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample. James A. Overton gamma-glutamyltransferase activity level assay @@ -25259,7 +25259,7 @@ - An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. + An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. James A. Overton glutamate dehydrogenase activity level assay @@ -25285,7 +25285,7 @@ - An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. + An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. James A. Overton isocitrate dehydrogenase activity level assay @@ -25311,7 +25311,7 @@ - An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. + An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. James A. Overton lactate dehydrogenase activity level assay @@ -25337,7 +25337,7 @@ - An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. + An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. James A. Overton sorbitol dehydrogenase activity level assay @@ -25363,7 +25363,7 @@ - An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. + An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. James A. Overton acyl-CoA oxidase activity level assay @@ -25389,7 +25389,7 @@ - An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. + An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. James A. Overton N-acetyl-beta-glucosaminidase activity level assay @@ -25415,7 +25415,7 @@ - An enzymatic activity level assay that measures the activity of ribonuclease in a sample. + An enzymatic activity level assay that measures the activity of ribonuclease in a sample. James A. Overton ribonuclease activity level assay @@ -25441,7 +25441,7 @@ - An enzymatic activity level assay that measures the activity of galactosidase in a sample. + An enzymatic activity level assay that measures the activity of galactosidase in a sample. James A. Overton galactosidase activity level assay @@ -25452,7 +25452,7 @@ - An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. + An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. Hector Guzman-Orozco survival after infectious challenge IEDB @@ -25466,7 +25466,7 @@ - An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. + An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. Hector Guzman-Orozco burden after tumor challenge IEDB @@ -25480,7 +25480,7 @@ - An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. + An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. Hector Guzman-Orozco survival after tumor challenge IEDB @@ -25494,7 +25494,7 @@ - An organism detection assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall. + An organism detection assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall. Gram-positive bacteria retain the violet stain whereas gram-negative bacteria do not. John Judkins ORCID:0000-0001-6595-0902 American Heritage Medical Dictionary @@ -25526,7 +25526,7 @@ - An assay that detects a type of organism and/or the quantity of individuals of a type of organism. + An assay that detects a type of organism and/or the quantity of individuals of a type of organism. This term is a generalized version of the term previously known as 'organism identification assay', to include classification other than species and to include quantities as outputs. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB @@ -25541,7 +25541,7 @@ A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. - A mass spectrometry assay that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). + A mass spectrometry assay that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). Discussed on the OBI developer call 2022-03-07: 'tandem mass spectrometry' OBI:0200198 is under 'data transformation' but is actually defined like an assay. Moving OBI:0200198 from 'data transformation' to 'assay' is a major logical change, so the OBI development team supports obsoleting 'tandem mass spectrometry' OBI:0200198 and replacing it with ‘tandem mass spectrometry assay’ OBI:0003540. Hector Guzman-Orozco, ORCID:0000-0003-3430-8997 http://purl.obolibrary.org/obo/OBI_0200198 @@ -25599,7 +25599,7 @@ - An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi. + An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 @@ -25656,7 +25656,7 @@ - A microarray assay that detects the IgM antibody that binds Dengue. + A microarray assay that detects the IgM antibody that binds Dengue. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 @@ -25693,7 +25693,7 @@ - A microarray assay that detects NS1. + A microarray assay that detects NS1. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 @@ -25750,7 +25750,7 @@ - Analytical chromatography that detects the IgM antibody that binds Chikungunya. + Analytical chromatography that detects the IgM antibody that binds Chikungunya. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 @@ -25807,7 +25807,7 @@ - An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Chikungunya. + An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Chikungunya. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 @@ -25864,7 +25864,7 @@ - An enzyme-linked immunosorbent assay that uses a microarray as the solid support and detects the IgM antibody that binds Chikungunya. + An enzyme-linked immunosorbent assay that uses a microarray as the solid support and detects the IgM antibody that binds Chikungunya. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 @@ -25883,7 +25883,7 @@ - A chromosome conformation capture assay in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation. Immunopreciptation with an antibody that targets a transcription factor or histone modification allows for selection and enrichment of specific genomic regions for investigation of long-range chromosomal interactions. + A chromosome conformation capture assay in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation. Immunopreciptation with an antibody that targets a transcription factor or histone modification allows for selection and enrichment of specific genomic regions for investigation of long-range chromosomal interactions. Hector Guzman-Orozco PLAC-seq https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5143423/ @@ -25978,7 +25978,7 @@ - An organism detection assay that detects microorganisms in a skin of body specimen. + An organism detection assay that detects microorganisms in a skin of body specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 @@ -26072,7 +26072,7 @@ - An organism detection assay that detects microorganisms in a bone marrow specimen. + An organism detection assay that detects microorganisms in a bone marrow specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 @@ -26166,7 +26166,7 @@ - An organism detection assay that detects microorganisms in a nasal aspirate specimen. + An organism detection assay that detects microorganisms in a nasal aspirate specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 @@ -26189,7 +26189,7 @@ - A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division. + A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 cell proliferation assay using carboxyfluorescein succinimidyl ester staining @@ -26216,7 +26216,7 @@ - A cytometry assay which measures the number of living cells in a population. + A cytometry assay which measures the number of living cells in a population. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 cell viability assay @@ -26238,7 +26238,7 @@ - A cell viability assay that uses Annexin V staining to detect apoptotic cells. + A cell viability assay that uses Annexin V staining to detect apoptotic cells. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 cell viability assay using Annexin V staining @@ -26272,7 +26272,7 @@ - An assay that has cell culture as an input. + An assay that has cell culture as an input. Randi Vita Sebastian Duesing cell culture assay @@ -26364,7 +26364,7 @@ - An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. + An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. Randi Vita Sebastian Duesing EBV @@ -26415,7 +26415,7 @@ - A CMV antibody assay that has serum as an input. + A CMV antibody assay that has serum as an input. Randi Vita Sebastian Duesing CMV @@ -26463,7 +26463,7 @@ single cell B cell receptor repertoire sequencing assay - A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. + A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. Randi Vita Sebastian Duesing single-cell BCR assay @@ -26511,7 +26511,7 @@ single cell T cell receptor repertoire sequencing assay - A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. + A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. Randi Vita Sebastian Duesing single-cell TCR assay @@ -26525,7 +26525,7 @@ quartz crystal microbalance assay - An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. + An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. Bjoern Peters Randi Vita Sebastian Duesing @@ -26541,7 +26541,7 @@ - A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. + A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. Sebastian Duesing MERFISH https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH @@ -26556,7 +26556,7 @@ - A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. + A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. Sebastian Duesing smFISH https://doi.org/10.21769/BioProtoc.3070 @@ -26567,6 +26567,105 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single-nucleus methylcytosine and transcriptome sequencing assay + https://www.biorxiv.org/content/10.1101/434845v1 + A DNA methylation profiling by high throughput sequencing assay that measures the cytosine DNA methylation and gene expression signature of single nuclei. + Jennifer Jou + Sebastian Duesing + snmCT-seq + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1785 + Jennifer Jou + single-nucleus methylcytosine and transcriptome sequencing assay + + + + @@ -26731,7 +26830,7 @@ PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. - An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis + An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis Philippe Rocca-Serra SCGE assay single cell gel electrophoresis assay @@ -26778,7 +26877,7 @@ PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? - An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions + An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions Philippe Rocca-Serra polymerase chain reaction-single strand conformation polymorphism assay PMID:18219595 @@ -26875,7 +26974,7 @@ - An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. + An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney grading of tumor OBI branch derived; submitted by MO @@ -26925,7 +27024,7 @@ Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present - An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached + An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached Matthew Brush OBI developer call, 3-12-12 assay detecting a molecular label @@ -26976,7 +27075,7 @@ the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated - An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. + An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. Adam Witney Helen Parkinson histology @@ -27045,7 +27144,7 @@ the detection of phycoerytherin by means of flow cytometry - An assay that detects a specified substance + An assay that detects a specified substance Kevin Clancy OBI branch derived substance detection assay @@ -27071,7 +27170,7 @@ The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection - An assay that measures the mass of a material at two or more time points + An assay that measures the mass of a material at two or more time points Helen Parkinson OBI branch derived longitudinal mass measurement assay @@ -27148,7 +27247,7 @@ Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. - A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. + A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. IEDB ELISPOT assay IEDB @@ -27172,7 +27271,7 @@ The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. - An assay that determines the 3-dimensional configuration of an input material. + An assay that determines the 3-dimensional configuration of an input material. IEDB IEDB 3D structure determination assay @@ -27293,7 +27392,7 @@ The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template - An assay the uses chemical or biochemical means to infer the sequence of a biomaterial + An assay the uses chemical or biochemical means to infer the sequence of a biomaterial PlanAndPlannedProcess Branch OBI branch derived sequencing assay @@ -27369,7 +27468,7 @@ An IFN-g ELISPOT is an assay detecting ifn-gamma production - An assay that determines information about the production of the cytokine interferon gamma + An assay that determines information about the production of the cytokine interferon gamma Bjoern Peters IFNg release IEDB @@ -27434,7 +27533,7 @@ - An analyte assay that measures the abundance of carbon dioxide + An analyte assay that measures the abundance of carbon dioxide Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27475,7 +27574,7 @@ - An analyte assay that measures the abundance of sodium(1+) + An analyte assay that measures the abundance of sodium(1+) Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27516,7 +27615,7 @@ - An analyte assay that measures the abundance of creatinine + An analyte assay that measures the abundance of creatinine Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27557,7 +27656,7 @@ - An analyte assay that measures the abundance of potassium(1+) + An analyte assay that measures the abundance of potassium(1+) Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27581,7 +27680,7 @@ - A cytometry assay that measures the count of basophils + A cytometry assay that measures the count of basophils Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27605,7 +27704,7 @@ - A cytometry assay that measures the count of neutrophils + A cytometry assay that measures the count of neutrophils Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27629,7 +27728,7 @@ - A cytometry assay that measures the count of eosinophils + A cytometry assay that measures the count of eosinophils Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27653,7 +27752,7 @@ - A cytometry assay that measures the count of lymphocytes + A cytometry assay that measures the count of lymphocytes Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27677,7 +27776,7 @@ - A cytometry assay that measures the count of monocytes + A cytometry assay that measures the count of monocytes Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27718,7 +27817,7 @@ - An analyte assay that measures the abundance of chloride + An analyte assay that measures the abundance of chloride Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27742,7 +27841,7 @@ - A cytometry assay that measures the count of erythrocytes + A cytometry assay that measures the count of erythrocytes Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27766,7 +27865,7 @@ - A cytometry assay that measures the count of platelets + A cytometry assay that measures the count of platelets Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27790,7 +27889,7 @@ - A cytometry assay that measures the count of leukocytes + A cytometry assay that measures the count of leukocytes Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27831,7 +27930,7 @@ - An analyte assay that measures the abundance of hemoglobin + An analyte assay that measures the abundance of hemoglobin Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27872,7 +27971,7 @@ - An analyte assay that measures the abundance of phosphate ion + An analyte assay that measures the abundance of phosphate ion Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27913,7 +28012,7 @@ - An analyte assay that measures the abundance of alanine aminotransferase + An analyte assay that measures the abundance of alanine aminotransferase Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27954,7 +28053,7 @@ - An analyte assay that measures the abundance of alkaline phosphatase (human) + An analyte assay that measures the abundance of alkaline phosphatase (human) Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -27995,7 +28094,7 @@ - An analyte assay that measures the abundance of bilirubin IXalpha + An analyte assay that measures the abundance of bilirubin IXalpha Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28036,7 +28135,7 @@ - An analyte assay that measures the abundance of aspartate aminotransferase (human) + An analyte assay that measures the abundance of aspartate aminotransferase (human) Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28077,7 +28176,7 @@ - An analyte assay that measures the abundance of glucose + An analyte assay that measures the abundance of glucose Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28118,7 +28217,7 @@ - An analyte assay that measures the abundance of magnesium cation + An analyte assay that measures the abundance of magnesium cation Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28159,7 +28258,7 @@ - An analyte assay that measures the abundance of albumin + An analyte assay that measures the abundance of albumin Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28200,7 +28299,7 @@ - An analyte assay that measures the abundance of protein + An analyte assay that measures the abundance of protein Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28241,7 +28340,7 @@ - An analyte assay that measures the abundance of calcium cation + An analyte assay that measures the abundance of calcium cation Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28282,7 +28381,7 @@ - An analyte assay that measures the abundance of creatine kinase + An analyte assay that measures the abundance of creatine kinase Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28306,7 +28405,7 @@ - A cytometry assay that measures the count of nucleate erythrocytes + A cytometry assay that measures the count of nucleate erythrocytes Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28330,7 +28429,7 @@ - A cytometry assay that measures the count of segmented neutrophil of bone marrows + A cytometry assay that measures the count of segmented neutrophil of bone marrows Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28358,7 +28457,7 @@ - An assay that measures lactate dehydrogenase complex + An assay that measures lactate dehydrogenase complex Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28399,7 +28498,7 @@ - An analyte assay that measures the abundance of triglyceride + An analyte assay that measures the abundance of triglyceride Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28440,7 +28539,7 @@ - An analyte assay that measures the abundance of high-density lipoprotein cholesterol + An analyte assay that measures the abundance of high-density lipoprotein cholesterol Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28481,7 +28580,7 @@ - An analyte assay that measures the abundance of cholesterol + An analyte assay that measures the abundance of cholesterol Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28522,7 +28621,7 @@ - An analyte assay that measures the abundance of low-density lipoprotein cholesterol + An analyte assay that measures the abundance of low-density lipoprotein cholesterol Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28563,7 +28662,7 @@ - An analyte assay that measures the abundance of thyroid stimulating hormone + An analyte assay that measures the abundance of thyroid stimulating hormone Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28604,7 +28703,7 @@ - An analyte assay that measures the abundance of prostate-specific antigen + An analyte assay that measures the abundance of prostate-specific antigen Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28645,7 +28744,7 @@ - An analyte assay that measures the abundance of thyroxine + An analyte assay that measures the abundance of thyroxine Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28686,7 +28785,7 @@ - An analyte assay that measures the abundance of elemental oxygen + An analyte assay that measures the abundance of elemental oxygen Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28727,7 +28826,7 @@ - An analyte assay that measures the abundance of folic acids + An analyte assay that measures the abundance of folic acids Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28751,7 +28850,7 @@ - A cytometry assay that measures the count of reticulocytes + A cytometry assay that measures the count of reticulocytes Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28779,7 +28878,7 @@ - An assay that measures osmolality + An assay that measures osmolality Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28820,7 +28919,7 @@ - An analyte assay that measures the abundance of methemoglobin + An analyte assay that measures the abundance of methemoglobin Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28848,7 +28947,7 @@ - An assay that measures cytosolic creatine kinase complex, MB-type + An assay that measures cytosolic creatine kinase complex, MB-type Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28876,7 +28975,7 @@ - An assay that measures rac-lactic acid + An assay that measures rac-lactic acid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28917,7 +29016,7 @@ - An analyte assay that measures the abundance of hydrogencarbonate + An analyte assay that measures the abundance of hydrogencarbonate Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28958,7 +29057,7 @@ - An analyte assay that measures the abundance of vancomycin + An analyte assay that measures the abundance of vancomycin Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -28999,7 +29098,7 @@ - An analyte assay that measures the abundance of tobramycin + An analyte assay that measures the abundance of tobramycin Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29040,7 +29139,7 @@ - An analyte assay that measures the abundance of 3,3',5'-triiodothyronine + An analyte assay that measures the abundance of 3,3',5'-triiodothyronine Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29081,7 +29180,7 @@ - An analyte assay that measures the abundance of C-reactive protein + An analyte assay that measures the abundance of C-reactive protein Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29105,7 +29204,7 @@ - A cytometry assay that measures the count of megakaryocytes + A cytometry assay that measures the count of megakaryocytes Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29129,7 +29228,7 @@ - A cytometry assay that measures the count of mesothelial cells + A cytometry assay that measures the count of mesothelial cells Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29153,7 +29252,7 @@ - A cytometry assay that measures the count of macrophages + A cytometry assay that measures the count of macrophages Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29194,7 +29293,7 @@ - An analyte assay that measures the abundance of 3-hydroxybutyric acid + An analyte assay that measures the abundance of 3-hydroxybutyric acid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29265,7 +29364,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29336,7 +29435,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order + An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29407,7 +29506,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order + An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29478,7 +29577,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order + An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29536,7 +29635,7 @@ - A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order + A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29594,7 +29693,7 @@ - A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order + A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29652,7 +29751,7 @@ - A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order + A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29710,7 +29809,7 @@ - A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order + A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29768,7 +29867,7 @@ - A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order + A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29839,7 +29938,7 @@ - An analyte assay that measures the abundance of chloride in venous blood + An analyte assay that measures the abundance of chloride in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29897,7 +29996,7 @@ - A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -29955,7 +30054,7 @@ - A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order + A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30013,7 +30112,7 @@ - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30071,7 +30170,7 @@ - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30142,7 +30241,7 @@ - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30213,7 +30312,7 @@ - An analyte assay that measures the abundance of phosphate in venous blood + An analyte assay that measures the abundance of phosphate in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30284,7 +30383,7 @@ - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30355,7 +30454,7 @@ - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30426,7 +30525,7 @@ - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30497,7 +30596,7 @@ - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30568,7 +30667,7 @@ - An analyte assay that measures the abundance of glucose in venous blood + An analyte assay that measures the abundance of glucose in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30639,7 +30738,7 @@ - An analyte assay that measures the abundance of magnesium in venous blood + An analyte assay that measures the abundance of magnesium in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30697,7 +30796,7 @@ - A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30755,7 +30854,7 @@ - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30813,7 +30912,7 @@ - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30871,7 +30970,7 @@ - A cytometry assay that measures the count of platelets in venous blood as part of a CBC order + A cytometry assay that measures the count of platelets in venous blood as part of a CBC order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -30942,7 +31041,7 @@ - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31000,7 +31099,7 @@ - A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order + A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31071,7 +31170,7 @@ - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31142,7 +31241,7 @@ - An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order + An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31213,7 +31312,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order + An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31284,7 +31383,7 @@ - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31355,7 +31454,7 @@ - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31426,7 +31525,7 @@ - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31497,7 +31596,7 @@ - An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order + An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31568,7 +31667,7 @@ - An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order + An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31639,7 +31738,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order + An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31710,7 +31809,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order + An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31781,7 +31880,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order + An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31852,7 +31951,7 @@ - An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order + An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31923,7 +32022,7 @@ - An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order + An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -31994,7 +32093,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32065,7 +32164,7 @@ - An analyte assay that measures the abundance of creatine kinase in venous blood + An analyte assay that measures the abundance of creatine kinase in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32136,7 +32235,7 @@ - An analyte assay that measures the abundance of calcium in venous blood + An analyte assay that measures the abundance of calcium in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32194,7 +32293,7 @@ - An assay that measures ferritin in venous blood + An assay that measures ferritin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32265,7 +32364,7 @@ - An analyte assay that measures the abundance of calcium in venous blood as part of a total order + An analyte assay that measures the abundance of calcium in venous blood as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32336,7 +32435,7 @@ - An analyte assay that measures the abundance of iron in venous blood + An analyte assay that measures the abundance of iron in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32394,7 +32493,7 @@ - A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32452,7 +32551,7 @@ - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32510,7 +32609,7 @@ - A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32568,7 +32667,7 @@ - A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32626,7 +32725,7 @@ - A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32684,7 +32783,7 @@ - A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32742,7 +32841,7 @@ - A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32800,7 +32899,7 @@ - A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32871,7 +32970,7 @@ - An analyte assay that measures the abundance of albumin in venous blood + An analyte assay that measures the abundance of albumin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -32942,7 +33041,7 @@ - An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order + An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33013,7 +33112,7 @@ - An analyte assay that measures the abundance of haptoglobin in venous blood + An analyte assay that measures the abundance of haptoglobin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33071,7 +33170,7 @@ - An assay that measures lactate dehydrogenase in venous blood + An assay that measures lactate dehydrogenase in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33142,7 +33241,7 @@ - An analyte assay that measures the abundance of prealbunin in venous blood + An analyte assay that measures the abundance of prealbunin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33213,7 +33312,7 @@ - An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order + An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33284,7 +33383,7 @@ - An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33355,7 +33454,7 @@ - An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order + An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33426,7 +33525,7 @@ - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33484,7 +33583,7 @@ - An assay that measures hemoglobin A1c in venous blood + An assay that measures hemoglobin A1c in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33555,7 +33654,7 @@ - An analyte assay that measures the abundance of uric acid in venous blood + An analyte assay that measures the abundance of uric acid in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33626,7 +33725,7 @@ - An analyte assay that measures the abundance of protein in venous blood as part of a total order + An analyte assay that measures the abundance of protein in venous blood as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33697,7 +33796,7 @@ - An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33768,7 +33867,7 @@ - An analyte assay that measures the abundance of prostate specific antigen in venous blood + An analyte assay that measures the abundance of prostate specific antigen in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33826,7 +33925,7 @@ - An assay that measures volume in urine as part of a 24 hour total order + An assay that measures volume in urine as part of a 24 hour total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33897,7 +33996,7 @@ - An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order + An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -33968,7 +34067,7 @@ - An analyte assay that measures the abundance of glucose in arterial blood + An analyte assay that measures the abundance of glucose in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34026,7 +34125,7 @@ - A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34097,7 +34196,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34168,7 +34267,7 @@ - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34239,7 +34338,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order + An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34310,7 +34409,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order + An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34381,7 +34480,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order + An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34452,7 +34551,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34523,7 +34622,7 @@ - An analyte assay that measures the abundance of folic acid in venous blood + An analyte assay that measures the abundance of folic acid in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34581,7 +34680,7 @@ - A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order + A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34652,7 +34751,7 @@ - An analyte assay that measures the abundance of potassium in venous blood + An analyte assay that measures the abundance of potassium in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34723,7 +34822,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood + An analyte assay that measures the abundance of carbon dioxide in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34794,7 +34893,7 @@ - An analyte assay that measures the abundance of transferrin in venous blood + An analyte assay that measures the abundance of transferrin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34865,7 +34964,7 @@ - An analyte assay that measures the abundance of sodium in venous blood + An analyte assay that measures the abundance of sodium in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -34936,7 +35035,7 @@ - An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order + An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35007,7 +35106,7 @@ - An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order + An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35078,7 +35177,7 @@ - An analyte assay that measures the abundance of creatinine in urine + An analyte assay that measures the abundance of creatinine in urine Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35136,7 +35235,7 @@ - An assay that measures osmolality in urine + An assay that measures osmolality in urine Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35207,7 +35306,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35278,7 +35377,7 @@ - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35349,7 +35448,7 @@ - An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order + An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35420,7 +35519,7 @@ - An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order + An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35491,7 +35590,7 @@ - An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order + An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35549,7 +35648,7 @@ - An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order + An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35607,7 +35706,7 @@ - An assay that measures fibrinogen in venous blood + An assay that measures fibrinogen in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35678,7 +35777,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35749,7 +35848,7 @@ - An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35820,7 +35919,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35891,7 +35990,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -35962,7 +36061,7 @@ - An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36033,7 +36132,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36104,7 +36203,7 @@ - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36175,7 +36274,7 @@ - An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36246,7 +36345,7 @@ - An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36317,7 +36416,7 @@ - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36388,7 +36487,7 @@ - An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36459,7 +36558,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36530,7 +36629,7 @@ - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36588,7 +36687,7 @@ - An assay that measures LDH in venous blood + An assay that measures LDH in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36646,7 +36745,7 @@ - An assay that measures creatine kinase MB in venous blood + An assay that measures creatine kinase MB in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36704,7 +36803,7 @@ - An assay that measures lactic acid in venous blood + An assay that measures lactic acid in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36762,7 +36861,7 @@ - A cytometry assay that measures the proportion of red blood cells in venous blood + A cytometry assay that measures the proportion of red blood cells in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36833,7 +36932,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood + An analyte assay that measures the abundance of creatinine in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36904,7 +37003,7 @@ - An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order + An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -36975,7 +37074,7 @@ - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37046,7 +37145,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37117,7 +37216,7 @@ - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37188,7 +37287,7 @@ - An analyte assay that measures the abundance of creatinine in arterial blood + An analyte assay that measures the abundance of creatinine in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37259,7 +37358,7 @@ - An analyte assay that measures the abundance of tacrolimus in venous blood + An analyte assay that measures the abundance of tacrolimus in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37330,7 +37429,7 @@ - An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order + An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37401,7 +37500,7 @@ - An analyte assay that measures the abundance of mycophenolic acid in venous blood + An analyte assay that measures the abundance of mycophenolic acid in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37472,7 +37571,7 @@ - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37543,7 +37642,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37614,7 +37713,7 @@ - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37672,7 +37771,7 @@ - An assay that measures IgG in venous blood as part of a quantitative order + An assay that measures IgG in venous blood as part of a quantitative order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37730,7 +37829,7 @@ - An assay that measures IgM in venous blood as part of a quantitative order + An assay that measures IgM in venous blood as part of a quantitative order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37788,7 +37887,7 @@ - An assay that measures IgA in venous blood as part of a quantitative order + An assay that measures IgA in venous blood as part of a quantitative order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37859,7 +37958,7 @@ - An analyte assay that measures the abundance of sodium in arterial blood + An analyte assay that measures the abundance of sodium in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -37930,7 +38029,7 @@ - An analyte assay that measures the abundance of potassium in arterial blood + An analyte assay that measures the abundance of potassium in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38001,7 +38100,7 @@ - An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order + An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38072,7 +38171,7 @@ - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38143,7 +38242,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38214,7 +38313,7 @@ - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38272,7 +38371,7 @@ - A cytometry assay that measures the proportion of red blood cells in arterial blood + A cytometry assay that measures the proportion of red blood cells in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38343,7 +38442,7 @@ - An analyte assay that measures the abundance of chloride in arterial blood + An analyte assay that measures the abundance of chloride in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38414,7 +38513,7 @@ - An analyte assay that measures the abundance of hemoglobin in arterial blood + An analyte assay that measures the abundance of hemoglobin in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38472,7 +38571,7 @@ - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38543,7 +38642,7 @@ - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38614,7 +38713,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38685,7 +38784,7 @@ - An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38756,7 +38855,7 @@ - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38827,7 +38926,7 @@ - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38898,7 +38997,7 @@ - An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -38969,7 +39068,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39027,7 +39126,7 @@ - An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order + An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39098,7 +39197,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39169,7 +39268,7 @@ - An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order + An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39240,7 +39339,7 @@ - An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order + An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39298,7 +39397,7 @@ - A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39356,7 +39455,7 @@ - An assay that measures lactic acid in arterial blood + An assay that measures lactic acid in arterial blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39427,7 +39526,7 @@ - An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood + An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39498,7 +39597,7 @@ - An analyte assay that measures the abundance of digoxin in venous blood + An analyte assay that measures the abundance of digoxin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39569,7 +39668,7 @@ - An analyte assay that measures the abundance of protein in urine + An analyte assay that measures the abundance of protein in urine Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39640,7 +39739,7 @@ - An analyte assay that measures the abundance of tobramycin in venous blood + An analyte assay that measures the abundance of tobramycin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39698,7 +39797,7 @@ - A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39769,7 +39868,7 @@ - An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order + An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39840,7 +39939,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order + An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39911,7 +40010,7 @@ - An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order + An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -39982,7 +40081,7 @@ - An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order + An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40053,7 +40152,7 @@ - An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order + An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40124,7 +40223,7 @@ - An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order + An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40195,7 +40294,7 @@ - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40266,7 +40365,7 @@ - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40337,7 +40436,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order + An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40408,7 +40507,7 @@ - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40466,7 +40565,7 @@ - An assay that measures glomerular filtration in venous blood as part of a estimated order + An assay that measures glomerular filtration in venous blood as part of a estimated order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40537,7 +40636,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order + An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40608,7 +40707,7 @@ - An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order + An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40679,7 +40778,7 @@ - An analyte assay that measures the abundance of amikacin in venous blood as part of a random order + An analyte assay that measures the abundance of amikacin in venous blood as part of a random order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40750,7 +40849,7 @@ - An analyte assay that measures the abundance of ammonia in venous blood + An analyte assay that measures the abundance of ammonia in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40821,7 +40920,7 @@ - An analyte assay that measures the abundance of GGT in venous blood + An analyte assay that measures the abundance of GGT in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40892,7 +40991,7 @@ - An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -40963,7 +41062,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order + An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41034,7 +41133,7 @@ - An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order + An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41105,7 +41204,7 @@ - An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order + An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41176,7 +41275,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41247,7 +41346,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order + An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41318,7 +41417,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order + An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41389,7 +41488,7 @@ - An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41460,7 +41559,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41531,7 +41630,7 @@ - An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order + An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41589,7 +41688,7 @@ - An assay that measures IgE in venous blood as part of a total order + An assay that measures IgE in venous blood as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41660,7 +41759,7 @@ - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41731,7 +41830,7 @@ - An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41802,7 +41901,7 @@ - An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41873,7 +41972,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -41944,7 +42043,7 @@ - An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order + An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42015,7 +42114,7 @@ - An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order + An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42086,7 +42185,7 @@ - An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order + An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42157,7 +42256,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order + An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42228,7 +42327,7 @@ - An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42299,7 +42398,7 @@ - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42370,7 +42469,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order + An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42441,7 +42540,7 @@ - An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order + An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42512,7 +42611,7 @@ - An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order + An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42583,7 +42682,7 @@ - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42654,7 +42753,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order + An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42725,7 +42824,7 @@ - An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order + An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42796,7 +42895,7 @@ - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42867,7 +42966,7 @@ - An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order + An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -42938,7 +43037,7 @@ - An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order + An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43009,7 +43108,7 @@ - An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43067,7 +43166,7 @@ - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43138,7 +43237,7 @@ - An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order + An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43209,7 +43308,7 @@ - An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order + An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43280,7 +43379,7 @@ - An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order + An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43351,7 +43450,7 @@ - An analyte assay that measures the abundance of PTH in venous blood as part of a intact order + An analyte assay that measures the abundance of PTH in venous blood as part of a intact order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43422,7 +43521,7 @@ - An analyte assay that measures the abundance of PSA in venous blood as part of a total order + An analyte assay that measures the abundance of PSA in venous blood as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43493,7 +43592,7 @@ - An analyte assay that measures the abundance of T3 in venous blood as part of a total order + An analyte assay that measures the abundance of T3 in venous blood as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43564,7 +43663,7 @@ - An analyte assay that measures the abundance of protein in urine as part of a 24 hour order + An analyte assay that measures the abundance of protein in urine as part of a 24 hour order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43635,7 +43734,7 @@ - An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order + An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43706,7 +43805,7 @@ - An analyte assay that measures the abundance of triglyceride in venous blood + An analyte assay that measures the abundance of triglyceride in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43764,7 +43863,7 @@ - A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43835,7 +43934,7 @@ - An analyte assay that measures the abundance of protein in cerebrospinal fluid + An analyte assay that measures the abundance of protein in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43906,7 +44005,7 @@ - An analyte assay that measures the abundance of glucose in cerebrospinal fluid + An analyte assay that measures the abundance of glucose in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -43964,7 +44063,7 @@ - A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44035,7 +44134,7 @@ - An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood + An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44106,7 +44205,7 @@ - An analyte assay that measures the abundance of cortisol in venous blood + An analyte assay that measures the abundance of cortisol in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44177,7 +44276,7 @@ - An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44248,7 +44347,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44319,7 +44418,7 @@ - An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44377,7 +44476,7 @@ - An assay that measures lactic acid in arterial blood as part of a ABL90 panel order + An assay that measures lactic acid in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44448,7 +44547,7 @@ - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44519,7 +44618,7 @@ - An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44590,7 +44689,7 @@ - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44648,7 +44747,7 @@ - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44719,7 +44818,7 @@ - An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44777,7 +44876,7 @@ - An assay that measures temperature in arterial blood as part of a ABL90 panel order + An assay that measures temperature in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44848,7 +44947,7 @@ - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44919,7 +45018,7 @@ - An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -44977,7 +45076,7 @@ - A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45048,7 +45147,7 @@ - An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45119,7 +45218,7 @@ - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45190,7 +45289,7 @@ - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45261,7 +45360,7 @@ - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45319,7 +45418,7 @@ - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45390,7 +45489,7 @@ - An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45461,7 +45560,7 @@ - An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45532,7 +45631,7 @@ - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45590,7 +45689,7 @@ - An assay that measures lactic acid in venous blood as part of a ABL90 panel order + An assay that measures lactic acid in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45661,7 +45760,7 @@ - An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45732,7 +45831,7 @@ - An analyte assay that measures the abundance of T4 in venous blood + An analyte assay that measures the abundance of T4 in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45803,7 +45902,7 @@ - An analyte assay that measures the abundance of T4 in venous blood as part of a free order + An analyte assay that measures the abundance of T4 in venous blood as part of a free order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45874,7 +45973,7 @@ - An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -45945,7 +46044,7 @@ - An analyte assay that measures the abundance of sodium in urine + An analyte assay that measures the abundance of sodium in urine Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46016,7 +46115,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order + An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46087,7 +46186,7 @@ - An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order + An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46158,7 +46257,7 @@ - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46229,7 +46328,7 @@ - An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order + An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46300,7 +46399,7 @@ - An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order + An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46371,7 +46470,7 @@ - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46442,7 +46541,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46513,7 +46612,7 @@ - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46571,7 +46670,7 @@ - A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46642,7 +46741,7 @@ - An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order + An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46713,7 +46812,7 @@ - An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order + An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46784,7 +46883,7 @@ - An analyte assay that measures the abundance of valproic acid in venous blood + An analyte assay that measures the abundance of valproic acid in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46855,7 +46954,7 @@ - An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46926,7 +47025,7 @@ - An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -46997,7 +47096,7 @@ - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47068,7 +47167,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47126,7 +47225,7 @@ - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47184,7 +47283,7 @@ - An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order + An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47255,7 +47354,7 @@ - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47326,7 +47425,7 @@ - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47397,7 +47496,7 @@ - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47468,7 +47567,7 @@ - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47539,7 +47638,7 @@ - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47610,7 +47709,7 @@ - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47681,7 +47780,7 @@ - An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order + An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47752,7 +47851,7 @@ - An analyte assay that measures the abundance of hemoglobin in venous blood + An analyte assay that measures the abundance of hemoglobin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47810,7 +47909,7 @@ - A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47881,7 +47980,7 @@ - An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -47952,7 +48051,7 @@ - An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order + An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48023,7 +48122,7 @@ - An analyte assay that measures the abundance of parathyroid hormone in venous blood + An analyte assay that measures the abundance of parathyroid hormone in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48094,7 +48193,7 @@ - An analyte assay that measures the abundance of protein in bodily fluid as part of a total order + An analyte assay that measures the abundance of protein in bodily fluid as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48165,7 +48264,7 @@ - An analyte assay that measures the abundance of glucose in bodily fluid + An analyte assay that measures the abundance of glucose in bodily fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48223,7 +48322,7 @@ - A cytometry assay that measures the count of cells in bodily fluid as part of a count order + A cytometry assay that measures the count of cells in bodily fluid as part of a count order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48281,7 +48380,7 @@ - A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order + A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48339,7 +48438,7 @@ - A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order + A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48397,7 +48496,7 @@ - A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order + A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48455,7 +48554,7 @@ - A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order + A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48513,7 +48612,7 @@ - A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order + A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48571,7 +48670,7 @@ - A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order + A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48629,7 +48728,7 @@ - A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order + A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48700,7 +48799,7 @@ - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48771,7 +48870,7 @@ - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48842,7 +48941,7 @@ - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48913,7 +49012,7 @@ - An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order + An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -48984,7 +49083,7 @@ - An analyte assay that measures the abundance of protein in venous blood as part of a liver function order + An analyte assay that measures the abundance of protein in venous blood as part of a liver function order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49055,7 +49154,7 @@ - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49126,7 +49225,7 @@ - An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order + An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49184,7 +49283,7 @@ - A cytometry assay that measures the count of cells in bodily fluid + A cytometry assay that measures the count of cells in bodily fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49242,7 +49341,7 @@ - A cytometry assay that measures the count of reticulocytes in venous blood + A cytometry assay that measures the count of reticulocytes in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49313,7 +49412,7 @@ - An analyte assay that measures the abundance of cholesterol in bodily fluid + An analyte assay that measures the abundance of cholesterol in bodily fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49384,7 +49483,7 @@ - An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49455,7 +49554,7 @@ - An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order + An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49526,7 +49625,7 @@ - An analyte assay that measures the abundance of T3 in venous blood as part of a free order + An analyte assay that measures the abundance of T3 in venous blood as part of a free order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49597,7 +49696,7 @@ - An analyte assay that measures the abundance of albumin in bodily fluid + An analyte assay that measures the abundance of albumin in bodily fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49668,7 +49767,7 @@ - An analyte assay that measures the abundance of triglyceride in bodily fluid + An analyte assay that measures the abundance of triglyceride in bodily fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49726,7 +49825,7 @@ - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49797,7 +49896,7 @@ - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49868,7 +49967,7 @@ - An analyte assay that measures the abundance of ionized calcium in venous blood + An analyte assay that measures the abundance of ionized calcium in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49926,7 +50025,7 @@ - An assay that measures temperature in venous blood + An assay that measures temperature in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -49997,7 +50096,7 @@ - An analyte assay that measures the abundance of bicarbonate in venous blood + An analyte assay that measures the abundance of bicarbonate in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50068,7 +50167,7 @@ - An analyte assay that measures the abundance of oxygen in venous blood + An analyte assay that measures the abundance of oxygen in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50126,7 +50225,7 @@ - An assay that measures osmolality in venous blood + An assay that measures osmolality in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50184,7 +50283,7 @@ - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50255,7 +50354,7 @@ - An analyte assay that measures the abundance of T3 in venous blood + An analyte assay that measures the abundance of T3 in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50313,7 +50412,7 @@ - A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50384,7 +50483,7 @@ - An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order + An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50455,7 +50554,7 @@ - An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood + An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50513,7 +50612,7 @@ - A cytometry assay that measures the count of megakaryocytes in venous blood + A cytometry assay that measures the count of megakaryocytes in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50571,7 +50670,7 @@ - A cytometry assay that measures the count of nucleated RBCs in venous blood + A cytometry assay that measures the count of nucleated RBCs in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50629,7 +50728,7 @@ - A cytometry assay that measures the count of WBCs in venous blood + A cytometry assay that measures the count of WBCs in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50687,7 +50786,7 @@ - A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order + A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50758,7 +50857,7 @@ - An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order + An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50829,7 +50928,7 @@ - An analyte assay that measures the abundance of Ceruloplasmin in venous blood + An analyte assay that measures the abundance of Ceruloplasmin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50900,7 +50999,7 @@ - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -50958,7 +51057,7 @@ - An assay that measures lactic acid in arterial blood as part of a GEM4 order + An assay that measures lactic acid in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51029,7 +51128,7 @@ - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51100,7 +51199,7 @@ - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51171,7 +51270,7 @@ - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51229,7 +51328,7 @@ - An assay that measures temperature in arterial blood as part of a GEM4 order + An assay that measures temperature in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51300,7 +51399,7 @@ - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51371,7 +51470,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51429,7 +51528,7 @@ - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51500,7 +51599,7 @@ - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51571,7 +51670,7 @@ - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51629,7 +51728,7 @@ - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51700,7 +51799,7 @@ - An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood + An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51758,7 +51857,7 @@ - A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order + A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51829,7 +51928,7 @@ - An analyte assay that measures the abundance of erythropoietin in venous blood + An analyte assay that measures the abundance of erythropoietin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51900,7 +51999,7 @@ - An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order + An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -51971,7 +52070,7 @@ - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52042,7 +52141,7 @@ - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52113,7 +52212,7 @@ - An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order + An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52171,7 +52270,7 @@ - A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid + A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52229,7 +52328,7 @@ - A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid + A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52287,7 +52386,7 @@ - A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid + A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52345,7 +52444,7 @@ - A cytometry assay that measures the count of macrophages in cerebrospinal fluid + A cytometry assay that measures the count of macrophages in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52403,7 +52502,7 @@ - A cytometry assay that measures the count of basophils in cerebrospinal fluid + A cytometry assay that measures the count of basophils in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52461,7 +52560,7 @@ - A cytometry assay that measures the count of monocytes in cerebrospinal fluid + A cytometry assay that measures the count of monocytes in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52519,7 +52618,7 @@ - A cytometry assay that measures the count of eosinophils in cerebrospinal fluid + A cytometry assay that measures the count of eosinophils in cerebrospinal fluid Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52590,7 +52689,7 @@ - An analyte assay that measures the abundance of beta-2-microglobulin in venous blood + An analyte assay that measures the abundance of beta-2-microglobulin in venous blood Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52661,7 +52760,7 @@ - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52732,7 +52831,7 @@ - An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order + An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52803,7 +52902,7 @@ - An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order + An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52874,7 +52973,7 @@ - An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X PennTURBO team https://github.com/obi-ontology/obi/issues/1253 @@ -52952,7 +53051,7 @@ Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones. - A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. + A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. Dan Berrios, ORCID: 0000-0003-4312-9552 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049660/ https://github.com/obi-ontology/obi/issues/1106 @@ -53004,7 +53103,7 @@ Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. + An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. IEDB PlanAndPlannedProcess Branch chromium release assay diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 47c9115b..8fb95a92 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -656,6 +656,7 @@ OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay +OBI:0003662 single-nucleus methylcytosine and transcriptome sequencing assay single-nucleus methylcytosine and transcriptome sequencing assay snmCT-seq A DNA methylation profiling by high throughput sequencing assay that measures the cytosine DNA methylation and gene expression signature of single nuclei. Jennifer Jou https://www.biorxiv.org/content/10.1101/434845v1 Sebastian Duesing|Jennifer Jou Jennifer Jou https://github.com/obi-ontology/obi/issues/1785 equivalent DNA methylation profiling by high throughput sequencing assay artificially induced reverse transcription RNA extract DNA sequencer RNA extract sequence data primary structure of RNA molecule OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course From a29d3b58b385a02a22a26f6d5904933ae6cc43cd Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 18 Jul 2024 10:43:23 -0500 Subject: [PATCH 03/23] Edit label of OBI:0003660 --- src/ontology/modules/assays.owl | 4 ++-- src/ontology/templates/assays.tsv | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index a9ec11ca..736011ac 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -26658,13 +26658,13 @@ - in vitro CRISPR screen using single RNA-Seq + in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 Jennifer Jou - in vitro CRISPR screen using single RNA-Seq + in vitro CRISPR screen using single-cell RNA-seq diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 56a4b328..dd09d688 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -657,7 +657,7 @@ OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay OBI:0003659 in vitro CRISPR screening assay in vitro CRISPR screening assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell -OBI:0003660 in vitro CRISPR screen using single RNA-Seq in vitro CRISPR screen using single RNA-Seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay +OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay OBI:0003661 in vitro CRISPR perturbation screen using FISH and flow cytometry in vitro CRISPR perturbation screen using FISH and flow cytometry An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay flow cytometry assay|fluorescence in-situ hybridization assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') From f7bf9047387d715f932e3b23c116d32b46df4eeb Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 30 Jul 2024 11:10:18 -0500 Subject: [PATCH 04/23] Add Illumina NovaSeq X & X Plus --- src/ontology/modules/devices.owl | 46 ++++++++++++++++++++++++++++++ src/ontology/templates/devices.tsv | 2 ++ 2 files changed, 48 insertions(+) diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index 745ec45a..8156f59b 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -9146,6 +9146,52 @@ + + + + + + + + + + + Illumina NovaSeq X + A DNA sequencer with three flow cell types manufactured by Illumina. The NovaSeq X provides an output of up to 8 Tb (26-52 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. + Morgana Barroso Oquendo + NovaSeq X Series + NovaSeq X System + https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html + https://github.com/obi-ontology/obi/issues/1802 + Morgana Barroso Oquendo + Illumina NovaSeq X + + + + + + + + + + + + + + + Illumina NovaSeq X Plus + A DNA sequencer with three flow cell types manufactured by Illumina. It features a dual-flow cell configuration, allowing to reach an output of up to 16 Tb (52-104 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. + Morgana Barroso Oquendo + NovaSeq X Series + NovaSeq X System + https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html + https://github.com/obi-ontology/obi/issues/1802 + Morgana Barroso Oquendo + Illumina NovaSeq X Plus + + + + diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index ee8e777e..1cb0b140 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -469,6 +469,8 @@ OBI:0003550 odor baited CDC light trap human odour baited light trap A CDC lig OBI:0003551 resting clay pot trap resting clay pot catch A resting arthropod trap that consists of a container composed primarily of clay. John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1651 resting arthropod trap OBI:0003606 Illumina NextSeq 1000 NextSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html Sebastian Duesing GENEPIO https://github.com/obi-ontology/obi/issues/1711 subclass DNA sequencer Illumina OBI:0003650 Illumina Infinium MethylationEPIC v2.0 BeadChip Illumina Infinium MethylationEPIC v2.0 BeadChip An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html Sebastian Duesing https://github.com/obi-ontology/obi/issues/1665 Illumina methylation BeadChip +OBI:0003663 Illumina NovaSeq X Illumina NovaSeq X NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. The NovaSeq X provides an output of up to 8 Tb (26-52 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass DNA sequencer Illumina +OBI:0003664 Illumina NovaSeq X Plus Illumina NovaSeq X Plus NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. It features a dual-flow cell configuration, allowing to reach an output of up to 16 Tb (52-104 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass DNA sequencer Illumina OBI:0400005 A10-Analyzer A10-Analyzer ready for release A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400006 A40-MiniFCM A40-MiniFCM ready for release A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400007 analog-to-digital converter analog-to-digital converter metadata incomplete A2D|A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. http://en.wiktionary.org/wiki/Analog-to-Digital_Converter The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. John Quinn|Melanie Courtot device signal conversion function From 1e1a3c2e8739912953982618a03cacc563ce1c09 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 15:59:46 -0500 Subject: [PATCH 05/23] Update ChEBI import --- src/ontology/OntoFox_outputs/ChEBI_imports.owl | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/ontology/OntoFox_outputs/ChEBI_imports.owl b/src/ontology/OntoFox_outputs/ChEBI_imports.owl index 3b1dc17e..dde2406b 100644 --- a/src/ontology/OntoFox_outputs/ChEBI_imports.owl +++ b/src/ontology/OntoFox_outputs/ChEBI_imports.owl @@ -86,7 +86,7 @@ water - An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. + An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms water @@ -352,7 +352,7 @@ cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses + A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -1097,9 +1097,10 @@ - ethylenediaminetetraacetic acid + EDTA(4-) + A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). - ethylenediaminetetraacetic acid + EDTA(4-) From 8d644a9df91dd4a0437330334ba0ed277f9f8e6f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:03:22 -0500 Subject: [PATCH 06/23] Add deoxyribonucleotide and methyl group imports --- src/ontology/OntoFox_inputs/ChEBI_input.txt | 6 +++++ .../OntoFox_outputs/ChEBI_imports.owl | 24 +++++++++++++++++++ 2 files changed, 30 insertions(+) diff --git a/src/ontology/OntoFox_inputs/ChEBI_input.txt b/src/ontology/OntoFox_inputs/ChEBI_input.txt index d0200298..0c9854ad 100755 --- a/src/ontology/OntoFox_inputs/ChEBI_input.txt +++ b/src/ontology/OntoFox_inputs/ChEBI_input.txt @@ -6,6 +6,7 @@ CHEBI [Low level source term URIs] http://purl.obolibrary.org/obo/CHEBI_23367 +http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide http://purl.obolibrary.org/obo/CHEBI_4705 http://purl.obolibrary.org/obo/CHEBI_15377 http://purl.obolibrary.org/obo/CHEBI_15956 @@ -25,6 +26,7 @@ http://purl.obolibrary.org/obo/CHEBI_31624 http://purl.obolibrary.org/obo/CHEBI_31642 http://purl.obolibrary.org/obo/CHEBI_31643 http://purl.obolibrary.org/obo/CHEBI_31991 +http://purl.obolibrary.org/obo/CHEBI_32875 # methyl group http://purl.obolibrary.org/obo/CHEBI_33359 http://purl.obolibrary.org/obo/CHEBI_33375 http://purl.obolibrary.org/obo/CHEBI_33376 @@ -124,6 +126,8 @@ http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/CHEBI_23367 subClassOf http://purl.obolibrary.org/obo/BFO_0000040 +http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide +subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity http://purl.obolibrary.org/obo/CHEBI_4705 subClassOf http://purl.obolibrary.org/obo/CHEBI_16991 http://purl.obolibrary.org/obo/CHEBI_15377 @@ -162,6 +166,8 @@ http://purl.obolibrary.org/obo/CHEBI_31643 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/CHEBI_31991 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +http://purl.obolibrary.org/obo/CHEBI_32875 # methyl group +subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity http://purl.obolibrary.org/obo/CHEBI_33359 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/CHEBI_33375 diff --git a/src/ontology/OntoFox_outputs/ChEBI_imports.owl b/src/ontology/OntoFox_outputs/ChEBI_imports.owl index dde2406b..5d2120d0 100644 --- a/src/ontology/OntoFox_outputs/ChEBI_imports.owl +++ b/src/ontology/OntoFox_outputs/ChEBI_imports.owl @@ -754,6 +754,18 @@ + + + + + methyl group + An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. + + methyl group + + + + @@ -1105,6 +1117,18 @@ + + + + + deoxyribonucleotide + A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. + + deoxyribonucleotide + + + + From fd676c198edf4ec0bbd44d14e4bff9462d47524f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:15:49 -0500 Subject: [PATCH 07/23] Remove references to obsolete DNA methylation term --- src/ontology/modules/assays.owl | 73 +++++++++++++++++++++++------- src/ontology/modules/devices.owl | 22 +++++++-- src/ontology/templates/assays.tsv | 2 +- src/ontology/templates/devices.tsv | 2 +- 4 files changed, 77 insertions(+), 22 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 59254ba4..1da20d22 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -470,6 +470,12 @@ + + + + + + @@ -560,6 +566,12 @@ + + + + + + @@ -1034,12 +1046,6 @@ - - - - - - @@ -2603,6 +2609,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2625,17 +2675,6 @@ - - - - - - - - - - - diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index 745ec45a..24db80e6 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -188,9 +188,15 @@ - + - + + + + + + + @@ -6230,7 +6236,17 @@ - + + + + + + + + + + + diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 47c9115b..bf96b8f5 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -27,7 +27,7 @@ OBI:0000615 protein expression profiling assay metadata complete proteomic anal OBI:0000623 NMR spectroscopy assay metadata incomplete Nuclear magnetic resonance spectroscopy An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 Philippe Rocca-Serra subclass assay OBI:0000626 DNA sequencing assay metadata incomplete nucleotide sequencing A sequencing assay which determines information on the sequence of a DNA molecule. url:https://en.wikipedia.org/wiki/DNA_sequencing Illumina (Solexa) sequencing is an example of DNA sequencing Philippe Rocca-Serra equivalent sequencing assay DNA extract DNA sequencer DNA sequence data primary structure of DNA macromolecule OBI:0000630 hematology assay metadata incomplete blood analysis|haematology An assay that studies blood and blood producing organs using a variety of techniques and instruments OBI branch derived Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 Philippe Rocca-Serra subclass assay ('information content entity' and ('is about' some hemopoiesis)) -OBI:0000634 DNA methylation profiling assay ready for release DNA methylation profiling An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. OBI branch derived Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 Philippe Rocca-Serra subclass epigenetic modification assay DNA extract (specimen and ('has part' some 'deoxyribonucleic acid')) data item DNA methylation epigenetic modification identification objective +OBI:0000634 DNA methylation profiling assay ready for release DNA methylation profiling An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. OBI branch derived Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 Philippe Rocca-Serra subclass epigenetic modification assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) (specimen and ('has part' some 'deoxyribonucleic acid')) data item epigenetic modification identification objective OBI:0000661 enzyme-linked immunosorbent assay ELISA An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. IEDB subclass logical definition does not capture details of processing analyte assay immunoglobulin complex, circulating OBI:0000664 BrdU incorporation assay A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. IEDB The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. IEDB subclass logical definition does not capture how exactly BRDU is utilized cell proliferation assay ""5-bromo-2'-deoxyuridine"" OBI:0000669 tritiated thymidine incorporation assay A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. IEDB The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. IEDB subclass logical definition does not capture how exactly thymidine is utilized cell proliferation assay radioactivity detection tritiated thymidine diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index ee8e777e..0a327b79 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -309,7 +309,7 @@ OBI:0001204 SNP microarray SNP microarray metadata complete A DNA microarray us OBI:0001307 tiling microarray tiling microarray metadata complete genome tiling array A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. EFO_0002704: tiling array Person: Helen Parkinson DNA microarray OBI:0001865 assay array metadata complete A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg device solid support function OBI:0001869 Illumina BeadChip metadata complete An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://www.illumina.com/technology/beadarray_technology.ilmn PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi assay array Illumina -OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg equivalent Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some 'DNA methylation'))))))) +OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg equivalent Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group'))))))))) OBI:0001871 LSRFortessa X-20 metadata complete A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg Anna Maria Masci flow cytometer analyzer Becton Dickinson (BD Biosciences) OBI:0001971 Ion 316 Chip v2 Ion 316 Chip v2 Ion PGM 316 Chip|Ion 316 Chip|Ion PGM 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ ion semiconductor chip OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ ion semiconductor chip From 55dab57d1e06ebd751d851c38649cdcfba5872a8 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:21:13 -0500 Subject: [PATCH 08/23] Remove references to obsolete 'regulation of DNA methylation' term --- src/ontology/modules/assays.owl | 279 +++++++++++++++++++++++------- src/ontology/templates/assays.tsv | 10 +- 2 files changed, 224 insertions(+), 65 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 1da20d22..ca1c6a8f 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -1184,12 +1184,6 @@ - - - - - - @@ -2951,6 +2945,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2988,17 +3026,6 @@ - - - - - - - - - - - @@ -3686,6 +3713,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3718,17 +3789,6 @@ - - - - - - - - - - - @@ -9326,20 +9386,53 @@ - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - + Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 @@ -9358,6 +9451,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -9370,17 +9507,6 @@ - - - - - - - - - - - @@ -10402,6 +10528,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -10433,17 +10603,6 @@ - - - - - - - - - - - diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index bf96b8f5..af01fc8d 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -31,7 +31,7 @@ OBI:0000634 DNA methylation profiling assay ready for release DNA methylation p OBI:0000661 enzyme-linked immunosorbent assay ELISA An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. IEDB subclass logical definition does not capture details of processing analyte assay immunoglobulin complex, circulating OBI:0000664 BrdU incorporation assay A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. IEDB The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. IEDB subclass logical definition does not capture how exactly BRDU is utilized cell proliferation assay ""5-bromo-2'-deoxyuridine"" OBI:0000669 tritiated thymidine incorporation assay A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. IEDB The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. IEDB subclass logical definition does not capture how exactly thymidine is utilized cell proliferation assay radioactivity detection tritiated thymidine -OBI:0000693 MeDIP-seq assay metadata complete Methylated DNA immunoprecipitation sequencing assay A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. Philippe Rocca-Serra subclass infer chip & sequecing assays DNA methylation profiling assay chromatin immunoprecipitation|library preparation sequencing assay DNA extract|('has part' some chromatin) DNA sequencer DNA extract sequence data regulation of DNA methylation epigenetic modification identification objective +OBI:0000693 MeDIP-seq assay metadata complete Methylated DNA immunoprecipitation sequencing assay A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. Philippe Rocca-Serra subclass infer chip & sequecing assays DNA methylation profiling assay chromatin immunoprecipitation|library preparation sequencing assay DNA extract|('has part' some chromatin) ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA extract sequence data epigenetic modification identification objective OBI:0000695 chain termination sequencing assay metadata complete Sanger sequencing|dye terminator sequencing A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position url:https://en.wikipedia.org/wiki/Sanger_sequencing PMID: 271968. DNA sequencing with chain-terminating inhibitors. Philippe Rocca-Serra subclass DNA sequencing by synthesis assay ('ABI 377 automated sequencer' or 'Li-Cor 4300 DNA Analysis System') PCR product OBI:0000697 Helicos sequencing assay metadata complete true single molecule sequencing A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Philippe Rocca-Serra subclass DNA sequencing by synthesis assay HeliScope Single Molecule Sequencer OBI:0000699 survival assessment assay metadata incomplete An assay that measures the occurrence of death events in one or more organisms over time subclass assay organism survival rate organism @@ -44,7 +44,7 @@ OBI:0000724 Solexa sequencing assay metadata complete reversible terminator seq OBI:0000730 pyrosequencing assay metadata complete A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. url:http://en.wikipedia.org/wiki/Pyrosequencing Pyrosequencing sheds light on DNA sequencing. PMID:1115661 Philippe Rocca-Serra subclass DNA sequencing by synthesis assay ('454 Genome Sequence 20' or '454 Genome Sequencer FLX') OBI:0000734 DNA sequencing by synthesis assay metadata incomplete A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing Philippe Rocca-Serra subclass DNA sequencing assay DNA polymerase complex OBI:0000743 immune response assay metadata incomplete An assay that determines information about an immune response IEDB Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. Bjoern Peters|Randi Vita subclass assay measurement datum immune response -OBI:0000748 bisulfite sequencing assay metadata complete A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. url:https://en.wikipedia.org/wiki/Bisulfite_sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Philippe Rocca-Serra|Sagar Jain subclass DNA meth profiling is a epigenetic mod assay, does not need inference DNA methylation profiling assay DNA sequencing assay DNA extract DNA sequencer DNA extract ('measurement datum' and 'DNA sequence data') regulation of DNA methylation epigenetic modification identification objective +OBI:0000748 bisulfite sequencing assay metadata complete A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. url:https://en.wikipedia.org/wiki/Bisulfite_sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Philippe Rocca-Serra|Sagar Jain subclass DNA meth profiling is a epigenetic mod assay, does not need inference DNA methylation profiling assay DNA sequencing assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA extract ('measurement datum' and 'DNA sequence data') epigenetic modification identification objective OBI:0000787 human antithrombin-III in blood assay ready for release AT-III assay An assay that measures the amount of antithrombin III in blood. url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. Alan Ruttenberg subclass analyte assay ('scattered molecular aggregate' and ('has grain' some antithrombin-III)) scalar measurement datum blood coagulation OBI:0000802 prothrombin time assay metadata complete An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). Alan Ruttenberg subclass assay scalar measurement datum blood coagulation OBI:0000805 antithrombin-III berichrome assay metadata complete AT-III assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 subclass human antithrombin-III in blood assay (has_specified_output some 'scalar measurement datum') and ('has participant' some 'Berichrom(r) Antithrombin III (A) Kit') and (has_specified_output exactly 1 Thing) @@ -162,8 +162,8 @@ OBI:0001680 Sos-recruitment assay ready for release SRS A binding assay that de OBI:0001681 yeast one-hybrid assay ready for release Y1H An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. PMID:22218861 Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 Philippe Rocca-Serra|Marcus Chibucos subclass binding assay genetically modified material data item sequence-specific DNA binding OBI:0001682 bacterial one-hybrid assay ready for release B1H An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence url:http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 Philippe Rocca-Serra|Marcus Chibucos subclass yeast one-hybrid assay genetically modified material data item sequence-specific DNA binding protein and DNA interaction identification objective OBI:0001683 chromosome organization assay by fluorescence in-situ hybridization ready for release An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 Philippe Rocca-Serra|Marcus Chibucos https://github.com/obi-ontology/obi/issues/788| subclass in-situ hybridization assay ('has part' some chromosome) molecular label data item chromosome organization biological feature identification objective -OBI:0001684 methylation-specific polymerase chain reaction assay ready for release MSP An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. PMID:8790415 Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 Philippe Rocca-Serra|Marcus Chibucos subclass assay data item regulation of DNA methylation -OBI:0001685 amplification of intermethylated sites assay ready for release AIMS assay|intermethylated site amplification An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. PMID:18987810 Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 Philippe Rocca-Serra|Marcus Chibucos subclass DNA methylation profiling assay high molecular weight DNA extract data item regulation of DNA methylation epigenetic modification identification objective +OBI:0001684 methylation-specific polymerase chain reaction assay ready for release MSP An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. PMID:8790415 Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 Philippe Rocca-Serra|Marcus Chibucos subclass assay ('deoxyribonucleotide' and ('has part' some 'methyl group')) data item +OBI:0001685 amplification of intermethylated sites assay ready for release AIMS assay|intermethylated site amplification An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. PMID:18987810 Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 Philippe Rocca-Serra|Marcus Chibucos subclass DNA methylation profiling assay ('deoxyribonucleotide' and ('has part' some 'methyl group')) high molecular weight DNA extract data item epigenetic modification identification objective OBI:0001686 in-situ hybridization assay ready for release ISH|in situ hybridization An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. PMID:9021518 Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 Philippe Rocca-Serra|Marcus Chibucos subclass assay nucleic acid hybridization labeled nucleic acid extract data item macromolecule localization biological feature identification objective OBI:0001689 cytochalasin-induced inhibition of actin polymerization assay ready for release An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). Philippe Rocca-Serra|Marcus Chibucos subclass assay cytochalasin data item actin filament polymerization biological feature identification objective OBI:0001699 antibody cross-blocking assay antibody inhibition of antibody binding A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. IEDB Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. IEDB subclass logical definition is not capturing how the different antibodies are used in relation to each other. competitive inhibition of binding assay immunoglobulin complex, circulating ('immunoglobulin complex, circulating' and ('has role' some 'positive reference substance role')) @@ -175,7 +175,7 @@ OBI:0001853 DNase I hypersensitive sites sequencing assay metadata complete An OBI:0001857 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay metadata complete RIP-seq assay|RIP-seq An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). PMID:21172659 Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer sequencing assay analyte assay immunoprecipitation|library preparation|cross linking RNA sequencing assay protein-containing complex DNA sequencer|sonicator DNA sequence data protein and RNA interaction identification objective OBI:0001858 cross-linking immunoprecipitation high-throughput sequencing assay metadata complete HITS-CLIP|CLIP-seq|CLIP-seq assay An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. PMID:18978773 Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer sequencing assay analyte assay immunoprecipitation|library preparation|cross linking RNA sequencing assay protein-containing complex DNA sequencer DNA sequence data protein and RNA interaction identification objective OBI:0001859 formaldehyde-assisted isolation of regulatory elements assay metadata complete FAIRE-seq assay|FAIRE-seq An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. url:http://en.wikipedia.org/wiki/FAIRE-Seq Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass sequencing assay library preparation|cross linking DNA sequencing assay DNA extract DNA sequence data regulatory_region protein and DNA interaction identification objective -OBI:0001861 methylation-sensitive restriction enzyme sequencing assay metadata complete MRE-seq|MRE-seq assay An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. PMID:20613842 Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer DNA sequencing assay DNA methylation profiling by high throughput sequencing assay library preparation|specific enzymatic cleavage DNA sequencing assay DNA extract DNA sequencer DNA sequence data regulation of DNA methylation epigenetic modification identification objective +OBI:0001861 methylation-sensitive restriction enzyme sequencing assay metadata complete MRE-seq|MRE-seq assay An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. PMID:20613842 Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer DNA sequencing assay DNA methylation profiling by high throughput sequencing assay library preparation|specific enzymatic cleavage DNA sequencing assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA sequence data epigenetic modification identification objective OBI:0001862 reduced representation bisulfite sequencing assay metadata complete reduced representation bisulfite-seq|RRBS|RRBS assay A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. PMC:1258174 Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass bisulfite sequencing assay library preparation|specific enzymatic cleavage OBI:0001863 shotgun bisulfite-seq assay metadata complete WGBS|Shotgun bisulfite sequencing|whole genome bisulfite sequencing|WGSBS|whole-genome shotgun bisulfite sequencing A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. PMID:18278030 Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. Venkat Malladi|Chris Stoeckert|Jie Zheng subclass bisulfite sequencing assay library preparation sonicator OBI:0001864 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay metadata complete RAMPAGE An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. PMID:22936248 Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer sequencing assay transcription profiling assay library preparation|non specific enzymatic cleavage sequencing assay RNA extract DNA sequencer DNA sequence data transcription start site identification objective From 5ec2369dbcd4da023f106dc54c59641352e613b1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:28:14 -0500 Subject: [PATCH 09/23] Remove imports for obsolete DNA methylation terms --- src/ontology/OntoFox_inputs/GO_input.txt | 6 ------ src/ontology/OntoFox_outputs/GO_imports.owl | 24 --------------------- 2 files changed, 30 deletions(-) diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt index a551396a..35c44954 100755 --- a/src/ontology/OntoFox_inputs/GO_input.txt +++ b/src/ontology/OntoFox_inputs/GO_input.txt @@ -47,7 +47,6 @@ http://purl.obolibrary.org/obo/GO_0005694 http://purl.obolibrary.org/obo/GO_0005739 # mitochondrion http://purl.obolibrary.org/obo/GO_0006006 http://purl.obolibrary.org/obo/GO_0006260 -http://purl.obolibrary.org/obo/GO_0006306 http://purl.obolibrary.org/obo/GO_0006338 http://purl.obolibrary.org/obo/GO_0006909 http://purl.obolibrary.org/obo/GO_0006955 @@ -139,7 +138,6 @@ http://purl.obolibrary.org/obo/GO_0042611 http://purl.obolibrary.org/obo/GO_0043227 http://purl.obolibrary.org/obo/GO_0043316 http://purl.obolibrary.org/obo/GO_0043565 -http://purl.obolibrary.org/obo/GO_0044030 http://purl.obolibrary.org/obo/GO_0044807 # macrophage migration inhibitory factor production http://purl.obolibrary.org/obo/GO_0044808 # Oncostatin M production http://purl.obolibrary.org/obo/GO_0044809 # chemokine (C-C motif) ligand 17 production @@ -398,8 +396,6 @@ http://purl.obolibrary.org/obo/GO_0043316 subClassOf http://purl.obolibrary.org/obo/GO_0001906 http://purl.obolibrary.org/obo/GO_0043565 subClassOf http://purl.obolibrary.org/obo/OBI_0001588 -http://purl.obolibrary.org/obo/GO_0044030 -subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0048869 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0050896 @@ -458,8 +454,6 @@ http://purl.obolibrary.org/obo/GO_0097391 subClassOf http://purl.obolibrary.org/obo/GO_0032602 http://purl.obolibrary.org/obo/GO_0097392 subClassOf http://purl.obolibrary.org/obo/GO_0032602 -http://purl.obolibrary.org/obo/GO_0006306 -subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0016570 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0005739 diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl index 277cf3c7..37d8e8a0 100644 --- a/src/ontology/OntoFox_outputs/GO_imports.owl +++ b/src/ontology/OntoFox_outputs/GO_imports.owl @@ -586,18 +586,6 @@ - - - - - DNA methylation - The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. - - DNA methylation - - - - @@ -1690,18 +1678,6 @@ - - - - - regulation of DNA methylation - Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. - - regulation of DNA methylation - - - - From 25aae6d451e873bc3b8902f4693784335b8989d9 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:34:07 -0500 Subject: [PATCH 10/23] Remove references to obsolete histone modification term --- src/ontology/modules/assays.owl | 28 ---------------------------- src/ontology/templates/assays.tsv | 4 ++-- 2 files changed, 2 insertions(+), 30 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index ca1c6a8f..274f2f8e 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -1112,12 +1112,6 @@ - - - - - - @@ -12642,17 +12636,6 @@ - - - - - - - - - - - @@ -12764,17 +12747,6 @@ - - - - - - - - - - - diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index af01fc8d..a181a7df 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -205,8 +205,8 @@ OBI:0001985 microarray assay An analyte assay where binding of the analyte to OBI:0001986 immunohistochemistry An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. IEDB Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. IEDB equivalent immuno staining assay specimen from organism material entity OBI:0002014 DNA methylation profiling by ChIP-chip assay DNA methylation ChIP-chip An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay epigenetic modification assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray epigenetic modification identification objective OBI:0002015 transcription profiling by MPSS assay expression MPSS A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing Chris Stoeckert|Jie Zheng subclass transcription profiling assay library preparation DNA sequencing assay assay bead -OBI:0002016 histone modification identification by ChIP-chip assay histone modification ChIP-chip An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay epigenetic modification assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray information content entity histone modification epigenetic modification identification objective -OBI:0002017 histone modification identification by ChIP-Seq assay histone modification ChIP-Seq An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-seq assay epigenetic modification assay chromatin immunoprecipitation ChIP-seq assay ('has part' some chromatin) DNA sequencer DNA sequence data histone modification epigenetic modification identification objective +OBI:0002016 histone modification identification by ChIP-chip assay histone modification ChIP-chip An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay epigenetic modification assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray information content entity epigenetic modification identification objective +OBI:0002017 histone modification identification by ChIP-Seq assay histone modification ChIP-Seq An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-seq assay epigenetic modification assay chromatin immunoprecipitation ChIP-seq assay ('has part' some chromatin) DNA sequencer DNA sequence data epigenetic modification identification objective OBI:0002018 transcription factor binding site identification by ChIP-chip assay TF Binding ChIP-chip A transcription factor binding site assay that utilizes ChIP-chip technology. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay transcription factor binding site assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray information content entity TF_binding_site protein and DNA interaction identification objective OBI:0002019 transcription factor binding site identification by ChIP-Seq assay TF Binding ChIP-Seq A transcription factor binding site assay that utilizes ChIP-seq technology. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-seq assay transcription factor binding site assay chromatin immunoprecipitation ChIP-seq assay ('has part' some chromatin) DNA sequencer DNA sequence data TF_binding_site protein and DNA interaction identification objective OBI:0002020 epigenetic modification assay An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. Penn group Chris Stoeckert|Jie Zheng equivalent assay epigenetic modification identification objective From 199cf481aa8f51e17a64706ca35241190b8ce0bd Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:35:39 -0500 Subject: [PATCH 11/23] Remove import of obsolete histone modification term --- src/ontology/OntoFox_inputs/GO_input.txt | 3 --- src/ontology/OntoFox_outputs/GO_imports.owl | 12 ------------ 2 files changed, 15 deletions(-) diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt index 35c44954..8a413b0a 100755 --- a/src/ontology/OntoFox_inputs/GO_input.txt +++ b/src/ontology/OntoFox_inputs/GO_input.txt @@ -65,7 +65,6 @@ http://purl.obolibrary.org/obo/GO_0015925 # galactosidase activity http://purl.obolibrary.org/obo/GO_0016064 http://purl.obolibrary.org/obo/GO_0016160 # amylase activity http://purl.obolibrary.org/obo/GO_0016231 # beta-N-acetylglucosaminidase activity -http://purl.obolibrary.org/obo/GO_0016570 # histone modification http://purl.obolibrary.org/obo/GO_0016788 #hydrolase activity, acting on ester bonds http://purl.obolibrary.org/obo/GO_0019814 http://purl.obolibrary.org/obo/GO_0019815 @@ -454,8 +453,6 @@ http://purl.obolibrary.org/obo/GO_0097391 subClassOf http://purl.obolibrary.org/obo/GO_0032602 http://purl.obolibrary.org/obo/GO_0097392 subClassOf http://purl.obolibrary.org/obo/GO_0032602 -http://purl.obolibrary.org/obo/GO_0016570 -subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0005739 subClassOf http://purl.obolibrary.org/obo/GO_0043227 http://purl.obolibrary.org/obo/GO_0140730 diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl index 37d8e8a0..d0f254c4 100644 --- a/src/ontology/OntoFox_outputs/GO_imports.owl +++ b/src/ontology/OntoFox_outputs/GO_imports.owl @@ -802,18 +802,6 @@ - - - - - histone modification - The covalent alteration of one or more amino acid residues within a histone protein. - - histone modification - - - - From c9132fd6011ec8f1a48d4b6d15bcfbf8c684986e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:37:40 -0500 Subject: [PATCH 12/23] Update imports --- src/ontology/OntoFox_outputs/CLO_imports.owl | 23 ------- src/ontology/OntoFox_outputs/CL_imports.owl | 53 +++++++--------- src/ontology/OntoFox_outputs/ENVO_imports.owl | 4 +- src/ontology/OntoFox_outputs/GO_imports.owl | 48 +++++++------- .../OntoFox_outputs/NCBITaxon_imports.owl | 63 +++++-------------- .../OntoFox_outputs/OMRSE_imports.owl | 30 +++++++++ src/ontology/OntoFox_outputs/OPL_imports.owl | 9 --- src/ontology/OntoFox_outputs/PR_imports.owl | 2 +- src/ontology/OntoFox_outputs/SO_imports.owl | 2 +- .../OntoFox_outputs/Uberon_imports.owl | 37 +---------- src/ontology/OntoFox_outputs/VO_imports.owl | 22 +------ 11 files changed, 101 insertions(+), 192 deletions(-) diff --git a/src/ontology/OntoFox_outputs/CLO_imports.owl b/src/ontology/OntoFox_outputs/CLO_imports.owl index 07386bc8..411e533b 100644 --- a/src/ontology/OntoFox_outputs/CLO_imports.owl +++ b/src/ontology/OntoFox_outputs/CLO_imports.owl @@ -56,18 +56,11 @@ cell line cell - cell line cell - 细胞系细胞 A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture - - 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 - 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 cell line cell - cell line cell - 细胞系细胞 @@ -77,14 +70,9 @@ mortal cell line cell - mortal cell line cell - 非永生细胞系细胞 A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. - A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. mortal cell line cell - mortal cell line cell - 非永生细胞系细胞 @@ -94,15 +82,9 @@ immortal cell line cell - immortal cell line cell - 永生细胞系细胞 A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. - A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. - 预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。 immortal cell line cell - immortal cell line cell - 永生细胞系细胞 @@ -112,16 +94,11 @@ cell line - 细胞系 A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). - - 一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 - 培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 cell line - 细胞系 diff --git a/src/ontology/OntoFox_outputs/CL_imports.owl b/src/ontology/OntoFox_outputs/CL_imports.owl index ee5bfcbd..2e376162 100644 --- a/src/ontology/OntoFox_outputs/CL_imports.owl +++ b/src/ontology/OntoFox_outputs/CL_imports.owl @@ -32,7 +32,10 @@ definition + definition + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition + definition @@ -64,12 +67,7 @@ - - material entity - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - - material entity - + @@ -101,10 +99,10 @@ - native cell - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + obsolete native cell + OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - native cell + obsolete native cell @@ -148,7 +146,7 @@ - + mesothelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. @@ -209,8 +207,7 @@ - - + platelet A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. @@ -282,9 +279,9 @@ - + megakaryocyte - A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. + A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. megakaryocyte @@ -306,8 +303,7 @@ - - + band form neutrophil A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. @@ -320,7 +316,7 @@ - + nucleate erythrocyte An erythrocyte having a nucleus. @@ -333,8 +329,7 @@ - - + monocyte @@ -408,8 +403,7 @@ - - + eosinophil Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. @@ -422,8 +416,7 @@ - - + neutrophil Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. @@ -496,8 +489,7 @@ - - + promyelocyte A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. @@ -533,8 +525,7 @@ - - + metamyelocyte A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. @@ -546,8 +537,7 @@ - - + myelocyte A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. @@ -571,8 +561,7 @@ - - + segmented neutrophil of bone marrow A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. @@ -585,7 +574,7 @@ - + peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. diff --git a/src/ontology/OntoFox_outputs/ENVO_imports.owl b/src/ontology/OntoFox_outputs/ENVO_imports.owl index 0baf7c5b..5e2a7aec 100644 --- a/src/ontology/OntoFox_outputs/ENVO_imports.owl +++ b/src/ontology/OntoFox_outputs/ENVO_imports.owl @@ -76,7 +76,7 @@ soil - Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. + An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms. soil @@ -100,7 +100,7 @@ environmental material - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. + A material entity which other material entities in an environmental system are primarily or partially composed of. environmental material diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl index d0f254c4..014e607f 100644 --- a/src/ontology/OntoFox_outputs/GO_imports.owl +++ b/src/ontology/OntoFox_outputs/GO_imports.owl @@ -77,7 +77,7 @@ - + chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. @@ -198,7 +198,7 @@ adaptive immune response - An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). + An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). adaptive immune response @@ -303,7 +303,7 @@ molecular_function - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular_function @@ -315,7 +315,7 @@ antigen binding - Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. + Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell. antigen binding @@ -338,10 +338,10 @@ - L-iditol 2-dehydrogenase activity - Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+. + L-iditol 2-dehydrogenase (NAD+) activity + Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+. Acts on a number of sugar alcohols, including (but not limited to) L-iditol, D-glucitol, D-xylitol, and D-galactitol. - L-iditol 2-dehydrogenase activity + L-iditol 2-dehydrogenase (NAD+) activity @@ -399,7 +399,7 @@ alkaline phosphatase activity - Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum. + Catalysis of the reaction: a phosphate monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum. alkaline phosphatase activity @@ -435,7 +435,7 @@ creatine kinase activity - Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). + Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H+. creatine kinase activity @@ -494,10 +494,10 @@ - ribonuclease activity + RNA nuclease activity Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. - ribonuclease activity + RNA nuclease activity @@ -506,10 +506,10 @@ - ion channel activity - Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). + monoatomic ion channel activity + Enables the facilitated diffusion of a monoatomic ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). - ion channel activity + monoatomic ion channel activity @@ -519,7 +519,7 @@ cellular_component - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). cellular_component @@ -579,7 +579,7 @@ DNA replication - The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. + The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. DNA replication @@ -626,10 +626,10 @@ - cellular response to DNA damage stimulus + DNA damage response Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. - cellular response to DNA damage stimulus + DNA damage response @@ -663,7 +663,7 @@ biological_process - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological_process @@ -735,7 +735,7 @@ gene expression - The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. + The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. gene expression @@ -974,10 +974,10 @@ - interferon-gamma production + type II interferon production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. - interferon-gamma production + type II interferon production @@ -1707,7 +1707,7 @@ D-glutamyltransferase activity - Catalysis of the reaction: L(or D)-glutamine + D-glutamyl-peptide = NH3 + 5-glutamyl-D-glutamyl-peptide. + Catalysis of the reaction: D-glutamate + D-glutamine = gamma-D-glutamyl-D-glutamate + NH4+. Can also transfer additional glutamyl residues to a peptide, extending the polypeptide chain. D-glutamyltransferase activity @@ -1767,7 +1767,7 @@ ferritin complex - A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain. + A protein complex that binds iron and acts as a major iron storage system. There are three major subclasses of ferritins: the classical ferritins (Ftn), the heme-containing bacterioferritins (Bfr) and the DNA-binding proteins from starved cells (Dps). Ftn and Bfr are made of 24 subunits, whereas Dps are smaller with 12 subunits. Ftn is found in most kindoms, while Bfr and Dps are restricted to prokaryotes. ferritin complex diff --git a/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl b/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl index eb0ca92f..804b4e0f 100644 --- a/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl +++ b/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl @@ -92,21 +92,10 @@ - - - - - Herpesviridae - - Herpesviridae - - - - - + Cytomegalovirus Cytomegalovirus @@ -117,15 +106,15 @@ - - Human gammaherpesvirus 4 + + human gammaherpesvirus 4 Epstein Barr virus Epstein-Barr virus Epstein-Barr virus EBV Human herpesvirus 4 Human herpesvirus type 4 - Human gammaherpesvirus 4 + human gammaherpesvirus 4 @@ -146,35 +135,6 @@ - - - - - Flaviviridae - Flavivirus (arbovirus group B) - - Flaviviridae - - - - - - - - - Hepacivirus C - Hepatitis C virus - hepatitis C virus HCV - human hepatitis C virus - human hepatitis C virus HCV - human hepatitis virus C HCV - post-transfusion hepatitis non A non B virus - - Hepacivirus C - - - - @@ -248,7 +208,7 @@ - + Dengue virus Dengue virus @@ -349,6 +309,17 @@ + + + + + Orthoherpesviridae + + Orthoherpesviridae + + + + @@ -519,7 +490,7 @@ Saccharomyces cerevisiae - S. cerevisiae + Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast diff --git a/src/ontology/OntoFox_outputs/OMRSE_imports.owl b/src/ontology/OntoFox_outputs/OMRSE_imports.owl index 222d6591..2d6dadba 100644 --- a/src/ontology/OntoFox_outputs/OMRSE_imports.owl +++ b/src/ontology/OntoFox_outputs/OMRSE_imports.owl @@ -84,6 +84,12 @@ + + + + + + @@ -93,6 +99,30 @@ health care provider role + + + + + + + + hospital role + A healthcare provider role that inheres in an organization and is realized by providing inpatient care. + + hospital role + + + + + + + + + hospital organization + An organization that is the bearer of a hospital role. + + hospital organization + diff --git a/src/ontology/OntoFox_outputs/OPL_imports.owl b/src/ontology/OntoFox_outputs/OPL_imports.owl index 359d0929..e0f63af5 100644 --- a/src/ontology/OntoFox_outputs/OPL_imports.owl +++ b/src/ontology/OntoFox_outputs/OPL_imports.owl @@ -50,15 +50,6 @@ - - - - label - label - - - - - - material entity - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - - material entity - + @@ -120,7 +116,6 @@ - lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. @@ -181,7 +176,6 @@ - blood A fluid that is composed of blood plasma and erythrocytes. @@ -194,7 +188,6 @@ - amnion The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. @@ -207,7 +200,6 @@ - breast The upper ventral region of the torso of an organism. @@ -233,7 +225,6 @@ - throat In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. @@ -330,7 +321,6 @@ - epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. @@ -355,7 +345,6 @@ - aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. @@ -489,7 +478,6 @@ - adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. @@ -782,7 +770,6 @@ - cheek A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. @@ -807,7 +794,6 @@ - coronary artery @@ -821,7 +807,6 @@ - artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. @@ -834,7 +819,6 @@ - vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. @@ -907,7 +891,6 @@ - nasal cavity mucosa The mucous membrane that lines the nasal cavity[MP]. @@ -920,7 +903,6 @@ - minor salivary gland One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. @@ -982,7 +964,6 @@ - milk @@ -1045,7 +1026,6 @@ - areola Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. @@ -1095,7 +1075,6 @@ - dermis The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. @@ -1108,7 +1087,6 @@ - hypodermis Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. @@ -1121,7 +1099,6 @@ - skin of body The organ covering the body that consists of the dermis and epidermis. @@ -1146,7 +1123,6 @@ - liver An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. @@ -1171,7 +1147,6 @@ - integument The dermis, epidermis and hypodermis. @@ -1184,7 +1159,6 @@ - peritoneum @@ -1308,7 +1282,6 @@ - esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. @@ -1345,7 +1318,6 @@ - trachea The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. @@ -1395,7 +1367,6 @@ - mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. @@ -1408,7 +1379,6 @@ - mucosa of oropharynx A mucosa that is part of a oropharynx [Automatically generated definition]. @@ -1517,7 +1487,6 @@ - tibial artery @@ -1543,7 +1512,6 @@ - tendon of biceps brachii A tendon that attaches_to a biceps brachii. @@ -1630,7 +1598,6 @@ - suprapubic skin Area of skin in the hypoastric region of the abdomen. diff --git a/src/ontology/OntoFox_outputs/VO_imports.owl b/src/ontology/OntoFox_outputs/VO_imports.owl index 29867e45..186d1125 100644 --- a/src/ontology/OntoFox_outputs/VO_imports.owl +++ b/src/ontology/OntoFox_outputs/VO_imports.owl @@ -25,17 +25,9 @@ - editor preferred label - editor preferred label - editor preferred term editor preferred term - editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - editor preferred label - editor preferred label - editor preferred term editor preferred term - editor preferred term~editor preferred label @@ -43,14 +35,9 @@ - definition definition - textual definition - The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - definition definition - textual definition @@ -65,10 +52,7 @@ - - label - label - + @@ -100,7 +84,7 @@ vaccine - A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. + Material entity that is manufactured to realize the vaccine function. vaccine @@ -112,7 +96,7 @@ vaccination - a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response. + A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. vaccination From da8c18cfa88d8fc7bef961c48bf441eb0c21f43f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:54:42 -0500 Subject: [PATCH 13/23] Relabel ion channel activity --- src/ontology/templates/assays.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index a181a7df..f8315797 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -18,8 +18,8 @@ OBI:0000435 genotyping assay metadata complete genotype profiling|SNP analysis OBI:0000438 DNA sequence variation detection assay ready for release An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. OBI Biomaterial Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 Philippe Rocca-Serra subclass assay DNA extract measurement datum sequence feature identification objective OBI:0000443 analyte assay ready for release An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Bjoern Peters|Helen Parkinson|Philippe Rocca-Serra|Alan Ruttenberg|OBI Planned process branch example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output Bjoern Peters|Helen Parkinson|Philippe Rocca-Serra|Alan Ruttenberg subclass assay measurement datum analyte measurement objective OBI:0000445 mass measurement assay metadata complete An assay that determines the mass of an evaluant OBI The patients was weighed and mass was determined to be 47 kilograms Helen Parkinson subclass assay material entity mass measurement datum -OBI:0000447 intracellular electrophysiology recording assay metadata incomplete An electrophysiology assay where the recording location of the electrode is intracellular. Frank Gibson Frank Gibson subclass electrophysiology assay mass measurement datum ion channel activity -OBI:0000454 extracellular electrophysiology recording assay metadata complete An electrophysiology assay where the recording location of the electrode is extracellular. Frank Gibson The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron Frank Gibson|Helen Parkinson subclass electrophysiology assay mass measurement datum ion channel activity +OBI:0000447 intracellular electrophysiology recording assay metadata incomplete An electrophysiology assay where the recording location of the electrode is intracellular. Frank Gibson Frank Gibson subclass electrophysiology assay mass measurement datum monoatomic ion channel activity +OBI:0000454 extracellular electrophysiology recording assay metadata complete An electrophysiology assay where the recording location of the electrode is extracellular. Frank Gibson The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron Frank Gibson|Helen Parkinson subclass electrophysiology assay mass measurement datum monoatomic ion channel activity OBI:0000470 mass spectrometry assay An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. Philippe Rocca-Serra Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. Philippe Rocca-Serra equivalent assay mass spectrometer OBI:0000520 clinical chemistry assay metadata complete detection of analyte in blood sample|chemical pathology An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. url:https://en.wikipedia.org/wiki/Clinical_chemistry Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Philippe Rocca-Serra subclass analyte assay bodily fluid specimen scattered molecular aggregate OBI:0000537 copy number variation profiling assay metadata complete CNV analysis An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 Philippe Rocca-Serra subclass assay measurement datum genetic characteristics information From 4735c9b63adb4215734ea7618f77f9fe7c89503e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:57:33 -0500 Subject: [PATCH 14/23] Replace reclassified Hepacivirus C term --- .../OntoFox_inputs/NCBITaxon_input.txt | 2 +- .../OntoFox_outputs/NCBITaxon_imports.owl | 32 ++++++++++++++++++- src/ontology/templates/assays.tsv | 4 +-- 3 files changed, 34 insertions(+), 4 deletions(-) diff --git a/src/ontology/OntoFox_inputs/NCBITaxon_input.txt b/src/ontology/OntoFox_inputs/NCBITaxon_input.txt index 0c2eeb45..f93d913d 100755 --- a/src/ontology/OntoFox_inputs/NCBITaxon_input.txt +++ b/src/ontology/OntoFox_inputs/NCBITaxon_input.txt @@ -30,7 +30,6 @@ http://purl.obolibrary.org/obo/NCBITaxon_11676 http://purl.obolibrary.org/obo/NCBITaxon_11709 http://purl.obolibrary.org/obo/NCBITaxon_388799 http://purl.obolibrary.org/obo/NCBITaxon_10407 -http://purl.obolibrary.org/obo/NCBITaxon_11103 http://purl.obolibrary.org/obo/NCBITaxon_10376 http://purl.obolibrary.org/obo/NCBITaxon_10358 http://purl.obolibrary.org/obo/NCBITaxon_160 @@ -41,6 +40,7 @@ http://purl.obolibrary.org/obo/NCBITaxon_33208 #Metazoa http://purl.obolibrary.org/obo/NCBITaxon_784 http://purl.obolibrary.org/obo/NCBITaxon_12637 #Dengue http://purl.obolibrary.org/obo/NCBITaxon_37124 #Chikungunya +http://purl.obolibrary.org/obo/NCBITaxon_3052230 # Hepacivirus hominis [Top level source term URIs and target direct superclass URIs] diff --git a/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl b/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl index 804b4e0f..cc1bfccb 100644 --- a/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl +++ b/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl @@ -135,6 +135,18 @@ + + + + + Flaviviridae + Flavivirus (arbovirus group B) + + Flaviviridae + + + + @@ -208,7 +220,7 @@ - + Dengue virus Dengue virus @@ -320,6 +332,24 @@ + + + + + Hepacivirus hominis + Hepacivirus C + Hepatitis C virus + hepatitis C virus HCV + human hepatitis C virus + human hepatitis C virus HCV + human hepatitis virus C HCV + post-transfusion hepatitis non A non B virus + + Hepacivirus hominis + + + + diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index f8315797..20ecb6da 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -260,7 +260,7 @@ OBI:0002147 HIV group O antibody assay HIV I/II Plus O assay An antigen specif OBI:0002148 surface HBV antibody assay HBsAb assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) OBI:0002149 core HBV antibody assay HBcAb assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) OBI:0002150 core HBV IgM antibody assay HBcAb-IgM assay An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) -OBI:0002151 HCV antibody assay HCV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepacivirus C')) +OBI:0002151 HCV antibody assay HCV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepacivirus hominis')) OBI:0002152 EBV IgG antibody assay EBV IgG Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) OBI:0002153 EBV IgM antibody assay EBV IgM Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) OBI:0002154 CMV antibody assay CMV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Cytomegalovirus')) @@ -268,7 +268,7 @@ OBI:0002155 venereal disease research laboratory test VDRL test An analyte ass OBI:0002156 rapid plasma reagin test RPR assay An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay immunoglobulin complex OBI:0002157 HBV surface antigen assay HBsAg assay An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay Hepatitis B virus OBI:0002158 HIV-1 nucleic acid testing HIV-1 NAT An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay ('nucleic acid' and ('part of' some 'Human immunodeficiency virus 1')) -OBI:0002159 HCV nucleic acid testing HCV NAT An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay ('nucleic acid' and ('part of' some 'Hepacivirus C')) +OBI:0002159 HCV nucleic acid testing HCV NAT An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay ('nucleic acid' and ('part of' some 'Hepacivirus hominis')) OBI:0002160 multiplexed indexed T7 ChIP-seq assay ready for release Mint-ChIP|Mint-ChIP-seq A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. url:http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00863-1 Jason Hilton|Chris Stoeckert ENCODE DCC https://github.com/obi-ontology/obi/issues/829 subclass ChIP-seq assay OBI:0002161 systematic evolution of ligands by exponential enrichment assay SELEX A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ PMID:21720957 Rebecca Jackson subclass binding assay OBI:0002162 footprinting assay An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. doi:10.1002/3527600906.mcb.200300025 Bjoern Peters subclass assay From 9b29611bfb56dcc88e74c3aa6e55ddce8b7bb79f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:09:43 -0500 Subject: [PATCH 15/23] Relabel Human gammaherpesvirus 4 term --- src/ontology/templates/assays.tsv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 20ecb6da..fda43767 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -261,8 +261,8 @@ OBI:0002148 surface HBV antibody assay HBsAb assay An antigen specific antibod OBI:0002149 core HBV antibody assay HBcAb assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) OBI:0002150 core HBV IgM antibody assay HBcAb-IgM assay An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) OBI:0002151 HCV antibody assay HCV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepacivirus hominis')) -OBI:0002152 EBV IgG antibody assay EBV IgG Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) -OBI:0002153 EBV IgM antibody assay EBV IgM Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) +OBI:0002152 EBV IgG antibody assay EBV IgG Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'human gammaherpesvirus 4')) +OBI:0002153 EBV IgM antibody assay EBV IgM Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'human gammaherpesvirus 4')) OBI:0002154 CMV antibody assay CMV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Cytomegalovirus')) OBI:0002155 venereal disease research laboratory test VDRL test An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay immunoglobulin complex OBI:0002156 rapid plasma reagin test RPR assay An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay immunoglobulin complex @@ -649,7 +649,7 @@ OBI:0003582 cell proliferation assay using carboxyfluorescein succinimidyl ester OBI:0003583 cell viability assay A cytometry assay which measures the number of living cells in a population. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 equivalent cytometry assay viability OBI:0003584 cell viability assay using Annexin V staining A cell viability assay that uses Annexin V staining to detect apoptotic cells. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 equivalent cell viability assay Annexin V staining OBI:0003587 cell culture assay An assay that has cell culture as an input. Sebastian Duesing|Randi Vita equivalent assay cultured cell population -OBI:0003589 serum anti-Epstein-Barr virus antibody level assay EBV An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. Sebastian Duesing|Randi Vita equivalent antigen specific antibodies assay blood serum specimen ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) +OBI:0003589 serum anti-Epstein-Barr virus antibody level assay EBV An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. Sebastian Duesing|Randi Vita equivalent antigen specific antibodies assay blood serum specimen ('immunoglobulin complex' and ('has disposition to bind' some 'human gammaherpesvirus 4')) OBI:0003590 serum anti-cytomegalovirus antibody level assay CMV A CMV antibody assay that has serum as an input. Sebastian Duesing|Randi Vita equivalent CMV antibody assay blood serum specimen OBI:0003598 single cell B cell receptor repertoire sequencing assay single cell B cell receptor repertoire sequencing assay single-cell BCR assay A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. Sebastian Duesing|Randi Vita subclass B cell receptor repertoire sequencing assay nucleic acid extract OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell T cell receptor repertoire sequencing assay single-cell TCR assay A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. Sebastian Duesing|Randi Vita subclass T cell receptor repertoire sequencing assay nucleic acid extract From b5cbd585f17ea0a986a5f56b6cd6fc52a2219162 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:12:40 -0500 Subject: [PATCH 16/23] Relabel L-iditol 2-dehydrogenase activity --- src/ontology/templates/assays.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index fda43767..4944d1c4 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -624,7 +624,7 @@ OBI:0003430 gamma-glutamyltransferase activity level assay An enzymatic activ OBI:0003431 glutamate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay glutamate dehydrogenase [NAD(P)+] activity OBI:0003432 isocitrate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay isocitrate dehydrogenase [NAD(P)+] activity OBI:0003433 lactate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay lactate dehydrogenase activity -OBI:0003434 sorbitol dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay L-iditol 2-dehydrogenase activity +OBI:0003434 sorbitol dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay L-iditol 2-dehydrogenase (NAD+) activity OBI:0003435 acyl-CoA oxidase activity level assay An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. James A. Overton equivalent enzymatic activity level assay acyl-CoA oxidase activity OBI:0003436 N-acetyl-beta-glucosaminidase activity level assay An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. James A. Overton equivalent enzymatic activity level assay beta-N-acetylglucosaminidase activity OBI:0003437 ribonuclease activity level assay An enzymatic activity level assay that measures the activity of ribonuclease in a sample. James A. Overton equivalent enzymatic activity level assay ribonuclease activity From 6b056324dea23e4722f84e7e6ab0cf2b2b41acc6 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:14:54 -0500 Subject: [PATCH 17/23] Relabel RNA nuclease activity --- src/ontology/templates/assays.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 4944d1c4..f2da68b8 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -627,7 +627,7 @@ OBI:0003433 lactate dehydrogenase activity level assay An enzymatic activity OBI:0003434 sorbitol dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay L-iditol 2-dehydrogenase (NAD+) activity OBI:0003435 acyl-CoA oxidase activity level assay An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. James A. Overton equivalent enzymatic activity level assay acyl-CoA oxidase activity OBI:0003436 N-acetyl-beta-glucosaminidase activity level assay An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. James A. Overton equivalent enzymatic activity level assay beta-N-acetylglucosaminidase activity -OBI:0003437 ribonuclease activity level assay An enzymatic activity level assay that measures the activity of ribonuclease in a sample. James A. Overton equivalent enzymatic activity level assay ribonuclease activity +OBI:0003437 ribonuclease activity level assay An enzymatic activity level assay that measures the activity of ribonuclease in a sample. James A. Overton equivalent enzymatic activity level assay RNA nuclease activity OBI:0003438 galactosidase activity level assay An enzymatic activity level assay that measures the activity of galactosidase in a sample. James A. Overton equivalent enzymatic activity level assay galactosidase activity OBI:0003457 epitope protection from infectious challenge experiment based on survival survival after infectious challenge An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. IEDB Hector Guzman-Orozco https://github.com/obi-ontology/obi/issues/1594 subclass epitope protection from infectious challenge experiment OBI:0003458 epitope protection from tumor challenge experiment based on burden burden after tumor challenge An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. IEDB Hector Guzman-Orozco https://github.com/obi-ontology/obi/issues/1594 subclass epitope protection from tumor challenge experiment From 195fd31aa054632c94f788b12cadae20a4ef94d2 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:16:27 -0500 Subject: [PATCH 18/23] Relabel cellular response to DNA damage stimulus --- src/ontology/templates/assays.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index f2da68b8..71399d18 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -656,7 +656,7 @@ OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay -OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus +OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity DNA damage response OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course OBI:0600017 assay detecting a molecular label pending final vetting An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached OBI developer call, 3-12-12 Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present Matthew Brush subclass assay molecular-labeled material measurement datum molecular-labeled material From 6a2d03592099b97a6d074fbaf0de6842fbed0cd4 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:32:29 -0500 Subject: [PATCH 19/23] Relabel interferon-gamma production --- src/ontology/templates/assays.tsv | 2 +- src/ontology/templates/epitope-assays.tsv | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 71399d18..a25ebd5a 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -666,7 +666,7 @@ OBI:0600026 longitudinal mass measurement assay metadata complete An assay tha OBI:0600031 enzyme-linked immunospot assay ELISPOT assay A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. IEDB Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. IEDB subclass logical definition does not capture details of processing cytometry assay cultured cell population immunoglobulin complex, circulating OBI:0600045 3D structure determination assay An assay that determines the 3-dimensional configuration of an input material. IEDB The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. IEDB equivalent assay 3D structural organization datum OBI:0600047 sequencing assay pending final vetting An assay the uses chemical or biochemical means to infer the sequence of a biomaterial OBI branch derived The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template PlanAndPlannedProcess Branch equivalent assay ('nucleic acid extract' or ('has part' some protein)) ('protein sequencer' or 'nucleic acid sequencer' or 'DNA sequencer') sequence data region -OBI:1110207 assay detecting IFN-gamma production ready for release IFNg release An assay that determines information about the production of the cytokine interferon gamma IEDB An IFN-g ELISPOT is an assay detecting ifn-gamma production Bjoern Peters equivalent assay ('measurement datum' and ('is about' some 'interferon-gamma production')) +OBI:1110207 assay detecting IFN-gamma production ready for release IFNg release An assay that determines information about the production of the cytokine interferon gamma IEDB An IFN-g ELISPOT is an assay detecting ifn-gamma production Bjoern Peters equivalent assay ('measurement datum' and ('is about' some 'type II interferon production')) OBI:2100001 carbon dioxide assay An analyte assay that measures the abundance of carbon dioxide PennTURBO team Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X https://github.com/obi-ontology/obi/issues/1253 equivalent analyte assay carbon dioxide OBI:2100002 sodium(1+) assay An analyte assay that measures the abundance of sodium(1+) PennTURBO team Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X https://github.com/obi-ontology/obi/issues/1253 equivalent analyte assay 'sodium(1+)' OBI:2100003 creatinine assay An analyte assay that measures the abundance of creatinine PennTURBO team Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X https://github.com/obi-ontology/obi/issues/1253 equivalent analyte assay creatinine diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv index bdd2534c..df7eb494 100644 --- a/src/ontology/templates/epitope-assays.tsv +++ b/src/ontology/templates/epitope-assays.tsv @@ -68,7 +68,7 @@ OBI:0001309 intracellular cytokine staining assay measuring epitope specific int OBI:0001311 X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex 3D structure|x-ray crystallography|angstroms A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent X-ray crystallography 3D molecular structure determination assay 3D structural organization datum epitope:MHC:TCR complex angstrom OBI:0001315 ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells CCL1/TCA-3 release|ELISA An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('chemokine (C-C motif) ligand 1 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001317 flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex T cell- APC binding|binding assay A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass flow cytometry assay categorical binding datum MHC:epitope complex binding to TCR -OBI:0001319 cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells IFNg release|bioassay A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent reporter cell line analyte detection bioassay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001319 cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells IFNg release|bioassay A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent reporter cell line analyte detection bioassay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001322 ELISPOT assay measuring epitope specific granzyme B release by T cells granzyme B release|ELISPOT An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('granzyme B release during T cell degranulation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001324 in vivo assay measuring T cell epitope specific tolerance induction tolerance|in vivo assay An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent epitope tolerance induction experiment ('T cell tolerance induction' and ('process is result of' some 'MHC:epitope complex binding to TCR')) (Metazoa and ('has quality' some alive)) OBI:0001325 detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells CCL5/RANTES release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. IEDB IEDB equivalent detection of specific nucleic acid polymers with complementary probes ('chemokine (C-C motif) ligand 5 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -85,7 +85,7 @@ OBI:0001345 assay measuring epitope specific chemokine (C-C motif) ligand 4 prod OBI:0001346 ELISA measuring epitope specific interleukin-21 production by T cells IL-21 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-21 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001348 in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity type IV hypersensitivity (DTH)|in vivo skin test An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent efficacy of epitope intervention experiment ('type IV hypersensitivity' and ('process is result of' some 'MHC:epitope complex binding to TCR')) (Metazoa and ('has quality' some alive)) OBI:0001349 cytometric bead array assay measuring epitope specific interleukin-13 production by T cells IL-13 release|cytometric bead array A cytometric bead array assay that detects interleukin-13 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('interleukin-13 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001350 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells IFNg release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001350 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells IFNg release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001353 cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|cytometric bead array A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001354 ELISPOT assay measuring epitope specific interleukin-17 production by T cells IL-17 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-17 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001356 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells IFNb release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('interferon-beta production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -98,7 +98,7 @@ OBI:0001368 cytometric bead array assay measuring epitope specific tumor necrosi OBI:0001370 intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells CCL4/MIP-1b release|ICS A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('chemokine (C-C motif) ligand 4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001376 intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells IL-3 release|ICS A flow cytometry assay that detects interleukin-3 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interleukin-3 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001378 ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells CCL4/MIP-1b release|ELISA An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('chemokine (C-C motif) ligand 4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001379 cytometric bead array assay measuring epitope specific interferon-gamma production by T cells IFNg release|cytometric bead array A cytometric bead array assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001379 cytometric bead array assay measuring epitope specific interferon-gamma production by T cells IFNg release|cytometric bead array A cytometric bead array assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001380 assay measuring epitope specific interleukin-18 production by T cells IL-18 release|biological activity A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('interleukin-18 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001382 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells IL-27 release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('interleukin-27 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001383 detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells CXCL10/IP-10 release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('IP-10 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -118,10 +118,10 @@ OBI:0001406 assay measuring epitope specific interleukin-3 production by T cells OBI:0001407 assay measuring epitope specific T cell activation activation|biological activity A T cell epitope dependent biological activity assay that detects T cell activation. IEDB IEDB equivalent assay ('T cell activation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001412 cytometric bead array assay measuring epitope specific RANTES production by T cells CCL5/RANTES release|cytometric bead array A cytometric bead array assay that detects RANTES production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('chemokine (C-C motif) ligand 5 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001413 cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells IL-6 release|bioassay A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent reporter cell line analyte detection bioassay ('interleukin-6 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001414 assay measuring epitope specific interferon-gamma production by T cells IFNg release|biological activity A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001414 assay measuring epitope specific interferon-gamma production by T cells IFNg release|biological activity A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001416 assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|biological activity An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001423 intracellular material detection measuring epitope specific granzyme B release by T cells granzyme B release|intracellular staining A flow cytometry assay that detects epitope specific granzyme B release by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('granzyme B release during T cell degranulation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001433 radio immuno assay measuring epitope specific interferon-gamma production by T cells IFNg release|radio immuno assay (RIA) A radio immuno assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent radio immuno assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001433 radio immuno assay measuring epitope specific interferon-gamma production by T cells IFNg release|radio immuno assay (RIA) A radio immuno assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent radio immuno assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001436 assay measuring epitope specific granzyme B release by T cells granzyme B release|biological activity A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('granzyme B release during T cell degranulation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001437 intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells CXCL9/MIG release|ICS A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('chemokine (C-X-C motif) ligand 9 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001438 ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells CCL9/MIP-1g release|ELISA An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('macrophage inflammatory protein-1 gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -504,7 +504,7 @@ OBI:0003612 electron microscopy assay determining the 3D structure of a T cell e OBI:0003613 electron microscopy assay determining the 3D structure of a MHC:ligand complex 3D structure|electron microscopy An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex. IEDB PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters equivalent electron-microscopy 3D molecular structure determination assay 3D structural organization datum MHC:ligand complex OBI:1110013 ELISPOT assay measuring epitope specific interleukin-2 production by T cells IL-2 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-2 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110037 assay measuring binding of a T cell epitope:MHC:TCR complex T cell binding|any method A T cell epitope assay that measures the binding of T cell receptor to an epitope. IEDB IEDB equivalent assay binding datum MHC:epitope complex binding to TCR -OBI:1110059 ELISPOT assay measuring epitope specific interferon-gamma production by T cells IFNg release|ELISPOT An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:1110059 ELISPOT assay measuring epitope specific interferon-gamma production by T cells IFNg release|ELISPOT An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110124 assay measuring qualitative binding of a T cell epitope:MHC:TCR complex qualitative binding|binding assay An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay categorical binding datum MHC:epitope complex binding to TCR OBI:1110125 assay measuring MHC ligand processing and presentation ligand presentation|any method A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. IEDB IEDB equivalent assay cell ('MHC protein complex binding to ligand' and ('process is result of' some 'antigen processing and presentation')) OBI:1110126 assay measuring binding of a MHC:ligand complex MHC binding|any method A MHC ligand assay that detects the binding of a ligand to an MHC molecule. IEDB IEDB equivalent assay binding datum MHC protein complex binding to ligand @@ -514,7 +514,7 @@ OBI:1110129 assay measuring epitope specific cytokine production by T cells c OBI:1110130 assay measuring epitope specific T cell killing cytotoxicity|biological activity A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. IEDB IEDB equivalent cell-cell killing assay ('T cell mediated cytotoxicity' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110131 assay measuring epitope specific proliferation of T cells proliferation|biological activity A T cell epitope dependent biological activity assay that detects T cell proliferation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('T cell proliferation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110150 51 chromium assay measuring epitope specific T cell killing cytotoxicity|51 chromium A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. IEDB IEDB equivalent chromium release assay ('T cell mediated cytotoxicity' and ('process is result of' some 'MHC:epitope complex binding to TCR')) cell culture -OBI:1110151 ELISA measuring epitope specific interferon-gamma production by T cells IFNg release|ELISA An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:1110151 ELISA measuring epitope specific interferon-gamma production by T cells IFNg release|ELISA An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110152 ELISA measuring epitope specific interleukin-2 production by T cells IL-2 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-2 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110153 ELISA measuring epitope specific interleukin-4 production by T cells IL-4 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110154 ELISA measuring epitope specific interleukin-5 production by T cells IL-5 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-5 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -531,7 +531,7 @@ OBI:1110167 ELISPOT assay measuring epitope specific interleukin-4 production by OBI:1110168 ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|ELISPOT An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells IEDB IEDB equivalent enzyme-linked immunospot assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110170 ELISPOT assay measuring epitope specific interleukin-10 production by T cells IL-10 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-10 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110171 ELISPOT assay measuring epitope specific interleukin-13 production by T cells IL-13 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-13 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:1110172 intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells IFNg release|ICS A flow cytometry assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:1110172 intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells IFNg release|ICS A flow cytometry assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110173 intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells IL-2 release|ICS A flow cytometry assay that detects interleukin-2 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interleukin-2 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110174 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|ICS A flow cytometry assay that detects tumor necrosis factor alpha production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110175 intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells IL-4 release|ICS A flow cytometry assay that detects interleukin-4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interleukin-4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) From 50c495ee5051d83fac678b67ef91382d1747dbf1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:35:27 -0500 Subject: [PATCH 20/23] Run make modules --- src/ontology/modules/assays.owl | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 274f2f8e..a294de99 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -1316,12 +1316,6 @@ - - - - - - @@ -1340,6 +1334,12 @@ + + + + + + @@ -14465,7 +14465,7 @@ - + @@ -14483,7 +14483,7 @@ - + @@ -14901,7 +14901,7 @@ - + @@ -14919,7 +14919,7 @@ - + From 6be7836c4575a5cbbdfdc404e1781b7f2d45e1a1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 16 Aug 2024 11:45:18 -0500 Subject: [PATCH 21/23] Add fourth assay term and standardize labels --- src/ontology/modules/assays.owl | 132 +++++++++++++++++++----------- src/ontology/templates/assays.tsv | 7 +- 2 files changed, 89 insertions(+), 50 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 736011ac..8a3beeff 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -26630,13 +26630,13 @@ - in vitro CRISPR screening assay + in vitro CRISPR screen assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 Jennifer Jou - in vitro CRISPR screening assay + in vitro CRISPR screen assay @@ -26644,22 +26644,26 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + in vitro CRISPR screen using single-cell RNA-seq - An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression + An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 @@ -26672,40 +26676,74 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - in vitro CRISPR perturbation screen using FISH and flow cytometry - An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes + + + + + + + + + + + + + + + + + + + in vitro CRISPR perturbation screen using flow cytometry + An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 Jennifer Jou - in vitro CRISPR perturbation screen using FISH and flow cytometry + in vitro CRISPR screen using flow cytometry + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry + An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. + Jennifer Jou + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index dd09d688..3676eb62 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -656,9 +656,10 @@ OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay -OBI:0003659 in vitro CRISPR screening assay in vitro CRISPR screening assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell -OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay -OBI:0003661 in vitro CRISPR perturbation screen using FISH and flow cytometry in vitro CRISPR perturbation screen using FISH and flow cytometry An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay flow cytometry assay|fluorescence in-situ hybridization assay +OBI:0003659 in vitro CRISPR screen assay in vitro CRISPR screen assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell +OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay single-cell RNA sequencing assay +OBI:0003661 in vitro CRISPR screen using flow cytometry in vitro CRISPR perturbation screen using flow cytometry An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay +OBI:0003668 in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Sebastian Duesing Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay|fluorescence imaging-based reporter gene assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course From a0a07c077919129e0aa654017685a511c95f5819 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 19 Aug 2024 14:32:19 -0500 Subject: [PATCH 22/23] Remove OBI:0003668 --- src/ontology/modules/assays.owl | 43 ------------------------------- src/ontology/templates/assays.tsv | 1 - 2 files changed, 44 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 8a3beeff..88cee146 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -26705,49 +26705,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry - An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. - Jennifer Jou - Sebastian Duesing - https://github.com/obi-ontology/obi/issues/1784 - Jennifer Jou - in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry - - - - diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 3676eb62..8ea6c7ed 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -659,7 +659,6 @@ OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluore OBI:0003659 in vitro CRISPR screen assay in vitro CRISPR screen assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay single-cell RNA sequencing assay OBI:0003661 in vitro CRISPR screen using flow cytometry in vitro CRISPR perturbation screen using flow cytometry An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay -OBI:0003668 in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Sebastian Duesing Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay|fluorescence imaging-based reporter gene assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course From 713dce86d9aafcc7ad9a4f6e84ff486478eb234e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 22 Aug 2024 14:18:11 -0500 Subject: [PATCH 23/23] Remove references to 3 obsoleted GO classes in obi-edit --- src/ontology/obi-edit.owl | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index f0ece3b6..a3e6d377 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -2259,12 +2259,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - @@ -2339,12 +2333,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - @@ -2667,12 +2655,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - -