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Add Fiber-seq and chromatin accessibility assays #1836

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Add Fiber-seq and chromatin accessibility assays #1836

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37 changes: 36 additions & 1 deletion src/ontology/modules/assays.owl
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<!-- http://purl.obolibrary.org/obo/OBI_0002039 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002039">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003686"/>
<obo:IAO_0000112>Kasinathan et al., (February 2014). &quot;High-resolution mapping of transcription factor binding sites on natitve chromatin.&quot; Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Stoeckert</obo:IAO_0000117>
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<!-- http://purl.obolibrary.org/obo/OBI_0003686 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003686">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<obo:IAO_0000111>chromatin accessibility assay</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">An assay that determines which regions of a DNA molecule are in the form of euchromatin and thus able to make direct physical contact with (i.e. are accessible to) other molecules such as RNA polymerase, transcription factors, etc.</obo:IAO_0000115>
<obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>Michelle Giglio</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000119>Michelle Giglio</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1813</obo:IAO_0000233>
<obo:IAO_0000234>Jennifer Jou</obo:IAO_0000234>
<rdfs:label>chromatin accessibility assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003687 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003687">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003686"/>
<obo:IAO_0000111>m6A-MTase sequencing assay</obo:IAO_0000111>
<obo:IAO_0000112>https://pubmed.ncbi.nlm.nih.gov/32587015/</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MTase) and then sequenced using single-molecule circular consensus sequencing to identify regions of accessible DNA at nucleotide resolution.</obo:IAO_0000115>
<obo:IAO_0000117>Jennifer Jou</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>Fiber-seq</obo:IAO_0000118>
<obo:IAO_0000119>Jennifer Jou</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1813</obo:IAO_0000233>
<obo:IAO_0000234>Jennifer Jou</obo:IAO_0000234>
<rdfs:label>m6A-MTase sequencing assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0100016 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100016"/>
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4 changes: 3 additions & 1 deletion src/ontology/templates/assays.tsv
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Expand Up @@ -220,7 +220,7 @@ OBI:0002035 peptide mass fingerprinting assay protein fingerprinting|PMF A mas
OBI:0002036 array based nucleic acid structure mapping assay An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. OBI:0000870 pmid:23580730 Janos Demeter|Chris Stoeckert https://sourceforge.net/p/obi/obi-terms/725/ subclass assay
OBI:0002037 micrococcal nuclease digestion followed by tiling array assay 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 pmid:17873876 Janos Demeter|Chris Stoeckert https://sourceforge.net/p/obi/obi-terms/725/ subclass array based nucleic acid structure mapping assay
OBI:0002038 ribosomal profiling by sequencing assay ribosomal profiling|Ribo-seq|Ribo-seq assay A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. PMID:24468696 Aspden et al., (August 2014). ""Extensive translation of small open reading frames revealed by poly-ribo-seq."" eLIFE 2014;3:e03528 Venkat Malladi|Chris Stoeckert|Jie Zheng subclass RNA-seq assay
OBI:0002039 assay for transposase-accessible chromatin using sequencing ATAC-seq|ATAC-seq assay An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. PMID:24097267 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. Venkat Malladi|Chris Stoeckert|Jie Zheng subclass assay
OBI:0002039 assay for transposase-accessible chromatin using sequencing ATAC-seq|ATAC-seq assay An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. PMID:24097267 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. Venkat Malladi|Chris Stoeckert|Jie Zheng subclass chromatin accessibility assay
OBI:0002040 chromatin isolation by RNA purification sequencing assay ChIRP-seq|Chromatin Isolation by RNA purification|ChIRP-seq assay 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. PMID:21963238 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. Venkat Malladi|Chris Stoeckert|Jie Zheng subclass detection of specific nucleic acid polymers with complementary probes DNA sequencing assay
OBI:0002041 self-transcribing active regulatory region sequencing assay self-transcribing active regulatory region sequencing|STARR-seq assay|STARR-seq 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. PMID:23328393 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. Venkat Malladi|Chris Stoeckert|Jie Zheng subclass RNA-seq assay
OBI:0002042 carbon-copy chromosome conformation capture assay followed by sequencing assay HiC|Carbon-copy chromosome conformation capture assay followed by sequencing|HiC assay 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. PMID:19815776 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. Venkat Malladi|Chris Stoeckert|Jie Zheng subclass Carbon-copy chromosome conformation capture assay
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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: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:0003686 chromatin accessibility assay chromatin accessibility assay An assay that determines which regions of a DNA molecule are in the form of euchromatin and thus able to make direct physical contact with (i.e. are accessible to) other molecules such as RNA polymerase, transcription factors, etc. Michelle Giglio Sebastian Duesing|Michelle Giglio|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1813 subclass assay
OBI:0003687 m6A-MTase sequencing assay m6A-MTase sequencing assay Fiber-seq A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MTase) and then sequenced using single-molecule circular consensus sequencing to identify regions of accessible DNA at nucleotide resolution. Jennifer Jou https://pubmed.ncbi.nlm.nih.gov/32587015/ Jennifer Jou|Sebastian Duesing Jennifer Jou https://github.com/obi-ontology/obi/issues/1813 subclass chromatin accessibility 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 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
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