diff --git a/src/ontology/modules/epitope-assays.owl b/src/ontology/modules/epitope-assays.owl
index 4f4ee941..15c3a55c 100644
--- a/src/ontology/modules/epitope-assays.owl
+++ b/src/ontology/modules/epitope-assays.owl
@@ -22784,6 +22784,70 @@
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+ An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR complex.
+ PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters
+ IEDB
+ 3D structure|electron microscopy
+ electron microscopy assay determining the 3D structure of a T cell epitope:MHC:TCR complex
+
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+ An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex.
+ PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters
+ IEDB
+ 3D structure|electron microscopy
+ electron microscopy assay determining the 3D structure of a MHC:ligand complex
+
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+
diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl
index 0018ad11..509f0623 100644
--- a/src/ontology/obi-edit.owl
+++ b/src/ontology/obi-edit.owl
@@ -502,12 +502,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
-
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reagent role
Buffer, dye, a catalyst, a solvating agent.
@@ -7132,9 +7126,9 @@ that has_part some material entity is a material entity. If we add as equivalent
manufacturing
A planned process with the objective to produce a processed material which will have a function for future use.
+ A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
- A person or organization (having manufacturer role) is a participant in this process
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
@@ -22361,6 +22355,73 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
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+ An objective specification that is fulfilled by causing a disease in a particular organism.
+ Sebastian Duesing
+ disease causation objective
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+ An objective specification that is fulfilled by reducing the severity of a disease in a particular organism.
+ Sebastian Duesing
+ disease severity reduction objective
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+
+ An objective specification that is fulfilled by preventing the development of a disease in a particular organism.
+ Sebastian Duesing
+ disease prevention objective
+
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+ A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction.
+ Sebastian Duesing
+ reactant role
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+ A role borne by a biological or chemical entity which serves as the core component of a chemical reaction process, upon which other reactants, like reagents or solvents, act.
+ Cameron More
+ Sebastian Duesing
+ precursor role
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+ An objective specification that is fulfilled by reducing the prevalence of a disease in a population of organisms.
+ Sebastian Duesing
+ disease prevalence reduction objective
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+
@@ -26941,7 +27002,7 @@ determinations of compounds.
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@@ -33435,5 +33496,5 @@ realizes some 'host of immune response role'
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diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv
index 88a78566..4443e87b 100644
--- a/src/ontology/templates/devices.tsv
+++ b/src/ontology/templates/devices.tsv
@@ -29,7 +29,7 @@ OBI:0000465 organic acid column organic acid column metadata complete An organi
OBI:0000466 thermal conductivity detector thermal conductivity detector metadata complete TCD, hot wire detector The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). WEB:|http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 PERSON:Daniel Schober gas chromatography detector
OBI:0000467 Bruker US 2 NMR magnet Bruker US 2 NMR magnet metadata complete An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189|WEB: PERSON:Daniel Schober NMR instrument Bruker NMR magnet
OBI:0000468 protein column protein column metadata complete A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238|GROUP: PERSON:Daniel Schober refactor as defined class chromatography column
-OBI:0000469 solvent mixer solvent mixer metadata complete A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. GROUP:|http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 PERSON:Daniel Schober check on definition ! chromatography instrument
+OBI:0000469 solvent mixer solvent mixer metadata complete A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. GROUP:|http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 PERSON:Daniel Schober chromatography instrument
OBI:0000473 Bruker NMR Case sample changer Bruker NMR Case sample changer metadata complete The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. WEB:|http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 PERSON:Daniel Schober NMR instrument Bruker autosampler
OBI:0000474 nano pump system nano pump system metadata complete A pump system optimized for nano flow chromatography. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052|GROUP: PERSON:Daniel Schober chromatography pump system
OBI:0000475 Bruker AutoClean system Bruker AutoClean system metadata complete NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. WEB:|http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 PERSON:Daniel Schober washing system/NMR tube washing system, XPS: device has function washing NMR tube washing system
@@ -85,7 +85,7 @@ OBI:0000528 liquid chromatography valve liquid chromatography valve metadata com
OBI:0000529 JEOL NMR probe JEOL NMR probe metadata complete An NMR probe that is manufactured by JEOL. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232|GROUP: PERSON:Daniel Schober NMR device NMR probe
OBI:0000530 Bruker UltraShield Plus NMR magnet Bruker UltraShield Plus NMR magnet metadata complete An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. WEB:|http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 PERSON:Daniel Schober NMR instrument Bruker NMR magnet
OBI:0000531 Bruker CryoProbe Bruker CryoProbe metadata complete The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:\n Significant S/N gains (with moderately salty samples also)\n Short pulse widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191|GROUP: PERSON:Daniel Schober NMR probe Bruker NMR probe
-OBI:0000532 column cartridge column cartridge metadata complete A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055|GROUP: PERSON:Daniel Schober chromatography device, check on definition ! chromatography device
+OBI:0000532 column cartridge column cartridge metadata complete A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055|GROUP: PERSON:Daniel Schober chromatography device
OBI:0000533 affinity column affinity column metadata complete An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. GROUP:|http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 PERSON:Daniel Schober chromatography column
OBI:0000534 tecmag NMR instrument tecmag NMR instrument metadata complete An NMR instrument that is manufactured by tecmag. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250|GROUP: PERSON:Daniel Schober NMR instrument NMR instrument
OBI:0000535 gel filtration column gel filtration column metadata complete A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104|GROUP: PERSON:Daniel Schober size exclusion column
@@ -99,9 +99,9 @@ OBI:0000544 Bruker SampleRail system Bruker SampleRail system metadata complete
OBI:0000545 column compartment column compartment metadata complete For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068|GROUP: PERSON:Daniel Schober chromatography device
OBI:0000546 capillary pump system capillary pump system metadata complete A pump system optimized for capillary chromatography. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051|GROUP: PERSON:Daniel Schober chromatography pump system
OBI:0000547 evaporative light scattering detector evaporative light scattering detector metadata complete The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. WEB:|http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 PERSON:Daniel Schober device measure function
-OBI:0000549 column cartridger column cartridger metadata complete A chromatography device where the column cartridge is inserted into and stabilised. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054|GROUP: PERSON:Daniel Schober check on definition ! chromatography instrument
+OBI:0000549 column cartridger column cartridger metadata complete A chromatography device where the column cartridge is inserted into and stabilised. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054|GROUP: PERSON:Daniel Schober chromatography instrument
OBI:0000550 nitrogen generator nitrogen generator metadata complete A gas generator that generates nitrogen gas. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034|GROUP: PERSON:Daniel Schober gas generator
-OBI:0000551 needle assembly needle assembly metadata complete The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065|GROUP: PERSON:Daniel Schober chromatography device, check on definition ! chromatography device
+OBI:0000551 needle assembly needle assembly metadata complete The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065|GROUP: PERSON:Daniel Schober chromatography device
OBI:0000553 Bruker Capillary LC-NMR platform Bruker Capillary LC-NMR platform metadata complete Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279|WEB: PERSON:Daniel Schober NMR instrument|hyphenated NMR instrument platform Bruker NMR instrument
OBI:0000554 gas chromatography oven gas chromatography oven metadata complete A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039|GROUP: PERSON:Daniel Schober gas chromatography equipment gas chromatography equipment
OBI:0000555 autosampler autosampler metadata complete An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. \n alt The autosampler is an automatic sample changer device. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002|GROUP: PERSON:Daniel Schober NMR instrument device
diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv
index 18012d47..728f93dd 100644
--- a/src/ontology/templates/epitope-assays.tsv
+++ b/src/ontology/templates/epitope-assays.tsv
@@ -500,6 +500,8 @@ OBI:0003486 intracellular cytokine staining assay measuring epitope specific int
OBI:0003487 ELISA measuring epitope specific interleukin-25 production by T cells IL-25 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. IEDB IEDB equivalent enzyme-linked immunosorbent assay ('interleukin-25 production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:0003488 cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells TNF release|bioassay A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. IEDB IEDB equivalent reporter cell line analyte detection bioassay ('tumor necrosis factor superfamily cytokine production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:0003602 quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex QCM measuring KD dissociation constant KD|quartz crystal microbalance|nM A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. IEDB Randi Vita|Bjoern Peters|Sebastian Duesing subclass quartz crystal microbalance assay equilibrium dissociation constant (KD) immunoglobulin binding to epitope nanomolar
+OBI:0003612 electron microscopy assay determining the 3D structure of a T cell epitope:MHC:TCR complex 3D structure|electron microscopy An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR complex. IEDB PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters equivalent electron-microscopy 3D molecular structure determination assay 3D structural organization datum epitope:MHC:TCR complex
+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'))
diff --git a/src/ontology/templates/specimen-assay-data.tsv b/src/ontology/templates/specimen-assay-data.tsv
index 8a7c2f4f..6b48dbdd 100644
--- a/src/ontology/templates/specimen-assay-data.tsv
+++ b/src/ontology/templates/specimen-assay-data.tsv
@@ -1,49 +1,49 @@
-ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item axiom
-ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item EC %
-OBI:0003243 blood assay datum A data item that is the specified output of a blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'blood assay')
-OBI:0003244 blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'blood microbiology assay')
-OBI:0003245 feces assay datum A data item that is the specified output of a feces assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'feces assay')
-OBI:0003246 feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'feces microbiology assay')
-OBI:0003247 urine assay datum A data item that is the specified output of a urine assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'urine assay')
-OBI:0003248 urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'urine microbiology assay')
-OBI:0003249 induced sputum assay datum A data item that is the specified output of a induced sputum assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'induced sputum assay')
-OBI:0003251 induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'induced sputum microbiology assay')
-OBI:0003252 cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'cerebrospinal fluid assay')
-OBI:0003253 cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'cerebrospinal fluid microbiology assay')
-OBI:0003254 endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'endotracheal aspirate assay')
-OBI:0003255 endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'endotracheal tube aspirate microbiology assay')
-OBI:0003256 lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'lung microbiology assay')
-OBI:0003257 nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'nasopharyngeal or oropharyngeal swab microbiology assay')
-OBI:0003258 pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'pleural fluid microbiology assay')
-OBI:0003259 umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'umbilical cord blood assay')
-OBI:0003260 umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'umbilical cord blood microbiology assay')
-OBI:0003261 bacteria in blood datum A blood microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Bacteria)
-OBI:0003262 virus in blood datum A blood microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Viruses)
-OBI:0003263 eukaryota in blood datum A blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Eukaryota)
-OBI:0003264 bacteria in feces datum A feces microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('feces microbiology datum' and 'is about' some Bacteria)
-OBI:0003265 eukaryota in feces datum A feces microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('feces microbiology datum' and 'is about' some Eukaryota)
-OBI:0003266 virus in feces datum A feces microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('feces microbiology datum' and 'is about' some Viruses)
-OBI:0003267 eukaryota in urine datum A urine microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('urine microbiology datum' and 'is about' some Eukaryota)
-OBI:0003268 bacteria in induced sputum datum An induced sputum microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('induced sputum microbiology datum' and 'is about' some Bacteria)
-OBI:0003269 eukaryota in induced sputum datum An induced sputum microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('induced sputum microbiology datum' and 'is about' some Eukaryota)
-OBI:0003270 virus in induced sputum datum An induced sputum microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('induced sputum microbiology datum' and 'is about' some Viruses)
-OBI:0003271 bacteria in endotracheal tube aspirate datum An endotracheal tube aspirate microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('endotracheal tube aspirate microbiology datum' and 'is about' some Bacteria)
-OBI:0003272 bacteria in lung datum A lung microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('lung microbiology datum' and 'is about' some Bacteria)
-OBI:0003273 eukaryota in lung datum A lung microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('lung microbiology datum' and 'is about' some Eukaryota)
-OBI:0003274 virus in lung datum A lung microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('lung microbiology datum' and 'is about' some Viruses)
-OBI:0003275 bacteria in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('nasopharyngeal or oropharyngeal swab microbiology datum' and 'is about' some Bacteria)
-OBI:0003276 eukaryota in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('nasopharyngeal or oropharyngeal swab microbiology datum' and 'is about' some Eukaryota)
-OBI:0003277 virus in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('nasopharyngeal or oropharyngeal swab microbiology datum' and 'is about' some Viruses)
-OBI:0003278 bacteria in pleural fluid datum A pleural fluid microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Bacteria)
-OBI:0003279 eukaryota in pleural fluid datum A pleural fluid microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Eukaryota)
-OBI:0003280 virus in pleural fluid datum A pleural fluid microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Viruses)
-OBI:0003281 eukaryota in umbilical cord blood datum An umbilical cord blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('umbilical cord blood microbiology datum' and 'is about' some Eukaryota)
-OBI:0003365 milk assay datum A data item that is the specified output of a milk assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1515 ('data item' and is_specified_output_of some 'milk assay')
-OBI:0003382 placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('organism detection datum' and is_specified_output_of some 'placental blood microbiology assay')
-OBI:0003383 eukaryota in placental blood datum A placental blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('placental blood microbiology datum' and 'is about' some Eukaryota)
-OBI:0003417 antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('data item' and is_specified_output_of some 'antigen specific antibodies assay')
-OBI:0003420 antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'blood assay')
-OBI:0003421 antigen specific antibodies in milk assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'milk assay')
-OBI:0003577 skin of body microbiology datum An organism detection datum that is the specified output of a skin of body microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'skin of body microbiology assay')
-OBI:0003579 bone marrow microbiology datum An organism detection datum that is the specified output of a bone marrow microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'bone marrow microbiology assay')
-OBI:0003581 nasal aspirate microbiology datum An organism detection datum that is the specified output of a nasal aspirate microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'nasal aspirate microbiology assay')
\ No newline at end of file
+ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item axiom
+ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item EC %
+OBI:0003243 blood assay datum A data item that is the specified output of a blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'blood assay')
+OBI:0003244 blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'blood microbiology assay')
+OBI:0003245 feces assay datum A data item that is the specified output of a feces assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'feces assay')
+OBI:0003246 feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'feces microbiology assay')
+OBI:0003247 urine assay datum A data item that is the specified output of a urine assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'urine assay')
+OBI:0003248 urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'urine microbiology assay')
+OBI:0003249 induced sputum assay datum A data item that is the specified output of a induced sputum assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'induced sputum assay')
+OBI:0003251 induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'induced sputum microbiology assay')
+OBI:0003252 cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'cerebrospinal fluid assay')
+OBI:0003253 cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'cerebrospinal fluid microbiology assay')
+OBI:0003254 endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'endotracheal aspirate assay')
+OBI:0003255 endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'endotracheal tube aspirate microbiology assay')
+OBI:0003256 lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'lung microbiology assay')
+OBI:0003257 nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'nasopharyngeal or oropharyngeal swab microbiology assay')
+OBI:0003258 pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'pleural fluid microbiology assay')
+OBI:0003259 umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'umbilical cord blood assay')
+OBI:0003260 umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'umbilical cord blood microbiology assay')
+OBI:0003261 bacteria in blood datum A blood microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Bacteria)
+OBI:0003262 virus in blood datum A blood microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Viruses)
+OBI:0003263 eukaryota in blood datum A blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Eukaryota)
+OBI:0003264 bacteria in feces datum A feces microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('feces microbiology datum' and 'is about' some Bacteria)
+OBI:0003265 eukaryota in feces datum A feces microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('feces microbiology datum' and 'is about' some Eukaryota)
+OBI:0003266 virus in feces datum A feces microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('feces microbiology datum' and 'is about' some Viruses)
+OBI:0003267 eukaryota in urine datum A urine microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('urine microbiology datum' and 'is about' some Eukaryota)
+OBI:0003268 bacteria in induced sputum datum An induced sputum microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('induced sputum microbiology datum' and 'is about' some Bacteria)
+OBI:0003269 eukaryota in induced sputum datum An induced sputum microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('induced sputum microbiology datum' and 'is about' some Eukaryota)
+OBI:0003270 virus in induced sputum datum An induced sputum microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('induced sputum microbiology datum' and 'is about' some Viruses)
+OBI:0003271 bacteria in endotracheal tube aspirate datum An endotracheal tube aspirate microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('endotracheal tube aspirate microbiology datum' and 'is about' some Bacteria)
+OBI:0003272 bacteria in lung datum A lung microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('lung microbiology datum' and 'is about' some Bacteria)
+OBI:0003273 eukaryota in lung datum A lung microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('lung microbiology datum' and 'is about' some Eukaryota)
+OBI:0003274 virus in lung datum A lung microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('lung microbiology datum' and 'is about' some Viruses)
+OBI:0003275 bacteria in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('nasopharyngeal or oropharyngeal swab microbiology datum' and 'is about' some Bacteria)
+OBI:0003276 eukaryota in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('nasopharyngeal or oropharyngeal swab microbiology datum' and 'is about' some Eukaryota)
+OBI:0003277 virus in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('nasopharyngeal or oropharyngeal swab microbiology datum' and 'is about' some Viruses)
+OBI:0003278 bacteria in pleural fluid datum A pleural fluid microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Bacteria)
+OBI:0003279 eukaryota in pleural fluid datum A pleural fluid microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Eukaryota)
+OBI:0003280 virus in pleural fluid datum A pleural fluid microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Viruses)
+OBI:0003281 eukaryota in umbilical cord blood datum An umbilical cord blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('umbilical cord blood microbiology datum' and 'is about' some Eukaryota)
+OBI:0003365 milk assay datum A data item that is the specified output of a milk assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1515 ('data item' and is_specified_output_of some 'milk assay')
+OBI:0003382 placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('organism detection datum' and is_specified_output_of some 'placental blood microbiology assay')
+OBI:0003383 eukaryota in placental blood datum A placental blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('placental blood microbiology datum' and 'is about' some Eukaryota)
+OBI:0003417 antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('data item' and is_specified_output_of some 'antigen specific antibodies assay')
+OBI:0003420 antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'blood assay')
+OBI:0003421 antigen specific antibodies in milk assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'milk assay')
+OBI:0003577 skin of body microbiology datum An organism detection datum that is the specified output of a skin of body microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'skin of body microbiology assay')
+OBI:0003579 bone marrow microbiology datum An organism detection datum that is the specified output of a bone marrow microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'bone marrow microbiology assay')
+OBI:0003581 nasal aspirate microbiology datum An organism detection datum that is the specified output of a nasal aspirate microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'nasal aspirate microbiology assay')
diff --git a/src/scripts/release-candidate.sh b/src/scripts/release-candidate.sh
index afcd60a7..6654e785 100755
--- a/src/scripts/release-candidate.sh
+++ b/src/scripts/release-candidate.sh
@@ -78,7 +78,7 @@ EOF
if command -v himalaya > /dev/null
then
- himalaya --mailbox Drafts save < "${EMAIL}"
+ himalaya --folder Drafts save < "${EMAIL}"
echo "Draft email created"
else
echo "Draft email created in ${EMAIL}"
diff --git a/src/scripts/release.sh b/src/scripts/release.sh
index f2ad322a..7350a893 100755
--- a/src/scripts/release.sh
+++ b/src/scripts/release.sh
@@ -71,7 +71,7 @@ EOF
if command -v himalaya > /dev/null
then
- himalaya --mailbox Drafts save < "${EMAIL}"
+ himalaya --folder Drafts save < "${EMAIL}"
echo "Draft email created"
else
echo "Draft email created in ${EMAIL}"