Skip to content

Add new assay terms #14

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ubyndr merged 2 commits into from
Jun 4, 2025
Merged

Add new assay terms #14

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
dac382c
Add details of EFO_0030003 and EFO_0030004
ubyndr Jun 4, 2025
e2cb385
Add release artifacts
ubyndr Jun 4, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
60 changes: 52 additions & 8 deletions capo-base.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,16 @@
"obj": "http://www.ebi.ac.uk/efo/EFO_0030005",
"pred": "is_a",
"sub": "http://www.ebi.ac.uk/efo/EFO_0010961"
},
{
"obj": "http://www.ebi.ac.uk/efo/EFO_0030080",
"pred": "is_a",
"sub": "http://www.ebi.ac.uk/efo/EFO_0030003"
},
{
"obj": "http://www.ebi.ac.uk/efo/EFO_0030080",
"pred": "is_a",
"sub": "http://www.ebi.ac.uk/efo/EFO_0030004"
}
],
"id": "http://purl.obolibrary.org/obo/capo/capo-base.json",
Expand All @@ -154,10 +164,10 @@
},
{
"pred": "http://www.w3.org/2002/07/owl#versionInfo",
"val": "2024-09-25"
"val": "2025-06-04"
}
],
"version": "http://purl.obolibrary.org/obo/capo/releases/2024-09-25/capo-base.json"
"version": "http://purl.obolibrary.org/obo/capo/releases/2025-06-04/capo-base.json"
},
"nodes": [
{
Expand Down Expand Up @@ -642,6 +652,44 @@
},
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030003",
"lbl": "10x 3' transcription profiling",
"meta": {
"basicPropertyValues": [
{
"pred": "http://purl.org/dc/elements/1.1/creator",
"val": "paola"
}
],
"definition": {
"val": "10x 3' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3' end.",
"xrefs": [
"https://orcid.org/0000-0002-8674-0039"
]
}
},
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030004",
"lbl": "10x 5' transcription profiling",
"meta": {
"basicPropertyValues": [
{
"pred": "http://purl.org/dc/elements/1.1/creator",
"val": "paola"
}
],
"definition": {
"val": "10x 5' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5' end.",
"xrefs": [
"https://orcid.org/0000-0002-8674-0039"
]
}
},
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030019",
"lbl": "Seq-Well S3",
Expand Down Expand Up @@ -1579,15 +1627,11 @@
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030003",
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030004",
"id": "http://www.ebi.ac.uk/efo/EFO_0030005",
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030005",
"id": "http://www.ebi.ac.uk/efo/EFO_0030080",
"type": "CLASS"
}
]
Expand Down
28 changes: 21 additions & 7 deletions capo-base.obo
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
format-version: 1.2
data-version: capo/releases/2024-09-25/capo-base.owl
data-version: capo/releases/2025-06-04/capo-base.owl
idspace: dce http://purl.org/dc/elements/1.1/
idspace: dcterms http://purl.org/dc/terms/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
Expand All @@ -8,7 +8,7 @@ property_value: dce:type IAO:8000001
property_value: dcterms:description "An ontology that contains CAP related ontology terms gathered from different ontologies " xsd:string
property_value: dcterms:license https://creativecommons.org/licenses/by/4.0/
property_value: dcterms:title "CAP Ontology" xsd:string
property_value: owl:versionInfo "2024-09-25" xsd:string
property_value: owl:versionInfo "2025-06-04" xsd:string

[Term]
id: CAPO:0000000
Expand Down Expand Up @@ -87,7 +87,7 @@ synonym: "10X v2 sequencing" RELATED []
synonym: "10x v2 sequencing" RELATED []
synonym: "10x_v2" RELATED []
synonym: "10XV2" RELATED []
is_a: EFO:0030003
is_a: EFO:0030003 ! 10x 3' transcription profiling
property_value: IAO:0000117 "Dani Welter" xsd:string

[Term]
Expand All @@ -97,7 +97,7 @@ def: "10X 5' v2 is the second version of the 10x sequencing technology that sequ
synonym: "10X 5' v2" EXACT []
synonym: "10X 5' v2 sequencing" RELATED []
synonym: "10x 5' v2 sequencing" RELATED []
is_a: EFO:0030004
is_a: EFO:0030004 ! 10x 5' transcription profiling
property_value: IAO:0000117 "Dani Welter" xsd:string

[Term]
Expand All @@ -111,7 +111,7 @@ synonym: "10X v1" RELATED []
synonym: "10x v1" RELATED []
synonym: "10x v1 sequencing" RELATED []
synonym: "10XV1" RELATED []
is_a: EFO:0030003
is_a: EFO:0030003 ! 10x 3' transcription profiling
property_value: IAO:0000117 "Dani Welter" xsd:string

[Term]
Expand All @@ -125,7 +125,7 @@ synonym: "10x v3" RELATED []
synonym: "10X v3 sequencing" RELATED []
synonym: "10x v3 sequencing" RELATED []
synonym: "10XV3" RELATED []
is_a: EFO:0030003
is_a: EFO:0030003 ! 10x 3' transcription profiling
property_value: IAO:0000117 "Dani Welter" xsd:string

[Term]
Expand All @@ -151,7 +151,21 @@ synonym: "10X 5' v3" RELATED []
synonym: "10x 5' v3" RELATED []
synonym: "10x 5' v3 sequencing" RELATED []
synonym: "10x v1 5' sequencing" RELATED []
is_a: EFO:0030004
is_a: EFO:0030004 ! 10x 5' transcription profiling
property_value: dce:creator "paola" xsd:string

[Term]
id: EFO:0030003
name: 10x 3' transcription profiling
def: "10x 3' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3' end." [https://orcid.org/0000-0002-8674-0039]
is_a: EFO:0030080
property_value: dce:creator "paola" xsd:string

[Term]
id: EFO:0030004
name: 10x 5' transcription profiling
def: "10x 5' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5' end." [https://orcid.org/0000-0002-8674-0039]
is_a: EFO:0030080
property_value: dce:creator "paola" xsd:string

[Term]
Expand Down
36 changes: 32 additions & 4 deletions capo-base.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/capo/capo-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/capo/releases/2024-09-25/capo-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/capo/releases/2025-06-04/capo-base.owl"/>
<dce:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<dcterms:description>An ontology that contains CAP related ontology terms gathered from different ontologies </dcterms:description>
<dcterms:license rdf:resource="https://creativecommons.org/licenses/by/4.0/"/>
<dcterms:title>CAP Ontology</dcterms:title>
<owl:versionInfo>2024-09-25</owl:versionInfo>
<owl:versionInfo>2025-06-04</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -1222,13 +1222,35 @@

<!-- http://www.ebi.ac.uk/efo/EFO_0030003 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0030003"/>
<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0030003">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030080"/>
<obo:IAO_0000115>10x 3&apos; transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3&apos; end.</obo:IAO_0000115>
<dce:creator>paola</dce:creator>
<rdfs:label>10x 3&apos; transcription profiling</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030003"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>10x 3&apos; transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3&apos; end.</owl:annotatedTarget>
<oboInOwl:hasDbXref>https://orcid.org/0000-0002-8674-0039</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://www.ebi.ac.uk/efo/EFO_0030004 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0030004"/>
<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0030004">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030080"/>
<obo:IAO_0000115>10x 5&apos; transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5&apos; end.</obo:IAO_0000115>
<dce:creator>paola</dce:creator>
<rdfs:label>10x 5&apos; transcription profiling</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030004"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>10x 5&apos; transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5&apos; end.</owl:annotatedTarget>
<oboInOwl:hasDbXref>https://orcid.org/0000-0002-8674-0039</oboInOwl:hasDbXref>
</owl:Axiom>



Expand Down Expand Up @@ -1296,6 +1318,12 @@
<oboInOwl:hasDbXref>http://orcid.org/0000-0002-1196-4871</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>https://www.biorxiv.org/content/10.1101/434845v1</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://www.ebi.ac.uk/efo/EFO_0030080 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0030080"/>
</rdf:RDF>


Expand Down
60 changes: 52 additions & 8 deletions capo-full.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,16 @@
"obj": "http://www.ebi.ac.uk/efo/EFO_0030005",
"pred": "is_a",
"sub": "http://www.ebi.ac.uk/efo/EFO_0010961"
},
{
"obj": "http://www.ebi.ac.uk/efo/EFO_0030080",
"pred": "is_a",
"sub": "http://www.ebi.ac.uk/efo/EFO_0030003"
},
{
"obj": "http://www.ebi.ac.uk/efo/EFO_0030080",
"pred": "is_a",
"sub": "http://www.ebi.ac.uk/efo/EFO_0030004"
}
],
"id": "http://purl.obolibrary.org/obo/capo/capo-full.json",
Expand All @@ -150,10 +160,10 @@
},
{
"pred": "http://www.w3.org/2002/07/owl#versionInfo",
"val": "2024-09-25"
"val": "2025-06-04"
}
],
"version": "http://purl.obolibrary.org/obo/capo/releases/2024-09-25/capo-full.json"
"version": "http://purl.obolibrary.org/obo/capo/releases/2025-06-04/capo-full.json"
},
"nodes": [
{
Expand Down Expand Up @@ -638,6 +648,44 @@
},
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030003",
"lbl": "10x 3' transcription profiling",
"meta": {
"basicPropertyValues": [
{
"pred": "http://purl.org/dc/elements/1.1/creator",
"val": "paola"
}
],
"definition": {
"val": "10x 3' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3' end.",
"xrefs": [
"https://orcid.org/0000-0002-8674-0039"
]
}
},
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030004",
"lbl": "10x 5' transcription profiling",
"meta": {
"basicPropertyValues": [
{
"pred": "http://purl.org/dc/elements/1.1/creator",
"val": "paola"
}
],
"definition": {
"val": "10x 5' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5' end.",
"xrefs": [
"https://orcid.org/0000-0002-8674-0039"
]
}
},
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030019",
"lbl": "Seq-Well S3",
Expand Down Expand Up @@ -1570,15 +1618,11 @@
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030003",
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030004",
"id": "http://www.ebi.ac.uk/efo/EFO_0030005",
"type": "CLASS"
},
{
"id": "http://www.ebi.ac.uk/efo/EFO_0030005",
"id": "http://www.ebi.ac.uk/efo/EFO_0030080",
"type": "CLASS"
}
]
Expand Down
Loading