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Merge pull request #1798 from obi-ontology/1785_snmCT_seq_assay
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Add snmCT-seq assay
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@jamesaoverton
jamesaoverton authored Aug 26, 2024
2 parents 341a306 + 87dd311 commit 4f6585f
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105 changes: 102 additions & 3 deletions src/ontology/modules/assays.owl
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>in vitro CRISPR screen 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_0000115 xml:lang="en">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>
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</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000111>in vitro CRISPR screen using single-cell RNA-seq</obo:IAO_0000111>
<obo:IAO_0000115>An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression.</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">An in vitro CRISPR screen 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>
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</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000111>in vitro CRISPR perturbation screen using flow cytometry</obo:IAO_0000111>
<obo:IAO_0000115>An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes.</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">An in vitro CRISPR screen assay that uses 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>
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<!-- http://purl.obolibrary.org/obo/OBI_0003662 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003662">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001266"/>
<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/BFO_0000034"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
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</owl:Class>
<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/OBI_0000880"/>
</owl:Restriction>
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</owl:Class>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000973"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000845"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000111>single-nucleus methylcytosine and transcriptome sequencing assay</obo:IAO_0000111>
<obo:IAO_0000112>https://www.biorxiv.org/content/10.1101/434845v1</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A DNA methylation profiling by high throughput sequencing assay that measures the cytosine DNA methylation and gene expression signature of single nuclei.</obo:IAO_0000115>
<obo:IAO_0000117>Jennifer Jou</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>snmCT-seq</obo:IAO_0000118>
<obo:IAO_0000119>Jennifer Jou</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1785</obo:IAO_0000233>
<obo:IAO_0000234>Jennifer Jou</obo:IAO_0000234>
<rdfs:label>single-nucleus methylcytosine and transcriptome 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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1 change: 1 addition & 0 deletions src/ontology/templates/assays.tsv
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Expand Up @@ -659,6 +659,7 @@ OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluore
OBI:0003659 in vitro CRISPR screen assay in vitro CRISPR screen 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-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: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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