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Update OBO foundry metadata #2649

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Nov 6, 2024
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Update OBO foundry metadata #2649

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29 changes: 23 additions & 6 deletions _config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -894,6 +894,20 @@ ontologies:
Program.'
type: annotation
user: https://hubmapconsortium.org/
- description: The single-cell transcriptomics platform CZ CELLxGENE uses CL to
annotate all cell types. All datasets on CellXGene are annotated according to
a standard schema that specifies the use of CL to record Cell Type.
examples:
- description: A CELLxGENE Cell Guide entry for 'luminal adaptive secretory precursor
cell of mammary gland', which includes the CL ID (CL:4033057), CL definition
and a visualizer of CL hierarchy
url: https://cellxgene.cziscience.com/cellguide/CL:4033057
publications:
- id: https://doi.org/10.1101/2021.04.05.438318
title: 'CELLxGENE: a performant, scalable exploration platform for high dimensional
sparse matrices'
type: annotation
user: https://cellxgene.cziscience.com/
- description: The Human Cell Atlas (HCA) is an international group of researchers
using a combination of these new technologies to create cellular reference maps.
The HCA use CL to annotate cells in their reference maps.
Expand Down Expand Up @@ -6918,10 +6932,10 @@ ontologies:
path: archive/ontology
source_url: http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip
contact:
email: [email protected]
github: nicolevasilevsky
label: Nicole Vasilevsky
orcid: 0000-0001-5208-3432
email: [email protected]
github: jamesamcl
label: James McLaughlin
orcid: 0000-0002-8361-2795
description: The uPheno ontology integrates multiple phenotype ontologies into a
unified cross-species phenotype ontology.
domain: phenotype
Expand All @@ -6948,22 +6962,25 @@ ontologies:
page: https://github.com/obophenotype/upheno/tree/master/hp-mp
title: uPheno MP-HP equivalence axioms
- description: The new version of uPheno, along with species independent phenotypes
amd additional phenotype relations. The ontology is still in Beta status, but
and additional phenotype relations. The ontology is still in Beta status, but
we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1
is no longer actively maintained.
id: upheno/v2/upheno.owl
ontology_purl: http://purl.obolibrary.org/obo/upheno/v2/upheno.owl
page: https://github.com/obophenotype/upheno-dev
title: uPheno 2
publications:
- id: https://doi.org/10.1101/2024.09.18.613276
title: 'The Unified Phenotype Ontology (uPheno): A framework for cross-species
integrative phenomics'
- id: https://zenodo.org/record/2382757
title: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims
to reconcile logical definitions across species
- id: https://zenodo.org/record/3352149
title: 'Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd
edition'
repository: https://github.com/obophenotype/upheno
title: Unified phenotype ontology (uPheno)
title: Unified Phenotype Ontology (uPheno)
tracker: https://github.com/obophenotype/upheno/issues
usages:
- description: uPheno is used by the Monarch Initiative for cross-species inference.
Expand Down
33 changes: 27 additions & 6 deletions registry/ontologies.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -1221,6 +1221,23 @@
"type": "annotation",
"user": "https://hubmapconsortium.org/"
},
{
"description": "The single-cell transcriptomics platform CZ CELLxGENE uses CL to annotate all cell types. All datasets on CellXGene are annotated according to a standard schema that specifies the use of CL to record Cell Type.",
"examples": [
{
"description": "A CELLxGENE Cell Guide entry for 'luminal adaptive secretory precursor cell of mammary gland', which includes the CL ID (CL:4033057), CL definition and a visualizer of CL hierarchy",
"url": "https://cellxgene.cziscience.com/cellguide/CL:4033057"
}
],
"publications": [
{
"id": "https://doi.org/10.1101/2021.04.05.438318",
"title": "CELLxGENE: a performant, scalable exploration platform for high dimensional sparse matrices"
}
],
"type": "annotation",
"user": "https://cellxgene.cziscience.com/"
},
{
"description": "The Human Cell Atlas (HCA) is an international group of researchers using a combination of these new technologies to create cellular reference maps. The HCA use CL to annotate cells in their reference maps.",
"examples": [
Expand Down Expand Up @@ -9669,10 +9686,10 @@
"source_url": "http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip"
},
"contact": {
"email": "[email protected]",
"github": "nicolevasilevsky",
"label": "Nicole Vasilevsky",
"orcid": "0000-0001-5208-3432"
"email": "[email protected]",
"github": "jamesamcl",
"label": "James McLaughlin",
"orcid": "0000-0002-8361-2795"
},
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.",
"domain": "phenotype",
Expand Down Expand Up @@ -9703,14 +9720,18 @@
"title": "uPheno MP-HP equivalence axioms"
},
{
"description": "The new version of uPheno, along with species independent phenotypes amd additional phenotype relations. The ontology is still in Beta status, but we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 is no longer actively maintained.",
"description": "The new version of uPheno, along with species independent phenotypes and additional phenotype relations. The ontology is still in Beta status, but we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 is no longer actively maintained.",
"id": "upheno/v2/upheno.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/upheno/v2/upheno.owl",
"page": "https://github.com/obophenotype/upheno-dev",
"title": "uPheno 2"
}
],
"publications": [
{
"id": "https://doi.org/10.1101/2024.09.18.613276",
"title": "The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics"
},
{
"id": "https://zenodo.org/record/2382757",
"title": "Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species"
Expand All @@ -9721,7 +9742,7 @@
}
],
"repository": "https://github.com/obophenotype/upheno",
"title": "Unified phenotype ontology (uPheno)",
"title": "Unified Phenotype Ontology (uPheno)",
"tracker": "https://github.com/obophenotype/upheno/issues",
"usages": [
{
Expand Down
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