More error handling workaround for gsso failing.

EBISPOT · Aug 9, 2024 · cb90669 · cb90669
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diff --git a/dataload/configs/gsso.json b/dataload/configs/gsso.json
@@ -0,0 +1,57 @@
+{
+  "name": "OBO Foundry",
+  "title": "The OBO Foundry",
+  "markdown": "kramdown",
+  "highlighter": "rouge",
+  "baseurl": "/",
+  "imgurl": "/images",
+  "repo": "https://github.com/OBOFoundry/OBOFoundry.github.io/",
+  "repo_src": "https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/",
+  "author": {
+    "name": "OBO Technical WG"
+  },
+  "ontologies": [
+    {
+      "activity_status": "active",
+      "build": {
+        "checkout": "git clone https://github.com/Superraptor/GSSO.git",
+        "path": ".",
+        "system": "git"
+      },
+      "contact": {
+        "email": "[email protected]",
+        "github": "Superraptor",
+        "label": "Clair Kronk",
+        "orcid": "0000-0001-8397-8810"
+      },
+      "description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences.",
+      "domain": "organisms",
+      "homepage": "https://gsso.research.cchmc.org/",
+      "id": "gsso",
+      "layout": "ontology_detail",
+      "license": {
+        "label": "Apache 2.0 License",
+        "url": "http://www.apache.org/licenses/LICENSE-2.0"
+      },
+      "ontology_purl": "http://purl.obolibrary.org/obo/gsso.owl",
+      "preferredPrefix": "GSSO",
+      "products": [
+        {
+          "id": "gsso.owl",
+          "ontology_purl": "http://purl.obolibrary.org/obo/gsso.owl"
+        },
+        {
+          "id": "gsso.obo",
+          "ontology_purl": "http://purl.obolibrary.org/obo/gsso.obo"
+        },
+        {
+          "id": "gsso.json",
+          "ontology_purl": "http://purl.obolibrary.org/obo/gsso.json"
+        }
+      ],
+      "repository": "https://github.com/Superraptor/GSSO",
+      "title": "Gender, Sex, and Sexual Orientation (GSSO) ontology",
+      "tracker": "https://github.com/Superraptor/GSSO/issues"
+    }
+  ]
+}
diff --git a/dataload/configs/hp.json b/dataload/configs/hp.json
@@ -0,0 +1,110 @@
+{
+  "name": "OBO Foundry",
+  "title": "The OBO Foundry",
+  "markdown": "kramdown",
+  "highlighter": "rouge",
+  "baseurl": "/",
+  "imgurl": "/images",
+  "repo": "https://github.com/OBOFoundry/OBOFoundry.github.io/",
+  "repo_src": "https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/",
+  "author": {
+    "name": "OBO Technical WG"
+  },
+  "ontologies": [
+    {
+      "activity_status": "active",
+      "browsers": [
+        {
+          "label": "HPO",
+          "title": "JAX HPO Browser",
+          "url": "https://hpo.jax.org/app/"
+        },
+        {
+          "label": "Monarch",
+          "title": "Monarch Phenotype Page",
+          "url": "http://monarchinitiative.org/phenotype/HP:0000118"
+        }
+      ],
+      "build": {
+        "infallible": 1,
+        "method": "archive",
+        "path": "archive/hp",
+        "source_url": "http://compbio.charite.de/hudson/job/hpo/lastSuccessfulBuild/artifact/*zip*/archive.zip"
+      },
+      "contact": {
+        "email": "[email protected]",
+        "github": "drseb",
+        "label": "Sebastian Koehler",
+        "orcid": "0000-0002-5316-1399"
+      },
+      "depicted_by": "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png",
+      "description": "A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.",
+      "domain": "phenotype",
+      "homepage": "http://www.human-phenotype-ontology.org/",
+      "id": "hp",
+      "jobs": [
+        {
+          "id": "https://travis-ci.org/obophenotype/human-phenotype-ontology",
+          "type": "travis-ci"
+        }
+      ],
+      "layout": "ontology_detail",
+      "license": {
+        "label": "hpo",
+        "url": "https://hpo.jax.org/app/license"
+      },
+      "mailing_list": "https://groups.io/g/human-phenotype-ontology",
+      "ontology_purl": "http://purl.obolibrary.org/obo/hp.owl",
+      "preferredPrefix": "HP",
+      "products": [
+        {
+          "id": "hp.owl",
+          "ontology_purl": "http://purl.obolibrary.org/obo/hp.owl"
+        },
+        {
+          "id": "hp.obo",
+          "ontology_purl": "http://purl.obolibrary.org/obo/hp.obo"
+        }
+      ],
+      "publications": [
+        {
+          "id": "https://www.ncbi.nlm.nih.gov/pubmed/18950739",
+          "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease."
+        },
+        {
+          "id": "https://www.ncbi.nlm.nih.gov/pubmed/26119816",
+          "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease."
+        },
+        {
+          "id": "https://www.ncbi.nlm.nih.gov/pubmed/24217912",
+          "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data."
+        },
+        {
+          "id": "https://www.ncbi.nlm.nih.gov/pubmed/30476213",
+          "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources."
+        }
+      ],
+      "repository": "https://github.com/obophenotype/human-phenotype-ontology",
+      "taxon": {
+        "id": "NCBITaxon:9606",
+        "label": "Homo sapiens"
+      },
+      "title": "Human Phenotype Ontology",
+      "tracker": "https://github.com/obophenotype/human-phenotype-ontology/issues/",
+      "twitter": "hp_ontology",
+      "usages": [
+        {
+          "description": "HPO is used by the Monarch Initiative for phenotype annotations.",
+          "examples": [
+            {
+              "url": "https://monarchinitiative.org/phenotype/HP:0001300"
+            }
+          ],
+          "reference": "https://academic.oup.com/nar/article/45/D1/D712/2605791",
+          "type": "annotation",
+          "user": "https://monarchinitiative.org/"
+        }
+      ]
+    }
+  ]
+}
diff --git a/dataload/configs/kisao.json b/dataload/configs/kisao.json
@@ -0,0 +1,96 @@
+{
+  "name": "OBO Foundry",
+  "title": "The OBO Foundry",
+  "markdown": "kramdown",
+  "highlighter": "rouge",
+  "baseurl": "/",
+  "imgurl": "/images",
+  "repo": "https://github.com/OBOFoundry/OBOFoundry.github.io/",
+  "repo_src": "https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/",
+  "author": {
+    "name": "OBO Technical WG"
+  },
+  "ontologies": [
+    {
+      "activity_status": "active",
+      "browsers": [
+        {
+          "label": "OLS",
+          "title": "Ontology Lookup Service",
+          "url": "https://www.ebi.ac.uk/ols/ontologies/kisao"
+        },
+        {
+          "label": "BioPortal",
+          "title": "BioPortal",
+          "url": "https://bioportal.bioontology.org/ontologies/KISAO"
+        },
+        {
+          "label": "OntoBee",
+          "title": "OntoBee",
+          "url": "https://www.ontobee.org/ontology/KISAO"
+        }
+      ],
+      "build": {
+        "method": "owl2obo",
+        "source_url": "https://raw.githubusercontent.com/SED-ML/KiSAO/deploy/kisao.owl"
+      },
+      "contact": {
+        "email": "[email protected]",
+        "github": "jonrkarr",
+        "label": "Jonathan Karr",
+        "orcid": "0000-0002-2605-5080"
+      },
+      "description": "A classification of algorithms for simulating biology, their parameters, and their outputs",
+      "domain": "simulation",
+      "funded_by": [
+        "NIH P41EB023912",
+        "NIH R35GM119771"
+      ],
+      "homepage": "https://github.com/SED-ML/KiSAO",
+      "id": "kisao",
+      "layout": "ontology_detail",
+      "license": {
+        "label": "Artistic License 2.0",
+        "url": "http://opensource.org/licenses/Artistic-2.0"
+      },
+      "ontology_purl": "http://purl.obolibrary.org/obo/kisao.owl",
+      "preferredPrefix": "KISAO",
+      "products": [
+        {
+          "id": "kisao.owl",
+          "ontology_purl": "http://purl.obolibrary.org/obo/kisao.owl"
+        }
+      ],
+      "publications": [
+        {
+          "id": "https://www.ncbi.nlm.nih.gov/pubmed/22027554",
+          "title": "Controlled vocabularies and semantics in systems biology"
+        }
+      ],
+      "releases": "https://github.com/SED-ML/KiSAO/releases",
+      "repository": "https://github.com/SED-ML/KiSAO",
+      "tags": [
+        "systems biology",
+        "computational biology",
+        "mathematical modeling",
+        "numerical simulation",
+        "simulation algorithms"
+      ],
+      "title": "Kinetic Simulation Algorithm Ontology",
+      "tracker": "https://github.com/SED-ML/KiSAO/issues",
+      "usages": [
+        {
+          "description": "The Simulation Experiment Description Markup Language (SED-ML) is a language for describing simulations and visualizations of their results.",
+          "examples": [
+            {
+              "description": "Several examples of simulations encoded in SED-ML",
+              "url": "https://sed-ml.org/examples.html"
+            }
+          ],
+          "type": "annotation",
+          "user": "https://sed-ml.org/"
+        }
+      ]
+    }
+  ]
+}
diff --git a/dataload/configs/sbo.json b/dataload/configs/sbo.json
@@ -0,0 +1,49 @@
+{
+  "name": "OBO Foundry",
+  "title": "The OBO Foundry",
+  "markdown": "kramdown",
+  "highlighter": "rouge",
+  "baseurl": "/",
+  "imgurl": "/images",
+  "repo": "https://github.com/OBOFoundry/OBOFoundry.github.io/",
+  "repo_src": "https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/",
+  "author": {
+    "name": "OBO Technical WG"
+  },
+  "ontologies": [
+    {
+      "activity_status": "active",
+      "build": {
+        "insert_ontology_id": true,
+        "method": "obo2owl",
+        "source_url": "http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo"
+      },
+      "contact": {
+        "email": "[email protected]",
+        "github": "rsmsheriff",
+        "label": "Rahuman Sheriff",
+        "orcid": "0000-0003-0705-9809"
+      },
+      "description": "Terms commonly used in Systems Biology, and in particular in computational modeling.",
+      "domain": "chemistry and biochemistry",
+      "homepage": "http://www.ebi.ac.uk/sbo/",
+      "id": "sbo",
+      "layout": "ontology_detail",
+      "license": {
+        "label": "Artistic License 2.0",
+        "url": "http://opensource.org/licenses/Artistic-2.0"
+      },
+      "ontology_purl": "http://purl.obolibrary.org/obo/sbo.owl",
+      "preferredPrefix": "SBO",
+      "products": [
+        {
+          "id": "sbo.owl",
+          "ontology_purl": "http://purl.obolibrary.org/obo/sbo.owl"
+        }
+      ],
+      "repository": "https://github.com/EBI-BioModels/SBO",
+      "title": "Systems Biology Ontology",
+      "tracker": "https://github.com/EBI-BioModels/SBO/issues"
+    }
+  ]
+}