Merge branch 'main' into patch-1

biopragmatics · Nov 21, 2024 · ebadb84 · ebadb84
2 parents 68acba1 + 0de4b4f
commit ebadb84
Show file tree

Hide file tree

Showing 2 changed files with 159 additions and 1 deletion.
diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
@@ -79832,6 +79832,43 @@
     ],
     "uri_format": "http://purl.obolibrary.org/obo/$1"
   },
+  "oboe": {
+    "contact": {
+      "email": "[email protected]",
+      "github": "amoeba",
+      "name": "Bryce Mecum",
+      "orcid": "0000-0002-0381-3766"
+    },
+    "contributor": {
+      "github": "StroemPhi",
+      "name": "Philip Strömert",
+      "orcid": "0000-0002-1595-3213"
+    },
+    "description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.",
+    "download_owl": "https://raw.githubusercontent.com/NCEAS/oboe/refs/heads/master/oboe.owl",
+    "example": "Characteristic",
+    "github_request_issue": 1276,
+    "homepage": "https://github.com/NCEAS/oboe",
+    "license": "CC-BY-3.0",
+    "name": "The Extensible Observation Ontology",
+    "publications": [
+      {
+        "doi": "10.1016/j.ecoinf.2007.05.004",
+        "pmc": "PMC8612252",
+        "pubmed": "34817235",
+        "title": "An ontology for describing and synthesizing ecological observation data",
+        "year": 2007
+      }
+    ],
+    "repository": "https://github.com/NCEAS/oboe",
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#$1"
+  },
   "oboinowl": {
     "biocontext": {
       "prefix": "oboInOwl",
@@ -106932,6 +106969,41 @@
       "prefix": "sopharm"
     }
   },
+  "sosa": {
+    "contact": {
+      "email": "[email protected]",
+      "github": "dr-shorthair",
+      "name": "Simon Cox",
+      "orcid": "0000-0002-3884-3420"
+    },
+    "contributor": {
+      "github": "StroemPhi",
+      "name": "Philip Strömert",
+      "orcid": "0000-0002-1595-3213"
+    },
+    "description": "This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.",
+    "download_rdf": "https://www.w3.org/ns/sosa/",
+    "example": "FeatureOfInterest",
+    "github_request_issue": 1274,
+    "homepage": "https://www.w3.org/TR/vocab-ssn/",
+    "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document",
+    "name": "Sensor, Observation, Sample, and Actuator Ontology",
+    "publications": [
+      {
+        "doi": "10.1016/j.websem.2018.06.003",
+        "title": "SOSA: A lightweight ontology for sensors, observations, samples, and actuators",
+        "year": 2019
+      }
+    ],
+    "repository": "https://github.com/w3c/sdw",
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "http://www.w3.org/ns/sosa/$1"
+  },
   "soybase": {
     "biocontext": {
       "prefix": "SOYBASE"
@@ -107660,6 +107732,63 @@
     "pattern": "^\\d+$",
     "uri_format": "https://ssbd.riken.jp/database/project/$1"
   },
+  "ssn": {
+    "contact": {
+      "email": "[email protected]",
+      "github": "dr-shorthair",
+      "name": "Simon Cox",
+      "orcid": "0000-0002-3884-3420"
+    },
+    "contributor": {
+      "github": "StroemPhi",
+      "name": "Philip Strömert",
+      "orcid": "0000-0002-1595-3213"
+    },
+    "description": "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.",
+    "download_rdf": "https://www.w3.org/ns/ssn/",
+    "example": "hasProperty",
+    "github_request_issue": 1272,
+    "homepage": "https://www.w3.org/TR/vocab-ssn",
+    "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document",
+    "name": "Semantic Sensor Network Ontology",
+    "repository": "https://github.com/w3c/sdw-sosa-ssn",
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "http://www.w3.org/ns/ssn/$1"
+  },
+  "ssn.system": {
+    "contact": {
+      "email": "[email protected]",
+      "github": "dr-shorthair",
+      "name": "Simon Cox",
+      "orcid": "0000-0002-3884-3420"
+    },
+    "contributor": {
+      "email": "[email protected]",
+      "github": "StroemPhi",
+      "name": "Philip Strömert",
+      "orcid": "0000-0002-1595-3213"
+    },
+    "description": "This ontology describes system capabilities, operating ranges, and survival ranges. Please report any errors to the W3C Spatial Data on the Web Working Group via the SDW WG Public List [email protected]",
+    "download_rdf": "http://www.w3.org/ns/ssn/systems",
+    "example": "qualityOfObservation",
+    "github_request_issue": 1270,
+    "homepage": "https://www.w3.org/TR/vocab-ssn/",
+    "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document",
+    "name": "System capabilities, operating ranges, and survival ranges ontology",
+    "repository": "bioregistry",
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "http://www.w3.org/ns/ssn/systems/$1"
+  },
   "ssrn.article": {
     "contributor": {
       "email": "[email protected]",
@@ -117354,6 +117483,35 @@
       "uri_format_rdf": "http://viaf.org/viaf/$1"
     }
   },
+  "vibso": {
+    "contact": {
+      "email": "[email protected]",
+      "github": "StroemPhi",
+      "name": "Philip Strömert",
+      "orcid": "0000-0002-1595-3213"
+    },
+    "contributor": {
+      "email": "[email protected]",
+      "github": "StroemPhi",
+      "name": "Philip Strömert",
+      "orcid": "0000-0002-1595-3213"
+    },
+    "description": "The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.",
+    "example": "0000008",
+    "github_request_issue": 1278,
+    "homepage": "https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/",
+    "license": "CC-BY-4.0",
+    "name": "Vibrational Spectroscopy Ontology",
+    "pattern": "^\\d{7}$",
+    "repository": "https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology",
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "http://purl.obolibrary.org/obo/VIBSO_$1"
+  },
   "vido": {
     "aberowl": {
       "description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.",

diff --git a/src/bioregistry/data/curated_papers.tsv b/src/bioregistry/data/curated_papers.tsv
@@ -53,4 +53,4 @@ pubmed	relevant	orcid	date_curated	relevancy_type	pr_added	notes
 39341795	1	0009-0009-5240-7463	2024-10-19	new_prefix	1223	Identifiers for non-coding RNA biomarkers for cancers
 39341994	0	0009-0009-5240-7463	2024-10-15	not_identifiers_resource	1223	
 39345624	1	0009-0009-5240-7463	2024-10-19	new_publication	1223	Publication for sgd and sgd.pathways
-39401100	1	0009-0009-5240-7463	2024-11-20	new_publication	1264	Publication for intact and intact.molecule
+39401100	1	0009-0009-5240-7463	2024-11-20	new_publication	1264	Publication for intact and intact.molecule