Merge branch 'master' into add-atom-feed

OBOFoundry · Nov 13, 2024 · b0a05ba · b0a05ba
2 parents 241a39b + 5167cfb
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diff --git a/_config.yml b/_config.yml
@@ -897,6 +897,20 @@ 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.
@@ -6921,10 +6935,10 @@ 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
@@ -6951,22 +6965,25 @@ 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       is no longer actively maintained.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.

diff --git a/_data/operations.yml b/_data/operations.yml
@@ -342,6 +342,16 @@ members:
   name: Richard Scheuermann
   orcid: 0000-0003-1355-892X
   wikidata: Q30508615
+- affiliation:
+    name: La Jolla Institute for Immunology, La Jolla, CA
+    ror: 05vkpd318
+  country: USA
+  github: sebastianduesing
+  groups:
+  - technical
+  name: Sebastian Duesing
+  orcid: 0009-0009-4008-3801
+  wikidata: Q6463245
 - affiliation:
     name: Lawrence Berkeley National Laboratory, Berkeley, CA
     ror: 02jbv0t02

diff --git a/images/ofoc/sebastianduesing.png b/images/ofoc/sebastianduesing.png
diff --git a/ontology/cl.md b/ontology/cl.md
@@ -84,6 +84,15 @@ usages:
     title: 'The human body at cellular resolution: the NIH Human Biomolecular Atlas 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.
   examples:
   - description: HCA collection studies that are related B cell (CL:0000236) that is filtered through CL annotation
@@ -149,6 +158,10 @@ Uberon and various phenotype ontologies.
 
 The following are some applications of the cell ontology along with their publications: 
 
+**CZ CELLxGENE**
+
+CZI Single-Cell Biology Program, Shibla Abdulla, Brian Aevermann, Pedro Assis, Seve Badajoz, Sidney M. Bell, Emanuele Bezzi, et al. 2023. “CZ CELL×GENE Discover: A Single-Cell Data Platform for Scalable Exploration, Analysis and Modeling of Aggregated Data.” bioRxiv. [doi:10.1101/2023.10.30.563174](https://doi.org/10.1101/2023.10.30.563174).
+
 **HuBMAP**
 
 HuBMAP Consortium (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature, 574, 187–192

diff --git a/ontology/upheno.md b/ontology/upheno.md
@@ -1,16 +1,16 @@
 ---
 layout: ontology_detail
 id: upheno
-title: Unified phenotype ontology (uPheno)
+title: Unified Phenotype Ontology (uPheno)
 build:
   method: archive
   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
 homepage: https://github.com/obophenotype/upheno
@@ -30,9 +30,11 @@ products:
   page: https://github.com/obophenotype/upheno/tree/master/hp-mp
 - id: upheno/v2/upheno.owl
   title: uPheno 2
-  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.
   page: https://github.com/obophenotype/upheno-dev
 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

diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld
@@ -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": [
@@ -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",
@@ -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"
@@ -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": [
                 {