pymetadata 0.4.1__py2.py3-none-any.whl → 0.4.2__py2.py3-none-any.whl

pymetadata/resources/identifiers_registry.json

@@ -95,6 +95,102 @@
     "deprecated": false,
     "deprecationDate": null
   },
+  "synapse": {
+    "id": 3808,
+    "prefix": "synapse",
+    "name": "Synapse Data Repository",
+    "pattern": "[0-9]*\\.*[0-9]*",
+    "namespaceEmbeddedInLui": false,
+    "description": "Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.",
+    "mirId": "MIR:00001043",
+    "resources": [
+      {
+        "id": 3809,
+        "providerCode": "synapse",
+        "name": "Sage Bionetworks",
+        "urlPattern": "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn{$id}",
+        "mirId": "MIR:00001042",
+        "description": "Sage Bionetworks is a trusted leader in data sharing and reuse, enabling a rapid acceleration in biomedical discoveries and the transformation of medicine.",
+        "official": true,
+        "sampleId": "41455251.1",
+        "resourceHomeUrl": "https://sagebionetworks.org",
+        "institution": {
+          "id": 3807,
+          "name": "Sage Bionetworks",
+          "homeUrl": "https://www.sagebionetworks.org",
+          "description": "Sage Bionetworks is a trusted leader in data sharing and reuse, enabling a rapid acceleration in biomedical discoveries and the transformation of medicine.",
+          "rorId": null,
+          "location": {
+            "countryCode": "US",
+            "countryName": "United States"
+          }
+        },
+        "location": {
+          "countryCode": "US",
+          "countryName": "United States"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      }
+    ],
+    "created": "2024-03-20T10:13:27.272+0000",
+    "modified": "2024-03-20T10:13:27.272+0000",
+    "sampleId": "41455251.1",
+    "deprecated": false,
+    "deprecationDate": null
+  },
+  "cheminf": {
+    "id": 3819,
+    "prefix": "cheminf",
+    "name": "Chemical Information Ontology",
+    "pattern": "^CHEMINF:\\d+$",
+    "namespaceEmbeddedInLui": true,
+    "description": "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.",
+    "mirId": "MIR:00001045",
+    "resources": [
+      {
+        "id": 3820,
+        "providerCode": "ols",
+        "name": "CHEMINF via OLS",
+        "urlPattern": "https://www.ebi.ac.uk/ols4/ontologies/cheminf/classes?obo_id=CHEMINF:{$id}",
+        "mirId": "MIR:00001044",
+        "description": "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.",
+        "official": true,
+        "sampleId": "000306",
+        "resourceHomeUrl": "https://www.ebi.ac.uk/ols4/ontologies/cheminf",
+        "institution": {
+          "id": 2,
+          "name": "European Bioinformatics Institute",
+          "homeUrl": "https://www.ebi.ac.uk",
+          "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.",
+          "rorId": "https://ror.org/02catss52",
+          "location": {
+            "countryCode": "GB",
+            "countryName": "United Kingdom"
+          }
+        },
+        "location": {
+          "countryCode": "GB",
+          "countryName": "United Kingdom"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      }
+    ],
+    "created": "2024-03-20T10:24:50.346+0000",
+    "modified": "2024-03-20T10:29:26.220+0000",
+    "sampleId": "000306",
+    "deprecated": false,
+    "deprecationDate": null
+  },
   "bgee.stage": {
     "id": 1211,
     "prefix": "bgee.stage",
@@ -191,6 +287,54 @@
     "deprecated": false,
     "deprecationDate": null
   },
+  "opl": {
+    "id": 3827,
+    "prefix": "opl",
+    "name": "Ontology for Parasite Lifecycle",
+    "pattern": "^OPL:\\d+$",
+    "namespaceEmbeddedInLui": true,
+    "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.",
+    "mirId": "MIR:00001047",
+    "resources": [
+      {
+        "id": 3828,
+        "providerCode": "ols",
+        "name": "OPL via OLS",
+        "urlPattern": "https://www.ebi.ac.uk/ols4/ontologies/opl/classes?obo_id=OPL:{$id}",
+        "mirId": "MIR:00001046",
+        "description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc",
+        "official": true,
+        "sampleId": "0000134",
+        "resourceHomeUrl": "https://www.ebi.ac.uk/ols4/ontologies/opl",
+        "institution": {
+          "id": 2,
+          "name": "European Bioinformatics Institute",
+          "homeUrl": "https://www.ebi.ac.uk",
+          "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.",
+          "rorId": "https://ror.org/02catss52",
+          "location": {
+            "countryCode": "GB",
+            "countryName": "United Kingdom"
+          }
+        },
+        "location": {
+          "countryCode": "GB",
+          "countryName": "United Kingdom"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      }
+    ],
+    "created": "2024-03-20T10:39:56.678+0000",
+    "modified": "2024-03-20T10:39:56.678+0000",
+    "sampleId": "0000134",
+    "deprecated": false,
+    "deprecationDate": null
+  },
   "signaling-gateway": {
     "id": 169,
     "prefix": "signaling-gateway",
@@ -287,6 +431,54 @@
     "deprecated": true,
     "deprecationDate": "2023-07-04T10:26:56.707+0000"
   },
+  "ncbidrs": {
+    "id": 3730,
+    "prefix": "ncbidrs",
+    "name": "NCBI Data Repository Service",
+    "pattern": "^[0-9a-fA-F]{32}$",
+    "namespaceEmbeddedInLui": false,
+    "description": "This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. ",
+    "mirId": "MIR:00001034",
+    "resources": [
+      {
+        "id": 3731,
+        "providerCode": "ncbi",
+        "name": "National Center for Biotechnology Information",
+        "urlPattern": "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/{$id}",
+        "mirId": "MIR:00001033",
+        "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.",
+        "official": true,
+        "sampleId": "72ff6ff882ec447f12df018e6183de59",
+        "resourceHomeUrl": "https://www.ncbi.nlm.nih.gov/",
+        "institution": {
+          "id": 26,
+          "name": "National Center for Biotechnology Information",
+          "homeUrl": "https://www.ncbi.nlm.nih.gov/",
+          "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.",
+          "rorId": "https://ror.org/02meqm098",
+          "location": {
+            "countryCode": "US",
+            "countryName": "United States"
+          }
+        },
+        "location": {
+          "countryCode": "US",
+          "countryName": "United States"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      }
+    ],
+    "created": "2023-10-31T16:13:48.191+0000",
+    "modified": "2023-10-31T16:13:48.191+0000",
+    "sampleId": "72ff6ff882ec447f12df018e6183de59",
+    "deprecated": false,
+    "deprecationDate": null
+  },
   "miriam.collection": {
     "id": 41,
     "prefix": "miriam.collection",
@@ -330,44 +522,44 @@
       }
     ],
     "created": "2019-06-11T14:15:31.442+0000",
-    "modified": "2023-09-13T08:57:20.977+0000",
+    "modified": "2024-02-06T14:56:58.330+0000",
     "sampleId": "MIR:00000008",
     "deprecated": true,
     "deprecationDate": "2020-06-04T11:17:21.453+0000"
   },
-  "ncbidrs": {
-    "id": 3730,
-    "prefix": "ncbidrs",
-    "name": "NCBI Data Repository Service",
-    "pattern": "^[0-9a-fA-F]{32}$",
-    "namespaceEmbeddedInLui": false,
-    "description": "This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. ",
-    "mirId": "MIR:00001034",
+  "mcro": {
+    "id": 3832,
+    "prefix": "mcro",
+    "name": "Model Card Ontology",
+    "pattern": "^MCRO:\\d+$",
+    "namespaceEmbeddedInLui": true,
+    "description": "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ",
+    "mirId": "MIR:00001049",
     "resources": [
       {
-        "id": 3731,
-        "providerCode": "ncbi",
-        "name": "National Center for Biotechnology Information",
-        "urlPattern": "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/{$id}",
-        "mirId": "MIR:00001033",
-        "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.",
+        "id": 3833,
+        "providerCode": "ols",
+        "name": "MCRO via OLS",
+        "urlPattern": "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:{$id}",
+        "mirId": "MIR:00001048",
+        "description": "ontology modeling the model card report for machine learning model assests",
         "official": true,
-        "sampleId": "72ff6ff882ec447f12df018e6183de59",
-        "resourceHomeUrl": "https://www.ncbi.nlm.nih.gov/",
+        "sampleId": "0000027",
+        "resourceHomeUrl": "https://www.ebi.ac.uk/ols4/ontologies/mcro",
         "institution": {
-          "id": 26,
-          "name": "National Center for Biotechnology Information",
-          "homeUrl": "https://www.ncbi.nlm.nih.gov/",
-          "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.",
-          "rorId": "https://ror.org/02meqm098",
+          "id": 2,
+          "name": "European Bioinformatics Institute",
+          "homeUrl": "https://www.ebi.ac.uk",
+          "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.",
+          "rorId": "https://ror.org/02catss52",
           "location": {
-            "countryCode": "US",
-            "countryName": "United States"
+            "countryCode": "GB",
+            "countryName": "United Kingdom"
           }
         },
         "location": {
-          "countryCode": "US",
-          "countryName": "United States"
+          "countryCode": "GB",
+          "countryName": "United Kingdom"
         },
         "deprecated": false,
         "deprecationDate": null,
@@ -377,9 +569,9 @@
         "authHelpDescription": null
       }
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-    "created": "2023-10-31T16:13:48.191+0000",
-    "modified": "2023-10-31T16:13:48.191+0000",
-    "sampleId": "72ff6ff882ec447f12df018e6183de59",
+    "created": "2024-03-20T10:56:06.644+0000",
+    "modified": "2024-03-20T10:56:06.644+0000",
+    "sampleId": "0000027",
     "deprecated": false,
     "deprecationDate": null
   },
@@ -511,6 +703,54 @@
     "deprecated": false,
     "deprecationDate": null
   },
+  "stato": {
+    "id": 3842,
+    "prefix": "stato",
+    "name": "Statistical Ontology",
+    "pattern": "^STATO:\\d+$",
+    "namespaceEmbeddedInLui": true,
+    "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.",
+    "mirId": "MIR:00001051",
+    "resources": [
+      {
+        "id": 3843,
+        "providerCode": "ols",
+        "name": "European Bioinformatics Institute",
+        "urlPattern": "https://www.ebi.ac.uk/ols4/ontologies/stato/classes?obo_id=STATO:{$id}",
+        "mirId": "MIR:00001050",
+        "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.",
+        "official": true,
+        "sampleId": "0000138",
+        "resourceHomeUrl": "https://www.ebi.ac.uk",
+        "institution": {
+          "id": 2,
+          "name": "European Bioinformatics Institute",
+          "homeUrl": "https://www.ebi.ac.uk",
+          "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.",
+          "rorId": "https://ror.org/02catss52",
+          "location": {
+            "countryCode": "GB",
+            "countryName": "United Kingdom"
+          }
+        },
+        "location": {
+          "countryCode": "GB",
+          "countryName": "United Kingdom"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      }
+    ],
+    "created": "2024-03-20T11:10:30.918+0000",
+    "modified": "2024-03-20T11:10:30.918+0000",
+    "sampleId": "0000138",
+    "deprecated": false,
+    "deprecationDate": null
+  },
   "macie": {
     "id": 261,
     "prefix": "macie",
@@ -607,6 +847,86 @@
     "deprecated": false,
     "deprecationDate": null
   },
+  "edam": {
+    "id": 575,
+    "prefix": "edam",
+    "name": "EDAM Ontology",
+    "pattern": "^(data|topic|operation|format)\\_\\d{4}$",
+    "namespaceEmbeddedInLui": false,
+    "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).",
+    "mirId": "MIR:00000189",
+    "resources": [
+      {
+        "id": 576,
+        "providerCode": "bptl",
+        "name": "EDAM through BioPortal",
+        "urlPattern": "http://purl.bioontology.org/ontology/EDAM/{$id}",
+        "mirId": "MIR:00100536",
+        "description": "EDAM through BioPortal",
+        "official": false,
+        "sampleId": "data_1664",
+        "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/EDAM",
+        "institution": {
+          "id": 5,
+          "name": "National Center for Biomedical Ontology, Stanford",
+          "homeUrl": "https://ncbo.bioontology.org/",
+          "description": "The goal of the National Center for Biomedical Ontology is to support biomedical researchers in their knowledge-intensive work, by providing online tools and a Web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of our work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments.",
+          "rorId": null,
+          "location": {
+            "countryCode": "US",
+            "countryName": "United States"
+          }
+        },
+        "location": {
+          "countryCode": "US",
+          "countryName": "United States"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      },
+      {
+        "id": 577,
+        "providerCode": "ols",
+        "name": "EDAM through OLS",
+        "urlPattern": "https://www.ebi.ac.uk/ols4/ontologies/edam/terms?short_form={$id}",
+        "mirId": "MIR:00100762",
+        "description": "EDAM through OLS",
+        "official": false,
+        "sampleId": "data_1664",
+        "resourceHomeUrl": "https://www.ebi.ac.uk/ols4/ontologies/edam",
+        "institution": {
+          "id": 2,
+          "name": "European Bioinformatics Institute",
+          "homeUrl": "https://www.ebi.ac.uk",
+          "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.",
+          "rorId": "https://ror.org/02catss52",
+          "location": {
+            "countryCode": "GB",
+            "countryName": "United Kingdom"
+          }
+        },
+        "location": {
+          "countryCode": "GB",
+          "countryName": "United Kingdom"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      }
+    ],
+    "created": "2019-06-11T14:16:22.318+0000",
+    "modified": "2024-03-20T11:53:50.927+0000",
+    "sampleId": "data_1664",
+    "deprecated": false,
+    "deprecationDate": null
+  },
   "neuromorpho": {
     "id": 312,
     "prefix": "neuromorpho",
@@ -703,6 +1023,54 @@
     "deprecated": false,
     "deprecationDate": null
   },
+  "obcs": {
+    "id": 3852,
+    "prefix": "obcs",
+    "name": " Ontology of Biological and Clinical Statistics",
+    "pattern": "^OBCS:\\d+$",
+    "namespaceEmbeddedInLui": true,
+    "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)",
+    "mirId": "MIR:00001053",
+    "resources": [
+      {
+        "id": 3853,
+        "providerCode": "ols",
+        "name": "OBCS via OLS",
+        "urlPattern": "https://www.ebi.ac.uk/ols4/ontologies/obcs/classes?obo_id=OBCS:{$id}",
+        "mirId": "MIR:00001052",
+        "description": "OBCS stands for the Ontology of Biological and Clinical Statistics",
+        "official": true,
+        "sampleId": "0000086",
+        "resourceHomeUrl": "https://www.ebi.ac.uk/ols4/ontologies/obcs",
+        "institution": {
+          "id": 2,
+          "name": "European Bioinformatics Institute",
+          "homeUrl": "https://www.ebi.ac.uk",
+          "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.",
+          "rorId": "https://ror.org/02catss52",
+          "location": {
+            "countryCode": "GB",
+            "countryName": "United Kingdom"
+          }
+        },
+        "location": {
+          "countryCode": "GB",
+          "countryName": "United Kingdom"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      }
+    ],
+    "created": "2024-03-21T14:43:39.901+0000",
+    "modified": "2024-03-21T14:43:39.901+0000",
+    "sampleId": "0000086",
+    "deprecated": false,
+    "deprecationDate": null
+  },
   "glycomedb": {
     "id": 363,
     "prefix": "glycomedb",
@@ -799,6 +1167,86 @@
     "deprecated": false,
     "deprecationDate": null
   },
+  "mzspec": {
+    "id": 1735,
+    "prefix": "mzspec",
+    "name": "Universal Spectrum Identifier",
+    "pattern": "^mzspec:.+$",
+    "namespaceEmbeddedInLui": true,
+    "description": "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.",
+    "mirId": "MIR:00000625",
+    "resources": [
+      {
+        "id": 2394,
+        "providerCode": "pc",
+        "name": "Institute for Systems Biology, Seattle, USA",
+        "urlPattern": "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:{$id}",
+        "mirId": "MIR:00000771",
+        "description": "Institute for Systems Biology (ISB), Seattle, USA is an independent research institute focusing on systems biology.",
+        "official": true,
+        "sampleId": "PXD000865:00603_F01_P004608_B00F_A00_R1:scan:14453:SSLLDVLAAR/2",
+        "resourceHomeUrl": "http://proteomecentral.proteomexchange.org/",
+        "institution": {
+          "id": 193,
+          "name": "Institute for Systems Biology",
+          "homeUrl": "https://isbscience.org/",
+          "description": "ISB was created in 2000 as the first-ever institute dedicated to systems biology.",
+          "rorId": "https://ror.org/02tpgw303",
+          "location": {
+            "countryCode": "US",
+            "countryName": "United States"
+          }
+        },
+        "location": {
+          "countryCode": "US",
+          "countryName": "United States"
+        },
+        "deprecated": false,
+        "deprecationDate": null,
+        "protectedUrls": false,
+        "renderProtectedLanding": false,
+        "authHelpUrl": null,
+        "authHelpDescription": null
+      },
+      {
+        "id": 1737,
+        "providerCode": "CURATOR_REVIEW",
+        "name": "Universal Spectrum Identifier through Peptide Atlas",
+        "urlPattern": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:{$id}",
+        "mirId": "MIR:00100829",
+        "description": "Universal Spectrum Identifier through Peptide Atlas",
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