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Add license for ORDO and update OBO Foundry patterns/examples (#1059)
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The ORDO license is stated as CC BY 4.0 in the ontology

The OBO Foundry patterns need updating since MCRO decided to submit
information with a banana to identifiers.org
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@cthoyt
cthoyt authored Mar 22, 2024
1 parent 3b653c4 commit 73ee861
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103 changes: 100 additions & 3 deletions src/bioregistry/data/bioregistry.json
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"biocontext": "CHEMINF",
"bioportal": "CHEMINF",
"fairsharing": "FAIRsharing.sjhvyy",
"miriam": "cheminf",
"obofoundry": "cheminf",
"ols": "cheminf",
"ontobee": "CHEMINF"
},
"miriam": {
"deprecated": false,
"description": "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/cheminf",
"id": "00001045",
"name": "Chemical Information Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^CHEMINF:\\d+$",
"prefix": "cheminf",
"sampleId": "000306",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/cheminf/classes?obo_id=CHEMINF:$1"
},
"name": "Chemical Information Ontology",
"obofoundry": {
"appears_in": [
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"biocontext": {
"prefix": "EV"
},
"example": "0100011",
"mappings": {
"biocontext": "EV",
"obofoundry": "ev",
Expand All @@ -35285,6 +35299,7 @@
"name": "eVOC (Expressed Sequence Annotation for Humans)",
"prefix": "ev"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1013",
"description": "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.",
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"library": "Library",
"name": "Plant Gall Ontology",
"prefix": "GALLONT"
}
},
"pattern": "^\\d{7}$"
},
"gard": {
"contributor": {
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"biocontext": {
"prefix": "MAO"
},
"example": "0000061",
"mappings": {
"biocontext": "MAO",
"obofoundry": "mao",
Expand All @@ -61067,6 +61084,7 @@
"name": "Multiple alignment",
"prefix": "mao"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1026",
"description": "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.",
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"example": "0000001",
"mappings": {
"aberowl": "MCRO",
"miriam": "mcro",
"obofoundry": "mcro",
"ontobee": "MCRO"
},
"miriam": {
"deprecated": false,
"description": "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/mcro",
"id": "00001049",
"name": "Model Card Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^MCRO:\\d+$",
"prefix": "mcro",
"sampleId": "0000027",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1"
},
"obofoundry": {
"contact": "muamith@utmb.edu",
"contact.github": "ProfTuan",
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"library": "Library",
"name": "Model Card Report Ontology",
"prefix": "MCRO"
}
},
"pattern": "^\\d{7}$"
},
"mdm": {
"aberowl": {
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"name": "Medaka Fish Anatomy and Development Ontology",
"prefix": "MFO"
},
"example": "0000001",
"mappings": {
"aberowl": "MFO",
"biocontext": "MFO",
Expand All @@ -63933,6 +63966,7 @@
"name": "Medaka fish anatomy and development",
"prefix": "mfo"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1027",
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, <i>Oryzias latipes</i>.",
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"name": "Next Generation Biobanking Ontology",
"prefix": "NGBO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/NGBO_$1"
},
"ngl": {
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"biocontext": "OBCS",
"bioportal": "OBCS",
"fairsharing": "FAIRsharing.5p12xh",
"miriam": "obcs",
"obofoundry": "obcs",
"ols": "obcs",
"ontobee": "OBCS"
},
"miriam": {
"deprecated": false,
"description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/obcs",
"id": "00001053",
"name": " Ontology of Biological and Clinical Statistics",
"namespaceEmbeddedInLui": true,
"pattern": "^OBCS:\\d+$",
"prefix": "obcs",
"sampleId": "0000086",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/obcs/classes?obo_id=OBCS:$1"
},
"obofoundry": {
"contact": "jiezhen@med.umich.edu",
"contact.github": "zhengj2007",
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"library": "Library",
"name": "Occupation Ontology",
"prefix": "OCCO"
}
},
"pattern": "^\\d+$"
},
"oci": {
"biocontext": {
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"biocontext": "OPL",
"bioportal": "OPL",
"fairsharing": "FAIRsharing.ez2nhb",
"miriam": "opl",
"obofoundry": "opl",
"ols": "opl",
"ontobee": "OPL"
},
"miriam": {
"deprecated": false,
"description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/opl",
"id": "00001047",
"name": "Ontology for Parasite Lifecycle",
"namespaceEmbeddedInLui": true,
"pattern": "^OPL:\\d+$",
"prefix": "opl",
"sampleId": "0000134",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/opl/classes?obo_id=OPL:$1"
},
"obofoundry": {
"contact": "zhengj2007@gmail.com",
"contact.github": "zhengj2007",
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"Biomedical Science"
]
},
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "ordo",
"biocontext": "ORPHANET.ORDO",
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"biocontext": "STATO",
"bioportal": "STATO",
"fairsharing": "FAIRsharing.na5xp",
"miriam": "stato",
"obofoundry": "stato",
"ols": "stato",
"ontobee": "STATO"
},
"miriam": {
"deprecated": false,
"description": "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.",
"homepage": "https://www.ebi.ac.uk",
"id": "00001051",
"name": "Statistical Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^STATO:\\d+$",
"prefix": "stato",
"sampleId": "0000138",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/stato/classes?obo_id=STATO:$1"
},
"obofoundry": {
"appears_in": [
"ontoavida",
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"uri_format": "https://www.ebi.ac.uk/ols/ontologies/symp/terms?iri=http://purl.obolibrary.org/obo/SYMP_$1"
}
},
"synapse": {
"mappings": {
"miriam": "synapse"
},
"miriam": {
"deprecated": false,
"description": "Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.",
"homepage": "https://sagebionetworks.org",
"id": "00001043",
"name": "Synapse Data Repository",
"namespaceEmbeddedInLui": false,
"pattern": "[0-9]*\\.*[0-9]*",
"prefix": "synapse",
"sampleId": "41455251.1",
"uri_format": "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1"
}
},
"syoid": {
"contributor": {
"email": "cthoyt@gmail.com",
Expand Down Expand Up @@ -113150,6 +113243,7 @@
"publication": "http://dx.plos.org/10.1371/journal.pone.0051070",
"version": "2012-11-06"
},
"example": "0000183",
"mappings": {
"aberowl": "VSAO",
"biocontext": "VSAO",
Expand Down Expand Up @@ -113179,6 +113273,7 @@
"version": "2012-11-06",
"version.iri": "http://purl.obolibrary.org/obo/vsao/2012-11-06/vsao.owl"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1555",
"description": "Vertebrate anatomy ontology. Currently covers the skeletal system",
Expand Down Expand Up @@ -116760,6 +116855,7 @@
"prefix": "ZEA",
"version": "1.2"
},
"example": "0015177",
"mappings": {
"aberowl": "ZEA",
"biocontext": "ZEA",
Expand All @@ -116777,6 +116873,7 @@
"name": "Maize gross anatomy",
"prefix": "zea"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1050",
"description": "Maize gross anatomy",
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72 changes: 72 additions & 0 deletions src/bioregistry/data/external/miriam/processed.json
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"sampleId": "57-27-2",
"uri_format": "https://chem.nlm.nih.gov/chemidplus/rn/$1"
},
"cheminf": {
"deprecated": false,
"description": "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/cheminf",
"id": "00001045",
"name": "Chemical Information Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^CHEMINF:\\d+$",
"prefix": "cheminf",
"sampleId": "000306",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/cheminf/classes?obo_id=CHEMINF:$1"
},
"chemspider": {
"deprecated": false,
"description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.",
Expand Down Expand Up @@ -5682,6 +5694,18 @@
"sampleId": "0001073",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/maxo/terms?obo_id=MAXO:$1"
},
"mcro": {
"deprecated": false,
"description": "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/mcro",
"id": "00001049",
"name": "Model Card Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^MCRO:\\d+$",
"prefix": "mcro",
"sampleId": "0000027",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1"
},
"mdm": {
"deprecated": false,
"description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.",
Expand Down Expand Up @@ -7003,6 +7027,18 @@
"sampleId": "880798137",
"uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1"
},
"obcs": {
"deprecated": false,
"description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/obcs",
"id": "00001053",
"name": " Ontology of Biological and Clinical Statistics",
"namespaceEmbeddedInLui": true,
"pattern": "^OBCS:\\d+$",
"prefix": "obcs",
"sampleId": "0000086",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/obcs/classes?obo_id=OBCS:$1"
},
"obi": {
"deprecated": false,
"description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).",
Expand Down Expand Up @@ -7219,6 +7255,18 @@
"sampleId": "OPB_00573",
"uri_format": "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$1"
},
"opl": {
"deprecated": false,
"description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/opl",
"id": "00001047",
"name": "Ontology for Parasite Lifecycle",
"namespaceEmbeddedInLui": true,
"pattern": "^OPL:\\d+$",
"prefix": "opl",
"sampleId": "0000134",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/opl/classes?obo_id=OPL:$1"
},
"opm": {
"deprecated": false,
"description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.",
Expand Down Expand Up @@ -9314,6 +9362,18 @@
"sampleId": "1a24",
"uri_format": "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"
},
"stato": {
"deprecated": false,
"description": "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.",
"homepage": "https://www.ebi.ac.uk",
"id": "00001051",
"name": "Statistical Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^STATO:\\d+$",
"prefix": "stato",
"sampleId": "0000138",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/stato/classes?obo_id=STATO:$1"
},
"stitch": {
"deprecated": false,
"description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.",
Expand Down Expand Up @@ -9443,6 +9503,18 @@
"sampleId": "AHR",
"uri_format": "http://swissregulon.unibas.ch/query/$1"
},
"synapse": {
"deprecated": false,
"description": "Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.",
"homepage": "https://sagebionetworks.org",
"id": "00001043",
"name": "Synapse Data Repository",
"namespaceEmbeddedInLui": false,
"pattern": "[0-9]*\\.*[0-9]*",
"prefix": "synapse",
"sampleId": "41455251.1",
"uri_format": "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1"
},
"t3db": {
"deprecated": false,
"description": "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.",
Expand Down
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