Skip to content

Commit

Permalink
Merge branch 'master' into ntr_1711
Browse files Browse the repository at this point in the history
  • Loading branch information
@jamesaoverton
jamesaoverton committed Sep 20, 2023
2 parents 8f17dae + 278a1cb commit badcad3
Show file tree
Hide file tree
Showing 2 changed files with 33 additions and 1 deletion.
30 changes: 30 additions & 0 deletions src/ontology/modules/assays.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26537,6 +26537,36 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003604 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003604">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003094"/>
<obo:IAO_0000115>A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging.</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>MERFISH</obo:IAO_0000118>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1724</obo:IAO_0000233>
<obo:IAO_0000234>Brain Image Library</obo:IAO_0000234>
<rdfs:label>multiplexed error-robust fluorescence in situ hybridization assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003605 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003605">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003094"/>
<obo:IAO_0000115>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.</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>smFISH</obo:IAO_0000118>
<obo:IAO_0000119>https://doi.org/10.21769/BioProtoc.3070</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1725</obo:IAO_0000233>
<obo:IAO_0000234>Brain Image Library</obo:IAO_0000234>
<rdfs:label>single molecule fluorescence in situ hybridization</rdfs:label>
</owl:Class>



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100016"/>
Expand Down
4 changes: 3 additions & 1 deletion src/ontology/templates/assays.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -650,10 +650,12 @@ OBI:0003583 cell viability assay A cytometry assay which measures the number
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: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: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
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: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
Expand Down

0 comments on commit badcad3

Please sign in to comment.