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Add three CRISPR assays #1796

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Aug 26, 2024
Merged

Add three CRISPR assays #1796

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585bceb
Add three CRISPR assays
sebastianduesing Jul 9, 2024
a29d3b5
Edit label of OBI:0003660
sebastianduesing Jul 18, 2024
6be7836
Add fourth assay term and standardize labels
sebastianduesing Aug 16, 2024
a0a07c0
Remove OBI:0003668
sebastianduesing Aug 19, 2024
c1fb85c
Merge branch 'master' into 1784_crispr_assays
jamesaoverton Aug 26, 2024
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143 changes: 143 additions & 0 deletions src/ontology/modules/assays.owl
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Expand Up @@ -21909,6 +21909,12 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003133 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003133"/>



<!-- http://purl.obolibrary.org/obo/OBI_0003148 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003148">
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<!-- http://purl.obolibrary.org/obo/OBI_0003659 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003659">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000067"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CL_0000000"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0003133"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0003368"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>in vitro CRISPR screening assay</obo:IAO_0000111>
<obo:IAO_0000115>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.</obo:IAO_0000115>
<obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>Jennifer Jou</obo:IAO_0000117>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1784</obo:IAO_0000233>
<obo:IAO_0000234>Jennifer Jou</obo:IAO_0000234>
<rdfs:label>in vitro CRISPR screening assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003660 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003660">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003659"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0002631"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0003368"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>in vitro CRISPR screen using single RNA-Seq</obo:IAO_0000111>
<obo:IAO_0000115>An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression</obo:IAO_0000115>
<obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>Jennifer Jou</obo:IAO_0000117>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1784</obo:IAO_0000233>
<obo:IAO_0000234>Jennifer Jou</obo:IAO_0000234>
<rdfs:label>in vitro CRISPR screen using single RNA-Seq</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003661 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003661">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003659"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000916"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0003368"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0003094"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0003368"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>in vitro CRISPR perturbation screen using FISH and flow cytometry</obo:IAO_0000111>
<obo:IAO_0000115>An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes</obo:IAO_0000115>
<obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>Jennifer Jou</obo:IAO_0000117>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1784</obo:IAO_0000233>
<obo:IAO_0000234>Jennifer Jou</obo:IAO_0000234>
<rdfs:label>in vitro CRISPR perturbation screen using FISH and flow cytometry</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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3 changes: 3 additions & 0 deletions src/ontology/templates/assays.tsv
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Expand Up @@ -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
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I noticed that the term name says "single RNA-seq"; I'm not sure if that's accidentally omitting the word "cell" (as in "single cell RNA-seq")?

Also, if it's OK, I'd like to share this pull request with some of our labs working on CRISPR screens to see if they are happy with the terminology.

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@jenjou Good catch—I believe that change was made while Bjoern was editing the template during the OBI call a couple weeks ago. I'll add a commit to change it to "single-cell RNA-Seq". Yes, please feel free to share this PR with the labs.

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
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