From 61460826656f110f118c8c35b0c3c64ea36b2c88 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 31 Aug 2023 16:44:49 -0500 Subject: [PATCH 1/2] Add single-cell BCR and TCR Adds single-cell BCR and TCR assay terms --- src/ontology/modules/assays.owl | 104 +++++++++++++++++++++++++++++- src/ontology/templates/assays.tsv | 2 + 2 files changed, 105 insertions(+), 1 deletion(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 3940fbf7..acf3ba24 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -22,6 +22,12 @@ + + + + + + @@ -26250,6 +26256,102 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + Randi Vita + Sebastian Duesing + single-cell BCR assay + single cell B cell receptor repertoire sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + Randi Vita + Sebastian Duesing + single-cell TCR assay + single cell T cell receptor repertoire sequencing assay + + + + @@ -53019,5 +53121,5 @@ - + diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 3935dedf..78f19981 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -648,6 +648,8 @@ OBI:0003580 nasal aspirate microbiology assay An organism detection assay tha OBI:0003582 cell proliferation assay using carboxyfluorescein succinimidyl ester staining A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 equivalent cell proliferation assay carboxyfluorescein succinimidyl ester staining 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: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 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 ec76a3ba734d6dfb3382d77396935cdd35389865 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 31 Aug 2023 16:58:16 -0500 Subject: [PATCH 2/2] Adds bulk BCR/TCR synonym Adds "bulk TCR assay" and "bulk BCR assay" as synonyms for TCR/BCR receptor repertoire sequencing assays respectively. --- src/ontology/modules/assays.owl | 2 ++ src/ontology/templates/assays.tsv | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index acf3ba24..dbd0162f 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -19680,6 +19680,7 @@ A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. Rebecca Jackson TCR repertoire sequencing assay + bulk TCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 T cell receptor repertoire sequencing assay @@ -19695,6 +19696,7 @@ Rebecca Jackson Antibody repertoire sequencing assay BCR repertoire sequencing assay + bulk BCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 B cell receptor repertoire sequencing assay diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 78f19981..834c4f9a 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -420,8 +420,8 @@ OBI:0002984 capture Hi-C assay cHi-C A Hi-C assay in which a selection step is OBI:0002985 magnetic resonance imaging assay MRI An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging Rebecca Jackson|Alexander D. Bartnik, ORCID:0000-0001-9676-7377|Lucas M. Serra, ORCID:0000-0002-2104-0568|Alexander D. Diehl, ORCID:0000-0001-9990-8331|Mackenzie T. Smith, ORCID:0000-0002-9821-4132|William D. Duncan, ORCID:0000-0001-9625-1899|Lauren M. Wishnie, ORCID:0000-0002-7245-3450 https://github.com/obi-ontology/obi/issues/1290 subclass imaging assay NMR instrument ('has role' some 'magnetic resonance imaging evaluant role') (realizes some (concretizes some 'magnetic resonance pulse sequence protocol')) OBI:0002986 computed tomography imaging assay CT scan|CAT scan|computed tomography scan 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. url:https://www.mayoclinic.org/tests-procedures/ct-scan/about/pac-20393675 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1290 subclass imaging assay computed tomography scanner OBI:0002987 positron emission tomography imaging assay PET scan|positron emission tomography scan An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. url:https://en.wikipedia.org/wiki/Positron_emission_tomography Rebecca Jackson https://github.com/obi-ontology/obi/issues/1290 subclass imaging assay positron emission tomography scanner -OBI:0002990 T cell receptor repertoire sequencing assay TCR repertoire sequencing assay A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay -OBI:0002991 B cell receptor repertoire sequencing assay BCR repertoire sequencing assay|Antibody repertoire sequencing assay 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. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay +OBI:0002990 T cell receptor repertoire sequencing assay TCR repertoire sequencing assay|bulk TCR assay A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay +OBI:0002991 B cell receptor repertoire sequencing assay BCR repertoire sequencing assay|Antibody repertoire sequencing assay|bulk BCR assay 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. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay OBI:0003009 ferritin assay An assay that measures ferritin OBI James A. Overton, ORCID:0000-0001-5139-5557 equivalent assay ferritin complex OBI:0003010 fibrinogen assay An assay that measures fibrinogen OBI James A. Overton, ORCID:0000-0001-5139-5558 equivalent assay fibrinogen complex OBI:0003011 iron assay An analyte assay that measures the abundance of iron OBI James A. Overton, ORCID:0000-0001-5139-5559 equivalent analyte assay iron cation