diff --git a/src/bioregistry/align/utils.py b/src/bioregistry/align/utils.py index fdaf90ed1..74f4a6c85 100644 --- a/src/bioregistry/align/utils.py +++ b/src/bioregistry/align/utils.py @@ -219,10 +219,12 @@ def get_curation_row(self, external_id, external_entry) -> Sequence[str]: rv.append("") elif isinstance(value, str): rv.append(value.strip()) + elif isinstance(value, bool): + rv.append("true" if value else "false") elif isinstance(value, (list, tuple, set)): rv.append("|".join(sorted(v.strip() for v in value))) else: - raise TypeError + raise TypeError(f"unexpected type in curation header: {value}") return rv def _iter_curation_rows(self) -> Iterable[Sequence[str]]: diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 6a14f26ef..9f3f5b028 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -2959,9 +2959,22 @@ "description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer", "homepage": "https://www.araport.org/", "mappings": { + "miriam": "tair.name", "ncbi": "Araport", "uniprot": "DB-0221" }, + "miriam": { + "deprecated": false, + "description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.", + "homepage": "https://www.arabidopsis.org/index.jsp", + "id": "00000976", + "name": "TAIR gene name", + "namespaceEmbeddedInLui": false, + "pattern": "^AT.G[0-9]{5}$", + "prefix": "tair.name", + "sampleId": "AT5G05330", + "uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1" + }, "name": "Arabidopsis Information Portal", "ncbi": { "example": "AT1G01010", @@ -3151,7 +3164,7 @@ "namespaceEmbeddedInLui": true, "pattern": "^(ark\\:)/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$", "prefix": "ark", - "sampleId": "/12345/fk1234", + "sampleId": "/87924/r4154jq8h", "uri_format": "http://n2t.net/ark:$1" }, "n2t": { @@ -7892,7 +7905,7 @@ "id": "00000694", "name": "BioStudies database", "namespaceEmbeddedInLui": false, - "pattern": "^S-[A-Z]{4}[A-Z\\d\\-]+$", + "pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$", "prefix": "biostudies", "sampleId": "S-EPMC6266652", "uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1" @@ -10575,7 +10588,7 @@ "id": "00000234", "name": "Cell Cycle Ontology", "namespaceEmbeddedInLui": true, - "pattern": "^CCO\\:\\w+$", + "pattern": "^CCO:\\w+$", "prefix": "cco", "sampleId": "0000003", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1" @@ -13915,6 +13928,23 @@ ], "uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1" }, + "clb": { + "mappings": { + "miriam": "clb" + }, + "miriam": { + "deprecated": false, + "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", + "homepage": "https://www.checklistbank.org", + "id": "00000964", + "name": "ChecklistBank", + "namespaceEmbeddedInLui": false, + "pattern": "^[0-9]+(LR)?$", + "prefix": "clb", + "sampleId": "1010", + "uri_format": "https://www.checklistbank.org/dataset/$1" + } + }, "cldb": { "biocontext": { "is_identifiers": true, @@ -16841,6 +16871,32 @@ "no_own_terms": true, "repository": "https://github.com/MIT-LCP/mimic-omop" }, + "col": { + "mappings": { + "miriam": "col" + }, + "miriam": { + "deprecated": false, + "description": "Identifier of a taxon or synonym in the Catalogue of Life", + "homepage": "https://www.checklistbank.org", + "id": "00000969", + "name": "Catalogue of Life", + "namespaceEmbeddedInLui": false, + "pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$", + "prefix": "col", + "providers": [ + { + "code": "col", + "description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.", + "homepage": "https://www.catalogueoflife.org", + "name": "Catalogue of Life (COL)", + "uri_format": "https://www.catalogueoflife.org/data/taxon/$1" + } + ], + "sampleId": "4QHKG", + "uri_format": "https://www.checklistbank.org/dataset/3LR/taxon/$1" + } + }, "col.taiwan": { "contributor": { "email": "meghan.balk@gmail.com", @@ -38105,7 +38161,7 @@ "mappings": { "biocontext": "GRAMENE.GROWTHSTAGE", "bioportal": "GRO-CPGA", - "miriam": "gramene.growthstage", + "miriam": "gro", "n2t": "gramene.growthstage", "obofoundry": "gro", "prefixcommons": "gramene.po" @@ -38117,8 +38173,8 @@ "id": "00000508", "name": "Gramene Growth Stage Ontology", "namespaceEmbeddedInLui": true, - "pattern": "^GRO\\:\\d+$", - "prefix": "gramene.growthstage", + "pattern": "^GRO:\\d+$", + "prefix": "gro", "sampleId": "0007133", "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" }, @@ -53377,7 +53433,7 @@ "prefixcommons": "aclame" }, "miriam": { - "deprecated": false, + "deprecated": true, "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", "homepage": "http://aclame.ulb.ac.be/", "id": "00000063", @@ -64624,7 +64680,7 @@ "namespaceEmbeddedInLui": true, "pattern": "^HOG:[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", "prefix": "oma.hog", - "sampleId": "HOG:0459895", + "sampleId": "0459895", "uri_format": "https://omabrowser.org/oma/hog/resolve/HOG:$1/" }, "pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", @@ -81363,6 +81419,23 @@ "name": "Scholia Registry", "uri_format": "https://bioregistry.io/metaregistry/scholia/$1" }, + "sciflection": { + "mappings": { + "miriam": "sciflection" + }, + "miriam": { + "deprecated": false, + "description": "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions", + "homepage": "https://sciformation.com/sciflection.html", + "id": "00000973", + "name": "Sciflection", + "namespaceEmbeddedInLui": false, + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", + "prefix": "sciflection", + "sampleId": "5ede4273-b26c-4ea4-adb7-3ce294ab3397", + "uri_format": "https://sciflection.com/$1" + } + }, "scomp": { "contributor": { "email": "cthoyt@gmail.com", @@ -83656,6 +83729,23 @@ "pattern": "^SKIP\\d+$", "uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1" }, + "skm": { + "mappings": { + "miriam": "skm" + }, + "miriam": { + "deprecated": false, + "description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ", + "homepage": "http://www.nib.si/eng/", + "id": "00000968", + "name": "Stress Knowledge Map", + "namespaceEmbeddedInLui": false, + "pattern": "^rx[0-9]{5}$", + "prefix": "skm", + "sampleId": "rx00408", + "uri_format": "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary" + } + }, "skos": { "aberowl": { "description": "This file is imported by vivo-core-1.5.owl. It contains terms relating to concepts from the http://www.w3.org/2004/02/skos/core# namespace of the SKOS (Simple Knowledge Organization System) ontology that are included in the vivo ontology.", diff --git a/src/bioregistry/data/external/miriam/processed.json b/src/bioregistry/data/external/miriam/processed.json index 3d16e4b12..bfd7e886d 100644 --- a/src/bioregistry/data/external/miriam/processed.json +++ b/src/bioregistry/data/external/miriam/processed.json @@ -281,7 +281,7 @@ "namespaceEmbeddedInLui": true, "pattern": "^(ark\\:)/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$", "prefix": "ark", - "sampleId": "/12345/fk1234", + "sampleId": "/87924/r4154jq8h", "uri_format": "http://n2t.net/ark:$1" }, "arrayexpress": { @@ -960,7 +960,7 @@ "id": "00000694", "name": "BioStudies database", "namespaceEmbeddedInLui": false, - "pattern": "^S-[A-Z]{4}[A-Z\\d\\-]+$", + "pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$", "prefix": "biostudies", "sampleId": "S-EPMC6266652", "uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1" @@ -1302,7 +1302,7 @@ "id": "00000234", "name": "Cell Cycle Ontology", "namespaceEmbeddedInLui": true, - "pattern": "^CCO\\:\\w+$", + "pattern": "^CCO:\\w+$", "prefix": "cco", "sampleId": "0000003", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1" @@ -3804,18 +3804,6 @@ "sampleId": "GR:0080039", "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" }, - "gramene.growthstage": { - "deprecated": false, - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", - "homepage": "http://www.gramene.org/", - "id": "00000508", - "name": "Gramene Growth Stage Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^GRO\\:\\d+$", - "prefix": "gramene.growthstage", - "sampleId": "0007133", - "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" - }, "gramene.protein": { "deprecated": false, "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.", @@ -3888,6 +3876,18 @@ "sampleId": "19333", "uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1" }, + "gro": { + "deprecated": false, + "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", + "homepage": "http://www.gramene.org/", + "id": "00000508", + "name": "Gramene Growth Stage Ontology", + "namespaceEmbeddedInLui": true, + "pattern": "^GRO:\\d+$", + "prefix": "gro", + "sampleId": "0007133", + "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" + }, "grsdb": { "deprecated": false, "description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.", @@ -5762,7 +5762,7 @@ "uri_format": "https://www.metabolome-express.org/datasetview.php?datasetid=$1" }, "mge": { - "deprecated": false, + "deprecated": true, "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", "homepage": "http://aclame.ulb.ac.be/", "id": "00000063", @@ -6953,7 +6953,7 @@ "namespaceEmbeddedInLui": true, "pattern": "^HOG:[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", "prefix": "oma.hog", - "sampleId": "HOG:0459895", + "sampleId": "0459895", "uri_format": "https://omabrowser.org/oma/hog/resolve/HOG:$1/" }, "oma.protein": { @@ -9243,6 +9243,18 @@ "sampleId": "2200950", "uri_format": "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1" }, + "tair.name": { + "deprecated": false, + "description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.", + "homepage": "https://www.arabidopsis.org/index.jsp", + "id": "00000976", + "name": "TAIR gene name", + "namespaceEmbeddedInLui": false, + "pattern": "^AT.G[0-9]{5}$", + "prefix": "tair.name", + "sampleId": "AT5G05330", + "uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1" + }, "tair.protein": { "deprecated": false, "description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept", diff --git a/src/bioregistry/data/external/miriam/raw.json b/src/bioregistry/data/external/miriam/raw.json index b98c1b592..bb651d12b 100644 --- a/src/bioregistry/data/external/miriam/raw.json +++ b/src/bioregistry/data/external/miriam/raw.json @@ -4,1271 +4,1179 @@ "payload": { "namespaces": [ { - "created": "2019-06-11T14:15:26.925+0000", + "created": "2019-06-11T14:15:50.652+0000", "deprecated": false, "deprecationDate": null, - "description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.", - "id": 1, - "mirId": "MIR:00000002", - "modified": "2019-06-11T14:15:26.925+0000", - "name": "ChEBI", - "namespaceEmbeddedInLui": true, - "pattern": "^CHEBI:\\d+$", - "prefix": "chebi", + "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.", + "id": 230, + "mirId": "MIR:00000066", + "modified": "2019-06-11T14:15:50.652+0000", + "name": "3DMET", + "namespaceEmbeddedInLui": false, + "pattern": "^B\\d{5}$", + "prefix": "3dmet", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ChEBI (Chemical Entities of Biological Interest)", - "id": 3, - "institution": { - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100009", - "name": "ChEBI (Chemical Entities of Biological Interest)", - "official": true, - "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/chebi/", - "sampleId": "36927", - "urlPattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{$id}" - }, - { - "deprecated": false, - "deprecationDate": null, - "description": "ChEBI through OLS", - "id": 4, + "description": "3DMET database", + "id": 232, "institution": { - "description": "At EMBL-EBI, we make the world’s 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.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, + "description": "The National Institute of Agrobiological Sciences (NIAS) is the largest agricultural research institute in Japan for basic life sciences. As a major research institute of the Ministry of Agriculture, Forestry and Fisheries (MAFF), it was formerly known as the National Institute of Agrobiological Resources (NIAR) until it was re-established as an independent administrative institution in April 1, 2001. The institute focuses on understanding the biological phenomena of agriculturally important plants, insects, microbes and animals to create innovative technologies, and eventually contribute to the solution of global issues such as food shortage due to rapid population growth and environmental problems due to climate change", + "homeUrl": "http://www.naro.affrc.go.jp/archive/nias/index_e.html", + "id": 231, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "JP", + "countryName": "Japan" }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" + "name": "National Institute of Agrobiological Sciences", + "rorId": "https://ror.org/01786mp71" }, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "JP", + "countryName": "Japan" }, - "mirId": "MIR:00100158", - "name": "ChEBI through OLS", + "mirId": "MIR:00100095", + "name": "3DMET database", "official": false, - "providerCode": "ols", - "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/chebi", - "sampleId": "36927", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/chebi/terms?obo_id=CHEBI:{$id}" - }, + "providerCode": "nias", + "resourceHomeUrl": "http://www.3dmet.dna.affrc.go.jp/", + "sampleId": "B00162", + "urlPattern": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc={$id}" + } + ], + "sampleId": "B00162" + }, + { + "created": "2022-02-27T20:31:54.933+0000", + "deprecated": false, + "deprecationDate": null, + "description": "NHLBI BioData Catalyst supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources.", + "id": 3152, + "mirId": "MIR:00001020", + "modified": "2022-02-27T20:31:54.933+0000", + "name": "BioData Catalyst", + "namespaceEmbeddedInLui": false, + "pattern": "[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}", + "prefix": "4503", + "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ChEBI through BioPortal", - "id": 6, + "description": "NHLBI BioData Catalyst supports the management, analysis and sharing of human disease data for the research community and aims to advance basic understanding of the genetic basis of complex traits and accelerate discovery and development of therapies, diagnostic tests, and other technologies for diseases like cancer. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources.", + "id": 3153, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 5, + "description": "The Open Commons Consortium (OCC) manages and operates cloud computing, data commons, and data ecosystems to advance scientific, medical, health care and environmental research for human and societal impact.", + "homeUrl": "https://www.occ-data.org/", + "id": 3145, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "National Center for Biomedical Ontology, Stanford", + "name": "Open Commons Consortium ", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100565", - "name": "ChEBI through BioPortal", - "official": false, - "providerCode": "bptl", - "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/CHEBI", - "sampleId": "36927", - "urlPattern": "http://purl.bioontology.org/ontology/CHEBI/CHEBI:{$id}" + "mirId": "MIR:00000921", + "name": "BioData Catalyst", + "official": true, + "providerCode": "dg.4503", + "resourceHomeUrl": "https://gen3.biodatacatalyst.nhlbi.nih.gov/", + "sampleId": "3dab719c-1fa0-461b-a543-5f0e564a9be4", + "urlPattern": "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/{$id}" } ], - "sampleId": "36927" + "sampleId": "3dab719c-1fa0-461b-a543-5f0e564a9be4" }, { - "created": "2019-06-11T14:15:28.483+0000", + "created": "2021-08-05T19:25:24.806+0000", "deprecated": false, "deprecationDate": null, - "description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.", - "id": 13, - "mirId": "MIR:00000004", - "modified": "2019-06-11T14:15:28.483+0000", - "name": "Enzyme Nomenclature", + "description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. 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Today it is considered one of the best young universities in the world.", - "homeUrl": "https://www.maastrichtuniversity.nl", - "id": 283, - "location": { - "countryCode": "NL", - "countryName": "Netherlands" - }, - "name": "Maastricht University", - "rorId": "https://ror.org/02jz4aj89" - }, - "location": { - "countryCode": "NL", - "countryName": "Netherlands" - }, - "mirId": "MIR:00000696", - "name": "Scholia", - "official": false, - "providerCode": "scholia", - "resourceHomeUrl": "https://scholia.toolforge.org/", - "sampleId": "WP111", - "urlPattern": "https://scholia.toolforge.org/wikipathways/{$id}" + "providerCode": "civicdb", + "resourceHomeUrl": "https://civicdb.org/", + "sampleId": "3", + "urlPattern": "https://civicdb.org/links/assertions/{$id}" } ], - "sampleId": "WP100" + "sampleId": "3" }, { - "created": "2019-06-11T14:15:57.451+0000", + "created": "2022-08-08T18:34:15.882+0000", "deprecated": false, "deprecationDate": null, - "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. 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The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", + "id": 3258, + "mirId": "MIR:00000957", + "modified": "2022-08-08T18:34:15.882+0000", + "name": "CIViC Disease", "namespaceEmbeddedInLui": false, - "pattern": "^PA\\d+$", - "prefix": "pharmgkb.drug", + "pattern": "^[0-9]+$", + "prefix": "civic.did", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "PharmGKB Drug at Stanford", - "id": 303, + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.https://civicdb.org/\n", + "id": 3259, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 298, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "homeUrl": "https://wustl.edu/", + "id": 2750, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Department of Genetics, School of Medicine, Stanford University, Stanford, California", + "name": "Washington University in St. Louis", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100122", - "name": "PharmGKB Drug at Stanford", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.pharmgkb.org/", - "sampleId": "PA448710", - "urlPattern": "http://www.pharmgkb.org/drug/{$id}" - } - ], - "sampleId": "PA448710" - }, - { - "created": "2019-06-11T14:15:57.654+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", - "id": 304, - "mirId": "MIR:00000092", - "modified": "2019-06-11T14:15:57.654+0000", - "name": "TTD Drug", - "namespaceEmbeddedInLui": false, - "pattern": "^DAP\\d+$", - "prefix": "ttd.drug", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Therapeutic Target Database Drug", - "id": 306, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 305, - "location": { - "countryCode": "SG", - "countryName": "Singapore" - }, - "name": "Computational Science Department, National University of Singapore", - "rorId": null - }, - "location": { - "countryCode": "SG", - "countryName": "Singapore" - }, - "mirId": "MIR:00100123", - "name": "Therapeutic Target Database Drug", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", - "sampleId": "DAP000773", - "urlPattern": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID={$id}" + "mirId": "MIR:00000956", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "official": true, + "providerCode": "civicdb", + "resourceHomeUrl": "https://civicdb.org/", + "sampleId": "46", + "urlPattern": "https://civicdb.org/links/diseases/{$id}" } ], - "sampleId": "DAP000773" + "sampleId": "46" }, { - "created": "2019-06-11T14:15:57.896+0000", + "created": "2021-08-08T09:28:56.816+0000", "deprecated": false, "deprecationDate": null, - "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", - "id": 307, - "mirId": "MIR:00000093", - "modified": "2019-06-11T14:15:57.896+0000", - "name": "TTD Target", + "description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).", + "id": 2784, + "mirId": "MIR:00000839", + "modified": "2021-08-08T09:28:56.816+0000", + "name": "CIViC Evidence", "namespaceEmbeddedInLui": false, - "pattern": "^TTDS\\d+$", - "prefix": "ttd.target", + "pattern": "^[0-9]+$", + "prefix": "civic.eid", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Therapeutic Target Database Target", - "id": 308, + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", + "id": 2785, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 305, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "homeUrl": "https://wustl.edu/", + "id": 2750, "location": { - "countryCode": "SG", - "countryName": "Singapore" + "countryCode": "US", + "countryName": "United States" }, - "name": "Computational Science Department, National University of Singapore", + "name": "Washington University in St. Louis", "rorId": null }, "location": { - "countryCode": "SG", - "countryName": "Singapore" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100124", - "name": "Therapeutic Target Database Target", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", - "sampleId": "TTDS00056", - "urlPattern": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID={$id}" + "mirId": "MIR:00000838", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "official": true, + "providerCode": "civicdb", + "resourceHomeUrl": "https://civicdb.org/", + "sampleId": "1199", + "urlPattern": "https://civicdb.org/links/evidence/{$id}" } ], - "sampleId": "TTDS00056" + "sampleId": "1199" }, { - "created": "2019-06-11T14:15:58.106+0000", + "created": "2022-01-29T10:47:57.098+0000", "deprecated": false, "deprecationDate": null, - "description": "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. 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Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis", + "id": 3039, + "mirId": "MIR:00000907", + "modified": "2022-01-29T10:47:57.098+0000", + "name": "CIViC Gene", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "neurondb", + "pattern": "^[0-9]+$", + "prefix": "civic.gid", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "NeuronDB at SenseLab", - "id": 311, + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", + "id": 3040, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 310, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "homeUrl": "https://wustl.edu/", + "id": 2750, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Yale University School of Medicine", + "name": "Washington University in St. Louis", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100125", - "name": "NeuronDB at SenseLab", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://senselab.med.yale.edu/NeuronDB/", - "sampleId": "265", - "urlPattern": "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id={$id}" + "mirId": "MIR:00000906", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "official": true, + "providerCode": "civicdb", + "resourceHomeUrl": "https://civicdb.org/", + "sampleId": "272", + "urlPattern": "https://civicdb.org/links/gene/{$id}" } ], - "sampleId": "265" + "sampleId": "272" }, { - "created": "2019-06-11T14:15:58.342+0000", + "created": "2022-08-08T18:32:17.171+0000", "deprecated": false, "deprecationDate": null, - "description": "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.", - "id": 312, - "mirId": "MIR:00000095", - "modified": "2019-06-11T14:15:58.342+0000", - "name": "NeuroMorpho", + "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", + "id": 3252, + "mirId": "MIR:00000953", + "modified": "2022-08-08T18:32:17.171+0000", + "name": "CIViC Source", "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "neuromorpho", + "pattern": "^[0-9]+$", + "prefix": "civic.sid", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "NeuroMorpho", - "id": 314, + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", + "id": 3253, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 313, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "homeUrl": "https://wustl.edu/", + "id": 2750, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Krasnow Institute, Virginia", + "name": "Washington University in St. Louis", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100126", - "name": "NeuroMorpho", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://neuromorpho.org/index.jsp", - "sampleId": "Rosa2", - "urlPattern": "http://neuromorpho.org/neuron_info.jsp?neuron_name={$id}" + "mirId": "MIR:00000952", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "official": true, + "providerCode": "civicdb", + "resourceHomeUrl": "https://civicdb.org/", + "sampleId": "62", + "urlPattern": "https://civicdb.org/links/sources/{$id}" } ], - "sampleId": "Rosa2" + "sampleId": "62" }, { - "created": "2019-06-11T14:15:58.577+0000", + "created": "2022-08-08T18:33:25.710+0000", "deprecated": false, "deprecationDate": null, - "description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.", - "id": 315, - "mirId": "MIR:00000096", - "modified": "2019-06-11T14:15:58.577+0000", - "name": "ChemIDplus", + "description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", + "id": 3255, + "mirId": "MIR:00000955", + "modified": "2022-08-08T18:33:25.710+0000", + "name": "CIViC Therapy", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+\\-\\d+\\-\\d+$", - "prefix": "chemidplus", + "pattern": "^[0-9]+$", + "prefix": "civic.tid", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ChemIDplus at National Library of Medicine", - "id": 317, + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", + "id": 3256, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 316, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "homeUrl": "https://wustl.edu/", + "id": 2750, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "National Library of Medicine, Maryland", + "name": "Washington University in St. Louis", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100127", - "name": "ChemIDplus at National Library of Medicine", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp", - "sampleId": "57-27-2", - "urlPattern": "https://chem.nlm.nih.gov/chemidplus/rn/{$id}" + "mirId": "MIR:00000954", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "official": true, + "providerCode": "civicdb", + "resourceHomeUrl": "https://civicdb.org/", + "sampleId": "14", + "urlPattern": "https://civicdb.org/links/drugs/{$id}" } ], - "sampleId": "57-27-2" + "sampleId": "14" }, { - "created": "2019-06-11T14:15:58.906+0000", + "created": "2022-01-29T10:48:56.640+0000", "deprecated": false, "deprecationDate": null, - "description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.", - "id": 318, - "mirId": "MIR:00000097", - "modified": "2019-06-11T14:15:58.906+0000", - "name": "BioSystems", + "description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.", + "id": 3042, + "mirId": "MIR:00000909", + "modified": "2022-01-29T10:48:56.640+0000", + "name": "CIViC Variant", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "biosystems", + "pattern": "^[0-9]+$", + "prefix": "civic.vid", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "BioSystems database at NCBI", - "id": 319, + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", + "id": 3043, "institution": { - "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", - "homeUrl": "https://www.ncbi.nlm.nih.gov/", - "id": 26, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "homeUrl": "https://wustl.edu/", + "id": 2750, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "National Center for Biotechnology Information", - "rorId": "https://ror.org/02meqm098" + "name": "Washington University in St. Louis", + "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100128", - "name": "BioSystems database at NCBI", - "official": false, - "providerCode": "ncbi", - "resourceHomeUrl": "https://www.ncbi.nlm.nih.gov/biosystems/", - "sampleId": "001", - "urlPattern": "https://www.ncbi.nlm.nih.gov/biosystems/{$id}" + "mirId": "MIR:00000908", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "official": true, + "providerCode": "civicdb", + "resourceHomeUrl": "https://civicdb.org/", + "sampleId": "12", + "urlPattern": "https://civicdb.org/links/variant/{$id}" } ], - "sampleId": "001" + "sampleId": "12" }, { - "created": "2019-06-11T14:15:59.108+0000", + "created": "2019-06-11T14:16:02.066+0000", "deprecated": false, "deprecationDate": null, - "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. 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Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.", + "id": 1977, + "mirId": "MIR:00000770", + "modified": "2019-09-05T11:46:36.162+0000", + "name": "ClassyFire", "namespaceEmbeddedInLui": false, - "pattern": "^D\\d+$", - "prefix": "ctd.disease", + "pattern": "^C[0-9]{7}$", + "prefix": "classyfire", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Comparative Toxicogenomics Database (Disease)", - "id": 324, + "description": "Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT). He has been with the University of Alberta since 1995. 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This collection references target information from version 4 of the database.", + "id": 1485, + "mirId": "MIR:00000528", + "modified": "2019-06-11T14:17:41.273+0000", + "name": "DrugBank Target v4", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sgn", + "pattern": "^BE\\d{7}$", + "prefix": "drugbankv4.target", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Sol Genomics Network at Boyce Thompson Institute for Plant Research", - "id": 566, + "description": "DrugBank Target information version 4", + "id": 1487, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 565, + "id": 1486, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CA", + "countryName": "Canada" }, - "name": "Boyce Thompson Institute for Plant Research, New York", + "name": "Departments of Computing Science, Biological Sciences, University of Alberta", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CA", + "countryName": "Canada" }, - "mirId": "MIR:00100231", - "name": "Sol Genomics Network at Boyce Thompson Institute for Plant Research", + "mirId": "MIR:00100687", + "name": "DrugBank Target information version 4", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://solgenomics.net/", - "sampleId": "0001", - "urlPattern": "http://solgenomics.net/phenome/locus_display.pl?locus_id={$id}" + "resourceHomeUrl": "http://www.drugbank.ca/targets", + "sampleId": "BE0000048", + "urlPattern": "http://www.drugbank.ca/biodb/bio_entities/{$id}" } ], - "sampleId": "0001" + "sampleId": "BE0000048" }, { - "created": "2019-06-11T14:16:21.882+0000", + "created": "2022-11-04T09:54:32.976+0000", "deprecated": false, "deprecationDate": null, - "description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. 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The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.", + "id": 3298, + "mirId": "MIR:00000966", + "modified": "2022-11-04T09:54:32.976+0000", + "name": "DrugCentral", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "bioportal", + "pattern": "^[0-9]+$", + "prefix": "drugcentral", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "BioPortal at National Center for Biomedical Ontology", - "id": 572, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", + "id": 3299, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 571, + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", + "homeUrl": "http://www.unm.edu/", + "id": 3297, "location": { "countryCode": "US", "countryName": "United States" }, - 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Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.", + "id": 1406, + "mirId": "MIR:00000496", + "modified": "2019-06-11T14:17:33.340+0000", + "name": "F-SNP", "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "scretf", + "pattern": "^rs\\d+$", + "prefix": "fsnp", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ScerTF at Washington University", - "id": 727, + "description": "F-SNP at Queen's University (Canada)", + "id": 1408, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 726, + "id": 1407, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CA", + "countryName": "Canada" }, - "name": "Department of Genetics, Washington University Medical School, St Louis, Missouri", + "name": "Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, Ontario", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CA", + "countryName": "Canada" }, - "mirId": "MIR:00100315", - "name": "ScerTF at Washington University", + "mirId": "MIR:00100637", + "name": "F-SNP at Queen's University (Canada)", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://stormo.wustl.edu/ScerTF/", - "sampleId": "RSC3", - "urlPattern": "http://stormo.wustl.edu/ScerTF/details/{$id}/" + "resourceHomeUrl": "http://compbio.cs.queensu.ca/F-SNP/", + "sampleId": "rs17852708", + "urlPattern": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val={$id}" } ], - "sampleId": "RSC3" + "sampleId": "rs17852708" }, { - "created": "2019-06-11T14:16:36.222+0000", + "created": "2019-06-11T14:17:25.854+0000", "deprecated": false, "deprecationDate": null, - "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. 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This datatype refers to gene information.", + "id": 541, + "mirId": "MIR:00000176", + "modified": "2019-06-11T14:16:19.420+0000", + "name": "Integrated Microbial Genomes Gene", "namespaceEmbeddedInLui": false, - "pattern": "^TS-\\d{4}$", - "prefix": "tissuelist", + "pattern": "^\\d+$", + "prefix": "img.gene", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Tissue List at Swiss Institute of Bioinformatics", - "id": 1035, + "description": "Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory", + "id": 542, "institution": { - "description": "SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide.", - "homeUrl": "https://www.sib.swiss", - "id": 1730, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 539, "location": { - "countryCode": "CH", - "countryName": "Switzerland" + "countryCode": "US", + "countryName": "United States" }, - "name": "SIB Swiss Institute of Bioinformatics", - "rorId": "https://ror.org/002n09z45" + "name": "Lawrence Berkeley National Laboratory, Berkeley", + "rorId": null }, "location": { - "countryCode": "CH", - "countryName": "Switzerland" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100457", - "name": "Tissue List at Swiss Institute of Bioinformatics", + "mirId": "MIR:00100222", + "name": "Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory", "official": false, - "providerCode": "sib", - "resourceHomeUrl": "https://www.uniprot.org/docs/tisslist.txt", - "sampleId": "TS-0285", - "urlPattern": "https://www.uniprot.org/tissues/{$id}" + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://img.jgi.doe.gov/", + "sampleId": "638309541", + "urlPattern": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid={$id}" } ], - "sampleId": "TS-0285" + "sampleId": "638309541" }, { - "created": "2019-06-11T14:17:01.735+0000", + "created": "2019-06-11T14:16:19.173+0000", "deprecated": false, "deprecationDate": null, - "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. 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This collection references allele information through the WHO nomenclature.", + "id": 950, + "mirId": "MIR:00000331", + "modified": "2019-06-11T14:16:54.535+0000", + "name": "IMGT HLA", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z-0-9_]+(\\@)?$", - "prefix": "hgnc.symbol", + "pattern": "^[A-Z0-9*:]+$", + "prefix": "imgt.hla", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "HGNC Symbol at HUGO Genome Nomenclature Committee", - "id": 1040, + "description": "IMGT HLA at EBI", + "id": 951, "institution": { "description": "At EMBL-EBI, we make the world’s 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.", "homeUrl": "https://www.ebi.ac.uk", @@ -17944,531 +18332,491 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100460", - "name": "HGNC Symbol at HUGO Genome Nomenclature Committee", + "mirId": "MIR:00100425", + "name": "IMGT HLA at EBI", "official": false, "providerCode": "ebi", - "resourceHomeUrl": "https://www.genenames.org/", - "sampleId": "DAPK1", - "urlPattern": "https://www.genenames.org/cgi-bin/gene_symbol_report?match={$id}" + "resourceHomeUrl": "https://www.ebi.ac.uk/imgt/hla/allele.html", + "sampleId": "A*01:01:01:01", + "urlPattern": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?{$id}" } ], - "sampleId": "DAPK1" + "sampleId": "A*01:01:01:01" }, { - "created": "2019-06-11T14:17:02.153+0000", + "created": "2019-06-11T14:16:45.469+0000", "deprecated": false, "deprecationDate": null, - "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. 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IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.", + "id": 842, + "mirId": "MIR:00000287", + "modified": "2019-06-11T14:16:45.469+0000", + "name": "IMGT LIGM", "namespaceEmbeddedInLui": false, - "pattern": "^P\\d{5}$", - "prefix": "panther.pathway", + "pattern": "^M\\d+$", + "prefix": "imgt.ligm", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "PANTHER Pathway at USC (Los Angeles)", - "id": 1042, + "description": "IMGT LIGM through DKFZ (SRS)", + "id": 844, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 94, + "id": 843, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "DE", + "countryName": "Germany" }, - "name": "Keck School of Medicine, University of Southern California", + "name": "DKFZ TP3, Heidelberg", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "DE", + "countryName": "Germany" }, - "mirId": "MIR:00100461", - "name": "PANTHER Pathway at USC (Los Angeles)", + "mirId": "MIR:00100369", + "name": "IMGT LIGM through DKFZ (SRS)", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.pantherdb.org/", - "sampleId": "P00024", - "urlPattern": "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession={$id}" - } - ], - "sampleId": "P00024" - }, - { - "created": "2019-06-11T14:17:02.358+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. 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"mirId": "MIR:00100473", - "name": "ENA at European Bioinformatics Institute", - "official": true, - "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/ena/", - "sampleId": "BN000065", - "urlPattern": "https://www.ebi.ac.uk/ena/browser/view/{$id}" - } - ], - "sampleId": "BN000065" - }, - { - "created": "2019-06-11T14:17:04.514+0000", - "deprecated": false, - "deprecationDate": null, - "description": "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.", - "id": 1071, - "mirId": "MIR:00000373", - "modified": "2019-06-11T14:17:04.514+0000", - "name": "DOMMINO", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9][A-Za-z0-9]{3}$", - "prefix": "dommino", - "resources": [ + "mirId": "MIR:00100807", + "name": "INSDC CDS through ENA", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "https://www.ebi.ac.uk/ena", + "sampleId": "AAA35559", + "urlPattern": "https://www.ebi.ac.uk/ena/data/view/{$id}" + }, { "deprecated": false, "deprecationDate": null, - "description": "DOMMINO at University of Missouri", - "id": 1073, + "description": "INSDC CDS through NCBI", + "id": 1683, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1072, + "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", + "homeUrl": "https://www.ncbi.nlm.nih.gov/", + "id": 26, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Informatics Institute and Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia", - "rorId": null + "name": "National Center for Biotechnology Information", + "rorId": "https://ror.org/02meqm098" }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100474", - "name": "DOMMINO at University of Missouri", + "mirId": "MIR:00100808", + "name": "INSDC CDS through NCBI", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://dommino.org/", - "sampleId": "2GC4", - "urlPattern": "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/{$id}" + "resourceHomeUrl": "https://www.ncbi.nlm.nih.gov/protein/", + "sampleId": "AAA35559", + "urlPattern": "https://www.ncbi.nlm.nih.gov/protein/{$id}" } ], - "sampleId": "2GC4" + "sampleId": "AAA35559" }, { - "created": "2019-06-11T14:17:04.735+0000", + "created": "2019-06-11T14:18:01.236+0000", "deprecated": false, "deprecationDate": null, - "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.", - "id": 1074, - "mirId": "MIR:00000374", - "modified": "2019-06-11T14:17:04.735+0000", - "name": "PANTHER Node", + "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.", + "id": 1685, + "mirId": "MIR:00000607", + "modified": "2020-03-31T12:32:16.941+0000", + "name": "Genome assembly database", "namespaceEmbeddedInLui": false, - "pattern": "^PTN\\d{9}$", - "prefix": "panther.node", + "pattern": "^GC[AF]_[0-9]{9}\\.[0-9]+$", + "prefix": "insdc.gca", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "PANTHER Node at USC (Los Angeles)", - "id": 1075, + "description": "Genome assembly database through ENA", + "id": 1686, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 94, + "description": "At EMBL-EBI, we make the world’s 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.", + "homeUrl": "https://www.ebi.ac.uk", + "id": 2, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "name": "Keck School of Medicine, University of Southern California", - "rorId": null + "name": "European Bioinformatics Institute", + "rorId": "https://ror.org/02catss52" }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "mirId": "MIR:00100475", - "name": "PANTHER Node at USC (Los Angeles)", + "mirId": "MIR:00100810", + "name": "Genome assembly database through ENA", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://pantree.org/", - "sampleId": "PTN000000026", - "urlPattern": "http://www.pantree.org/node/annotationNode.jsp?id={$id}" - } - ], - "sampleId": "PTN000000026" - }, - { - "created": "2019-06-11T14:17:04.925+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.", - "id": 1076, - "mirId": "MIR:00000375", - "modified": "2019-06-11T14:17:04.925+0000", - "name": "Consensus CDS", - "namespaceEmbeddedInLui": false, - "pattern": "^CCDS\\d+\\.\\d+$", - "prefix": "ccds", - "resources": [ + "resourceHomeUrl": "https://www.ebi.ac.uk/ena/browse/genome-assembly-database", + "sampleId": "GCA_000155495.1", + "urlPattern": "https://www.ebi.ac.uk/ena/data/view/{$id}" + }, { "deprecated": false, "deprecationDate": null, - "description": "Consensus CDS at NCBI", - "id": 1077, + "description": "Genome assembly database NCBI", + "id": 1687, "institution": { "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", "homeUrl": "https://www.ncbi.nlm.nih.gov/", @@ -18616,79 +18932,63 @@ "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100477", - "name": "Consensus CDS at NCBI", - "official": true, + "mirId": "MIR:00100811", + "name": "Genome assembly database NCBI", + "official": false, "providerCode": "ncbi", - "resourceHomeUrl": "http://www.ncbi.nlm.nih.gov/CCDS/", - "sampleId": "CCDS13573.1", - "urlPattern": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA={$id}" + "resourceHomeUrl": "https://www.ncbi.nlm.nih.gov/assembly/", + "sampleId": "GCA_000155495.1", + "urlPattern": "https://www.ncbi.nlm.nih.gov/assembly/{$id}" } ], - "sampleId": "CCDS13573.1" + "sampleId": "GCA_000155495.1" }, { - "created": "2019-06-11T14:17:05.741+0000", + "created": "2019-06-11T14:16:35.560+0000", "deprecated": false, "deprecationDate": null, - "description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.", - "id": 1086, - "mirId": "MIR:00000377", - "modified": "2019-06-11T14:17:05.741+0000", - "name": "HPRD", + "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", + "id": 721, + "mirId": "MIR:00000243", + "modified": "2019-06-11T14:16:35.560+0000", + "name": "Sequence Read Archive", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "hprd", + "pattern": "^[SED]R[APRSXZ]\\d+$", + "prefix": "insdc.sra", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Human Protein Reference Database", - "id": 1088, + "description": "Sequence Read Archive at NCBI", + "id": 722, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1087, + "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", + "homeUrl": "https://www.ncbi.nlm.nih.gov/", + "id": 26, "location": { - "countryCode": "IN", - "countryName": "India" + "countryCode": "US", + "countryName": "United States" }, - "name": "Institute of Bioinformatics, International Tech Park, Bangalore", - "rorId": null + "name": "National Center for Biotechnology Information", + "rorId": "https://ror.org/02meqm098" }, "location": { - "countryCode": "IN", - "countryName": "India" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100479", - "name": "Human Protein Reference Database", + "mirId": "MIR:00100312", + "name": "Sequence Read Archive at NCBI", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.hprd.org/", - "sampleId": "00001", - "urlPattern": "http://www.hprd.org/protein/{$id}" - } - ], - "sampleId": "00001" - }, - { - "created": "2019-06-11T14:17:05.964+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.", - "id": 1089, - "mirId": "MIR:00000378", - "modified": "2019-06-11T14:17:05.964+0000", - "name": "GXA Gene", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "gxa.gene", - "resources": [ + "providerCode": "ncbi", + "resourceHomeUrl": "https://www.ncbi.nlm.nih.gov/sra", + "sampleId": "SRX000007", + "urlPattern": "https://www.ncbi.nlm.nih.gov/sra/{$id}" + }, { "deprecated": false, "deprecationDate": null, - "description": "GXA Gene at EBI", - "id": 1090, + "description": "European Nucleotide Archive (ENA)", + "id": 723, "institution": { "description": "At EMBL-EBI, we make the world’s 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.", "homeUrl": "https://www.ebi.ac.uk", @@ -18704,35 +19004,63 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100482", - "name": "GXA Gene at EBI", + "mirId": "MIR:00100313", + "name": "European Nucleotide Archive (ENA)", "official": false, "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/gxa/", - "sampleId": "AT4G01080", - "urlPattern": "https://www.ebi.ac.uk/gxa/genes/{$id}" + "resourceHomeUrl": "https://www.ebi.ac.uk/ena", + "sampleId": "SRX000007", + "urlPattern": "https://www.ebi.ac.uk/ena/data/view/{$id}" + }, + { + "deprecated": false, + "deprecationDate": null, + "description": "DDBJ Sequence Read Archive (DRA)", + "id": 724, + "institution": { + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 121, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "name": "DNA Data Bank of Japan, Mishima, Shizuoka", + "rorId": null + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "mirId": "MIR:00100314", + "name": "DDBJ Sequence Read Archive (DRA)", + "official": false, + "providerCode": "ddbj", + "resourceHomeUrl": "http://trace.ddbj.nig.ac.jp/dra/", + "sampleId": "SRX000007", + "urlPattern": "http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc={$id}" } ], - "sampleId": "AT4G01080" + "sampleId": "SRX000007" }, { - "created": "2019-06-11T14:17:06.163+0000", + "created": "2019-06-11T14:15:31.920+0000", "deprecated": false, "deprecationDate": null, - "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.", - "id": 1091, - "mirId": "MIR:00000379", - "modified": "2019-06-11T14:17:06.163+0000", - "name": "GXA Expt", + "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.", + "id": 46, + "mirId": "MIR:00000010", + "modified": "2019-06-11T14:15:31.920+0000", + "name": "IntAct", "namespaceEmbeddedInLui": false, - "pattern": "^[AEP]-\\w{4}-\\d+$", - "prefix": "gxa.expt", + "pattern": "^EBI\\-[0-9]+$", + "prefix": "intact", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "GXA Expt at EBI", - "id": 1092, + "description": "IntAct at EBI", + "id": 47, "institution": { "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", "homeUrl": "https://www.ebi.ac.uk", @@ -18748,19 +19076,35 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100483", - "name": "GXA Expt at EBI", + "mirId": "MIR:00100017", + "name": "IntAct at EBI", "official": true, "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/gxa/", - "sampleId": "E-MTAB-2037", - "urlPattern": "https://www.ebi.ac.uk/gxa/experiments/{$id}" - }, + "resourceHomeUrl": "https://www.ebi.ac.uk/intact/", + "sampleId": "EBI-2307691", + "urlPattern": "https://www.ebi.ac.uk/intact/interaction/{$id}" + } + ], + "sampleId": "EBI-2307691" + }, + { + "created": "2019-06-11T14:17:17.850+0000", + "deprecated": false, + "deprecationDate": null, + "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.", + "id": 1227, + "mirId": "MIR:00000427", + "modified": "2019-06-11T14:17:17.850+0000", + "name": "IntAct Molecule", + "namespaceEmbeddedInLui": false, + "pattern": "^EBI\\-[0-9]+$", + "prefix": "intact.molecule", + "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "GXA Expt through OmicsDI", - "id": 1093, + "description": "IntAct Molecule at EBI", + "id": 1228, "institution": { "description": "At EMBL-EBI, we make the world’s 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.", "homeUrl": "https://www.ebi.ac.uk", @@ -18776,35 +19120,35 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100857", - "name": "GXA Expt through OmicsDI", + "mirId": "MIR:00100550", + "name": "IntAct Molecule at EBI", "official": false, - "providerCode": "omicsdi", - "resourceHomeUrl": "https://www.omicsdi.org/", - "sampleId": "E-MTAB-2037", - "urlPattern": "https://www.omicsdi.org/dataset/atlas-experiments/{$id}" + "providerCode": "ebi", + "resourceHomeUrl": "https://www.ebi.ac.uk/intact/", + "sampleId": "EBI-366083", + "urlPattern": "https://www.ebi.ac.uk/intact/molecule/{$id}" } ], - "sampleId": "E-MTAB-2037" + "sampleId": "EBI-366083" }, { - "created": "2019-06-11T14:17:06.457+0000", + "created": "2019-06-11T14:15:32.153+0000", "deprecated": false, "deprecationDate": null, - "description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.", - "id": 1094, - "mirId": "MIR:00000380", - "modified": "2019-06-11T14:17:06.457+0000", - "name": "MetaboLights", + "description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.", + "id": 48, + "mirId": "MIR:00000011", + "modified": "2019-06-11T14:15:32.153+0000", + "name": "InterPro", "namespaceEmbeddedInLui": false, - "pattern": "^MTBLS\\d+$", - "prefix": "metabolights", + "pattern": "^IPR\\d{6}$", + "prefix": "interpro", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "MetaboLights at EBI", - "id": 1095, + "description": "InterPro", + "id": 49, "institution": { "description": "At EMBL-EBI, we make the world’s 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.", "homeUrl": "https://www.ebi.ac.uk", @@ -18820,2347 +19164,2351 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100486", - "name": "MetaboLights at EBI", + "mirId": "MIR:00100018", + "name": "InterPro", "official": true, "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/metabolights/", - "sampleId": "MTBLS1", - "urlPattern": "https://www.ebi.ac.uk/metabolights/{$id}" + "resourceHomeUrl": "https://www.ebi.ac.uk/interpro/", + "sampleId": "IPR000100", + "urlPattern": "https://www.ebi.ac.uk/interpro/entry/{$id}" }, { "deprecated": false, "deprecationDate": null, - "description": "MataboLights through OmicsDI", - "id": 1096, + "description": "Bio2RDF", + "id": 50, "institution": { - "description": "At EMBL-EBI, we make the world’s 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.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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This collection references interactor molecules.", - "id": 1227, - "mirId": "MIR:00000427", - "modified": "2019-06-11T14:17:17.850+0000", - "name": "IntAct Molecule", - "namespaceEmbeddedInLui": false, - "pattern": "^EBI\\-[0-9]+$", - "prefix": "intact.molecule", - "resources": [ + "countryCode": "US", + "countryName": "United States" + }, + "mirId": "MIR:00100631", + "name": "Locus Reference Genomic through Ensembl mirror (US east)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://useast.ensembl.org/", + "sampleId": "LRG_1", + "urlPattern": "http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg={$id}" + }, { "deprecated": false, "deprecationDate": null, - "description": "IntAct Molecule at EBI", - "id": 1228, + "description": "Locus Reference Genomic", + "id": 1080, "institution": { "description": "At EMBL-EBI, we make the world’s 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.", "homeUrl": "https://www.ebi.ac.uk", @@ -21176,1587 +21524,1519 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100550", - "name": "IntAct Molecule at EBI", - "official": false, + "mirId": "MIR:00100478", + "name": "Locus Reference Genomic", + "official": true, "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/intact/", - "sampleId": "EBI-366083", - "urlPattern": "https://www.ebi.ac.uk/intact/molecule/{$id}" + "resourceHomeUrl": "http://www.lrg-sequence.org/", + "sampleId": "LRG_1", + "urlPattern": "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/{$id}.xml" } ], - "sampleId": "EBI-366083" + "sampleId": "LRG_1" }, { - "created": "2019-06-11T14:17:18.034+0000", + "created": "2019-06-11T14:17:21.919+0000", "deprecated": false, "deprecationDate": null, - "description": "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.", - "id": 1229, - "mirId": "MIR:00000428", - "modified": "2019-06-11T14:17:18.034+0000", - "name": "DEPOD", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z0-9]+$", - "prefix": "depod", + "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)", + "id": 1275, + "mirId": "MIR:00000445", + "modified": "2019-06-11T14:17:21.919+0000", + "name": "Mouse Adult Gross Anatomy", + "namespaceEmbeddedInLui": true, + "pattern": "^MA:\\d+$", + "prefix": "ma", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "DEPOD at EMBL", - "id": 1231, + "description": "Mouse Adult Gross Anatomy through BioPortal", + "id": 1276, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1230, + "id": 5, "location": { - "countryCode": "DE", - "countryName": "Germany" + "countryCode": "US", + "countryName": "United States" }, - "name": "European Molecular Biology Laboratory EMBL, Heidelberg", + "name": "National Center for Biomedical Ontology, Stanford", "rorId": null }, "location": { - "countryCode": "DE", - "countryName": "Germany" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100551", - "name": "DEPOD at EMBL", + "mirId": "MIR:00100576", + "name": "Mouse Adult Gross Anatomy through BioPortal", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.depod.bioss.uni-freiburg.de", - "sampleId": "PTPN1", - "urlPattern": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene={$id}" - } - ], - "sampleId": "PTPN1" - }, - { - "created": "2019-06-11T14:17:18.324+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. 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Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.", + "id": 261, + "mirId": "MIR:00000077", + "modified": "2019-06-11T14:15:53.388+0000", + "name": "MACiE", "namespaceEmbeddedInLui": false, - "pattern": "^BG\\d+$", - "prefix": "subtilist", + "pattern": "^M\\d{4}$", + "prefix": "macie", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "SubtiList at Pasteur Institute", - "id": 1246, + "description": "MACiE database of mechanisms, annotation and classification in enzymes", + "id": 262, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1245, + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "homeUrl": "https://www.ebi.ac.uk", + "id": 2, "location": { - "countryCode": "FR", - "countryName": "France" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "name": "Pasteur Institute, Paris", - "rorId": null + "name": "European Bioinformatics Institute", + "rorId": "https://ror.org/02catss52" }, "location": { - "countryCode": "FR", - "countryName": "France" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "mirId": "MIR:00100557", - "name": "SubtiList at Pasteur Institute", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://genolist.pasteur.fr/SubtiList/", - "sampleId": "BG11523", - "urlPattern": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+{$id}" + "mirId": "MIR:00100108", + "name": "MACiE database of mechanisms, annotation and classification in enzymes", + "official": true, + "providerCode": "ebi", + "resourceHomeUrl": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html", + "sampleId": "M0001", + "urlPattern": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id={$id}" } ], - "sampleId": "BG11523" + "sampleId": "M0001" }, { - "created": "2019-06-11T14:17:19.532+0000", + "created": "2019-06-11T14:16:19.610+0000", "deprecated": false, "deprecationDate": null, - "description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.", - "id": 1247, - "mirId": "MIR:00000434", - "modified": "2019-06-11T14:17:19.532+0000", - "name": "DailyMed", + "description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.", + "id": 543, + "mirId": "MIR:00000177", + "modified": "2019-06-11T14:16:19.610+0000", + "name": "MaizeGDB Locus", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9-]+", - "prefix": "dailymed", + "pattern": "^\\d+$", + "prefix": "maizegdb.locus", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "DailyMed at NLM", - "id": 1249, + "description": "MaizeGDB at Missouri", + "id": 545, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1248, + "id": 544, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "U.S. National Library of Medicine, Bethesda, Maryland", + "name": "Division of Plant Sciences, Missouri", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100558", - "name": "DailyMed at NLM", + "mirId": "MIR:00100223", + "name": "MaizeGDB at Missouri", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://dailymed.nlm.nih.gov/dailymed/", - "sampleId": "973a9333-fec7-46dd-8eb5-25738f06ee54", - "urlPattern": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid={$id}" + "resourceHomeUrl": "http://www.maizegdb.org/", + "sampleId": "25011", + "urlPattern": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id={$id}" } ], - "sampleId": "973a9333-fec7-46dd-8eb5-25738f06ee54" + "sampleId": "25011" }, { - "created": "2019-06-11T14:17:19.846+0000", + "created": "2019-06-11T14:17:38.625+0000", "deprecated": false, "deprecationDate": null, - "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. 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This collection references mouse.", - "id": 1326, - "mirId": "MIR:00000463", - "modified": "2019-06-11T14:17:26.285+0000", - "name": "FuncBase Mouse", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "funcbase.mouse", + "created": "2019-06-11T14:15:49.786+0000", + "deprecated": true, + "deprecationDate": "2023-01-10T13:18:19.506+0000", + "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", + "id": 220, + "mirId": "MIR:00000063", + "modified": "2023-01-10T13:18:19.511+0000", + "name": "Aclame", + "namespaceEmbeddedInLui": true, + "pattern": "^mge:\\d+$", + "prefix": "mge", "resources": [ { "deprecated": false, - "deprecationDate": null, - "description": "FuncBase Mouse at Harvard Medical School", - "id": 1327, + "deprecationDate": null, + "description": "Aclame database of mobile genetic elements", + "id": 222, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1322, + "id": 221, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "BE", + "countryName": "Belgium" }, - "name": "Harvard Medical School, Boston, Massachusetts", + "name": "Service de Conformation de Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "BE", + "countryName": "Belgium" }, - "mirId": "MIR:00100598", - "name": "FuncBase Mouse at Harvard Medical School", + "mirId": "MIR:00100091", + "name": "Aclame database of mobile genetic elements", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://func.mshri.on.ca/mouse/", - "sampleId": "1351341", - "urlPattern": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/{$id}" + "resourceHomeUrl": "http://aclame.ulb.ac.be/", + "sampleId": "2", + "urlPattern": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:{$id}" } ], - "sampleId": "1351341" + "sampleId": "2" }, { - "created": "2019-06-11T14:18:18.874+0000", + "created": "2019-06-11T14:15:42.331+0000", "deprecated": false, "deprecationDate": null, - "description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.", - "id": 1881, - "mirId": "MIR:00000679", - "modified": "2019-06-11T14:18:18.874+0000", - "name": "The cBioPortal for Cancer Genomics", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9\\_]+$", - "prefix": "cbioportal", + "description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.", + "id": 146, + "mirId": "MIR:00000037", + "modified": "2019-06-11T14:15:42.331+0000", + "name": "Mouse Genome Database", + "namespaceEmbeddedInLui": true, + "pattern": "^MGI:\\d+$", + "prefix": "mgi", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "The cBioPortal for Cancer Genomics", - "id": 1883, + "description": "Mouse Genome Informatics Database", + "id": 147, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1882, + "id": 91, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Memorial Sloan Kettering Cancer Center", + "name": "The Jackson Laboratory", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100909", - "name": "The cBioPortal for Cancer Genomics", - "official": false, + "mirId": "MIR:00100062", + "name": "Mouse Genome Informatics Database", + "official": true, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.cbioportal.org", - "sampleId": "laml_tcga_pub", - "urlPattern": "http://www.cbioportal.org/study?id={$id}#summary" - } - ], - "sampleId": "laml_tcga_pub" - }, - { - "created": "2019-06-11T14:17:26.470+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.", - "id": 1328, - "mirId": "MIR:00000464", - "modified": "2019-06-11T14:17:26.470+0000", - "name": "FuncBase Yeast", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "funcbase.yeast", - "resources": [ + "resourceHomeUrl": "http://www.informatics.jax.org/", + "sampleId": "2442292", + "urlPattern": "http://www.informatics.jax.org/accession/MGI:{$id}" + }, { "deprecated": false, "deprecationDate": null, - "description": "FuncBase Yeast at Harvard Medical School", - "id": 1329, + "description": "MGD through BioEntity Link", + "id": 148, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1322, + "id": 101, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Harvard Medical School, Boston, Massachusetts", + "name": "InSilico Inc, in Eugene, Oregon", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100599", - "name": "FuncBase Yeast at Harvard Medical School", + "mirId": "MIR:00100894", + "name": "MGD through BioEntity Link", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://func.mshri.on.ca/yeast", - "sampleId": "2701", - "urlPattern": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/{$id}" - } - ], - "sampleId": "2701" - }, - { - "created": "2019-06-11T14:17:26.654+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.", - "id": 1330, - "mirId": "MIR:00000465", - "modified": "2019-06-11T14:17:26.654+0000", - "name": "YDPM", - "namespaceEmbeddedInLui": false, - "pattern": "^Y[A-Z]{2}\\d+[CW]$", - "prefix": "ydpm", - "resources": [ + "providerCode": "bioentitylink", + "resourceHomeUrl": "https://bioentity.link/", + "sampleId": "2442292", + "urlPattern": "https://bioentity.link/#/lexicon/public/MGI:{$id}" + }, { "deprecated": false, "deprecationDate": null, - "description": "YDPM at Stanford University School of Medicine", - "id": 1332, + "description": "MGI through the Alliance of Genome Resources", + "id": 149, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1331, + "description": "The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.", + "homeUrl": "https://www.alliancegenome.org", + "id": 103, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Stanford University School of Medicine, Stanford, California", + "name": "Alliance of Genome Resources", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100600", - "name": "YDPM at Stanford University School of Medicine", + "mirId": "MIR:00100903", + "name": "MGI through the Alliance of Genome Resources", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www-deletion.stanford.edu/YDPM/", - "sampleId": "YAL001C", - "urlPattern": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id}" + "providerCode": "agr", + "resourceHomeUrl": "https://www.alliancegenome.org", + "sampleId": "2442292", + "urlPattern": "https://www.alliancegenome.org/gene/MGI:{$id}" } ], - "sampleId": "YAL001C" + "sampleId": "2442292" }, { - "created": "2019-06-11T14:17:26.886+0000", + "created": "2019-06-11T14:17:42.938+0000", "deprecated": false, "deprecationDate": null, - "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.", - "id": 1333, - "mirId": "MIR:00000466", - "modified": "2019-06-11T14:17:26.886+0000", - "name": "WormBase RNAi", + "description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", + "id": 1502, + "mirId": "MIR:00000535", + "modified": "2019-06-11T14:17:42.938+0000", + "name": "MGnify Project", "namespaceEmbeddedInLui": false, - "pattern": "^WBRNAi\\d{8}$", - "prefix": "wb.rnai", + "pattern": "^[A-Z]+[0-9]+$", + "prefix": "mgnify.proj", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "WormBase RNAi", - "id": 1334, + "description": "MGnify Project", + "id": 1503, "institution": { "description": "At EMBL-EBI, we make the world’s 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.", "homeUrl": "https://www.ebi.ac.uk", @@ -22772,2071 +23052,2063 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100601", - "name": "WormBase RNAi", + "mirId": "MIR:00100711", + "name": "MGnify Project", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://www.wormbase.org/", - "sampleId": "WBRNAi00086878", - "urlPattern": "https://www.wormbase.org/species/c_elegans/rnai/{$id}" + "providerCode": "ebi", + "resourceHomeUrl": "https://www.ebi.ac.uk/metagenomics", + "sampleId": "ERP004492", + "urlPattern": "https://www.ebi.ac.uk/metagenomics/projects/{$id}" } ], - "sampleId": "WBRNAi00086878" + "sampleId": "ERP004492" }, { - "created": "2019-06-11T14:17:27.086+0000", + "created": "2019-06-11T14:17:36.594+0000", "deprecated": false, "deprecationDate": null, - "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", - "id": 1335, - "mirId": "MIR:00000468", - "modified": "2019-06-11T14:17:27.086+0000", - "name": "PASS2", + "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", + "id": 1439, + "mirId": "MIR:00000510", + "modified": "2019-06-11T14:17:36.594+0000", + "name": "MGnify Sample", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pass2", + "pattern": "^[A-Z]+[0-9]+$", + "prefix": "mgnify.samp", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "PASS2 at National centre for Biological Sciences (India)", - "id": 1337, + "description": "MGnify Sample", + "id": 1440, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1336, + "description": "At EMBL-EBI, we make the world’s 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.", + "homeUrl": "https://www.ebi.ac.uk", + "id": 2, "location": { - "countryCode": "IN", - "countryName": "India" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "name": "National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka", - "rorId": null + "name": "European Bioinformatics Institute", + "rorId": "https://ror.org/02catss52" }, "location": { - "countryCode": "IN", - "countryName": "India" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "mirId": "MIR:00100603", - "name": "PASS2 at National centre for Biological Sciences (India)", + "mirId": "MIR:00100656", + "name": "MGnify Sample", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://caps.ncbs.res.in/pass2/", - "sampleId": "46977", - "urlPattern": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id={$id}" + "providerCode": "ebi", + "resourceHomeUrl": "https://www.ebi.ac.uk/metagenomics", + "sampleId": "SRS086444", + "urlPattern": "https://www.ebi.ac.uk/metagenomics/samples/{$id}" } ], - "sampleId": "46977" + "sampleId": "SRS086444" }, { - "created": "2019-06-11T14:17:27.338+0000", + "created": "2019-06-11T14:16:01.860+0000", "deprecated": false, "deprecationDate": null, - "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.", - "id": 1338, - "mirId": "MIR:00000469", - "modified": "2019-06-11T14:17:27.338+0000", - "name": "ICEberg element", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "iceberg.element", + "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", + "id": 350, + "mirId": "MIR:00000109", + "modified": "2020-06-26T10:17:31.752+0000", + "name": "Molecular Interactions Ontology", + "namespaceEmbeddedInLui": true, + "pattern": "^MI:\\d{4}$", + "prefix": "mi", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ICEberg element at Shanghai Jiaotong University", - "id": 1340, + "description": "Molecular Interactions Ontology through OLS", + "id": 351, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1339, + "description": "At EMBL-EBI, we make the world’s 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.", + "homeUrl": "https://www.ebi.ac.uk", + "id": 2, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "name": "State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai", - "rorId": null + "name": "European Bioinformatics Institute", + "rorId": "https://ror.org/02catss52" }, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "mirId": "MIR:00100604", - "name": "ICEberg element at Shanghai Jiaotong University", + "mirId": "MIR:00100142", + "name": "Molecular Interactions Ontology through OLS", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://db-mml.sjtu.edu.cn/ICEberg/", - "sampleId": "100", - "urlPattern": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id={$id}" + "providerCode": "ols", + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/mi", + "sampleId": "0308", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:{$id}" } ], - "sampleId": "100" + "sampleId": "0308" }, { - "created": "2019-06-11T14:17:27.601+0000", + "created": "2019-06-11T14:18:06.853+0000", "deprecated": false, "deprecationDate": null, - "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.", - "id": 1341, - "mirId": "MIR:00000470", - "modified": "2019-06-11T14:17:27.601+0000", - "name": "ICEberg family", + "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", + "id": 1752, + "mirId": "MIR:00000631", + "modified": "2019-06-11T14:18:06.853+0000", + "name": "MicroScope", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", - "prefix": "iceberg.family", + "prefix": "microscope", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ICEberg family at Shanghai Jiaotong University", - "id": 1343, + "description": "MicroScope", + "id": 1754, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1342, + "id": 1753, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "FR", + "countryName": "France" }, - "name": "State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp; Biotechnology, Shanghai Jiaotong University, Shanghai", + "name": "Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Evry", "rorId": null }, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "FR", + "countryName": "France" }, - "mirId": "MIR:00100605", - "name": "ICEberg family at Shanghai Jiaotong University", + "mirId": "MIR:00100836", + "name": "MicroScope", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://db-mml.sjtu.edu.cn/ICEberg/", - "sampleId": "1", - "urlPattern": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id={$id}" + "resourceHomeUrl": "http://www.genoscope.cns.fr/agc/microscope", + "sampleId": "5601141", + "urlPattern": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id={$id}" } ], - "sampleId": "1" + "sampleId": "5601141" }, { - "created": "2019-06-11T14:17:27.811+0000", + "created": "2019-06-11T14:16:13.630+0000", "deprecated": false, "deprecationDate": null, - "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.", - "id": 1344, - "mirId": "MIR:00000471", - "modified": "2019-06-11T14:17:27.811+0000", - "name": "VFDB Genus", + "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "id": 475, + "mirId": "MIR:00000152", + "modified": "2019-06-11T14:16:13.630+0000", + "name": "MicrosporidiaDB", "namespaceEmbeddedInLui": false, "pattern": "^\\w+$", - "prefix": "vfdb.genus", + "prefix": "microsporidia", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "VFDB Genus at Institute of Pathogen Biology", - "id": 1346, + "description": "MicrosporidiaDB at EuPathDB", + "id": 476, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1345, + "id": 467, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "US", + "countryName": "United States" }, - "name": "State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing", + "name": "Center for Tropical & Emerging Global Diseases, University of Georgia", "rorId": null }, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100606", - "name": "VFDB Genus at Institute of Pathogen Biology", + "mirId": "MIR:00100197", + "name": "MicrosporidiaDB at EuPathDB", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.mgc.ac.cn/VFs/", - "sampleId": "Chlamydia", - "urlPattern": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus={$id}" + "resourceHomeUrl": "http://microsporidiadb.org/micro/", + "sampleId": "ECU03_0820i", + "urlPattern": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id}" } ], - "sampleId": "Chlamydia" + "sampleId": "ECU03_0820i" }, { - "created": "2019-06-11T14:17:28.027+0000", + "created": "2019-06-11T14:15:33.878+0000", "deprecated": false, "deprecationDate": null, - "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.", - "id": 1347, - "mirId": "MIR:00000472", - "modified": "2019-06-11T14:17:28.027+0000", - "name": "VFDB Gene", + "description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.", + "id": 65, + "mirId": "MIR:00000016", + "modified": "2019-06-11T14:15:33.878+0000", + "name": "OMIM", "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "vfdb.gene", + "pattern": "^[*#+%^]?\\d{6}$", + "prefix": "mim", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "VFDB Gene at Institute of Pathogen Biology", - "id": 1348, + "description": "OMIM at John Hopkins", + "id": 67, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1345, + "id": 66, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "US", + "countryName": "United States" }, - "name": "State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing", + "name": "Johns Hopkins University, Baltimore, Maryland", "rorId": null }, "location": { - "countryCode": "CN", - "countryName": "China" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100607", - "name": "VFDB Gene at Institute of Pathogen Biology", - "official": false, + "mirId": "MIR:00100024", + "name": "OMIM at John Hopkins", + "official": true, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.mgc.ac.cn/VFs/", - "sampleId": "VFG2154", - "urlPattern": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID={$id}" - } - ], - "sampleId": "VFG2154" - }, - { - "created": "2019-06-11T14:17:28.224+0000", - "deprecated": false, - "deprecationDate": null, - "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. 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This collection references individual protein abundance levels.", - "id": 1387, - "mirId": "MIR:00000489", - "modified": "2019-06-11T14:17:31.566+0000", - "name": "PaxDb Protein", + "description": "MLCommons Association artifacts, including benchmark results, datasets, and saved models.", + "id": 2709, + "mirId": "MIR:00000828", + "modified": "2021-06-24T16:02:06.844+0000", + "name": "MLCommons Association", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "paxdb.protein", + "pattern": "^[0-9a-zA-Z\\.\\-\\_]+$", + "prefix": "mlc", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "PaxDb v3 at University of Zurich", - "id": 1388, + "description": "The MLCommons Association is a non-profit founded to \"make ML better for everyone\" through benchmarks, public datasets, and best practices. The MLCommons board has representatives from Alibaba, Google, GraphCore, Facebook, Intel, Qualcomm, Myrtle.ai, NVIDIA, and a Harvard faculty member, and the organization has over 50 members consisting of companies and academics.", + "id": 2710, "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1385, + "description": "The MLCommons Association is a non-profit founded to \"make ML better for everyone\" through benchmarks, public datasets, and best practices. 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The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.", + "id": 392, + "mirId": "MIR:00000124", + "modified": "2019-06-11T14:16:05.849+0000", + "name": "Microbial Protein Interaction Database", "namespaceEmbeddedInLui": false, "pattern": "^\\d+$", - "prefix": "chickenqtldb", + "prefix": "mpid", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Animal QTL Chicken at Iowa State University", - "id": 1432, + "description": "Microbial Protein Interaction Database", + "id": 394, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1429, + "id": 393, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa", + "name": "J. Craig Venter Institute, Maryland", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100646", - "name": "Animal QTL Chicken at Iowa State University", + "mirId": "MIR:00100157", + "name": "Microbial Protein Interaction Database", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://www.animalgenome.org/QTLdb", - "sampleId": "14362", - "urlPattern": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id}" + "resourceHomeUrl": "http://www.jcvi.org/mpidb/about.php", + "sampleId": "172", + "urlPattern": "http://www.jcvi.org/mpidb/experiment.php?interaction_id={$id}" + }, + { + "deprecated": false, + "deprecationDate": null, + "description": "Microbial Protein Interaction Database subset through IntAct", + "id": 395, + "institution": { + "description": "At EMBL-EBI, we make the world’s 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.", + "homeUrl": "https://www.ebi.ac.uk", + "id": 2, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "name": "European Bioinformatics Institute", + "rorId": "https://ror.org/02catss52" + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "mirId": "MIR:00100655", + "name": "Microbial Protein Interaction Database subset through IntAct", + "official": false, + "providerCode": "ebi", + "resourceHomeUrl": "https://www.ebi.ac.uk/intact/", + "sampleId": "1776", + "urlPattern": "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-{$id}" } ], - "sampleId": "14362" + "sampleId": "172" }, { - "created": "2019-06-11T14:17:35.969+0000", + "created": "2019-06-11T14:17:56.919+0000", "deprecated": false, "deprecationDate": null, - "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.", - "id": 1433, - "mirId": "MIR:00000506", - "modified": "2019-06-11T14:17:35.969+0000", - "name": "Animal Genome Pig QTL", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pigqtldb", + "description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.", + "id": 1641, + "mirId": "MIR:00000590", + "modified": "2019-06-11T14:17:56.919+0000", + "name": "Mass Spectrometry Controlled Vocabulary", + "namespaceEmbeddedInLui": true, + "pattern": "^MS:\\d{7}$", + "prefix": "ms", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Animal QTL Pig at Iowa State University", - "id": 1434, + "description": "Mass Spectrometry Controlled Vocabulary through OLS", + "id": 1642, + "institution": { + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "homeUrl": "https://www.ebi.ac.uk", + "id": 2, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "name": "European Bioinformatics Institute", + "rorId": "https://ror.org/02catss52" + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "mirId": "MIR:00100786", + "name": "Mass Spectrometry Controlled Vocabulary through OLS", + "official": false, + "providerCode": "ols", + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/ms", + "sampleId": "1000001", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:{$id}" + }, + { + "deprecated": false, + "deprecationDate": null, + "description": "Mass Spectrometry Controlled Vocabulary through BioPortal", + "id": 1643, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1429, + "id": 5, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa", + "name": "National Center for Biomedical Ontology, Stanford", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100647", - "name": "Animal QTL Pig at Iowa State University", + "mirId": "MIR:00100787", + "name": "Mass Spectrometry Controlled Vocabulary through BioPortal", "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://www.animalgenome.org/QTLdb", - "sampleId": "14", - "urlPattern": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id}" + "providerCode": "bptl", + "resourceHomeUrl": "https://bioportal.bioontology.org/ontologies/MS", + "sampleId": "1000001", + "urlPattern": "http://purl.bioontology.org/ontology/MS/MS:{$id}" } ], - "sampleId": "14" + "sampleId": "1000001" }, { - "created": "2019-06-11T14:17:36.183+0000", + "created": "2019-06-11T14:17:55.320+0000", "deprecated": false, "deprecationDate": null, - "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.", - "id": 1435, - "mirId": "MIR:00000507", - "modified": "2019-06-11T14:17:36.183+0000", - "name": "Animal Genome Sheep QTL", + "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", + "id": 1626, + "mirId": "MIR:00000584", + "modified": "2019-06-11T14:17:55.320+0000", + "name": "MultiCellDS Digital Cell Line", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sheepqtldb", + "pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$", + "prefix": "multicellds.cell_line", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Animal QTL Sheep at Iowa State University", - "id": 1436, + "description": "MultiCellDS Digital Cell Line at Keck School of Medicine", + "id": 1627, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1429, + "id": 1622, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa", + "name": "Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100648", - "name": "Animal QTL Sheep at Iowa State University", + "mirId": "MIR:00100781", + "name": "MultiCellDS Digital Cell Line at Keck School of Medicine", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://www.animalgenome.org/QTLdb", - "sampleId": "19803", - "urlPattern": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id}" + "resourceHomeUrl": "http://multicellds.org/MultiCellDB.php", + "sampleId": "MCDS_L_0000000001", + "urlPattern": "http://multicellds.org/MultiCellDB/{$id}" } ], - "sampleId": "19803" + "sampleId": "MCDS_L_0000000001" }, { - "created": "2019-06-11T14:17:36.384+0000", + "created": "2019-06-11T14:17:54.753+0000", "deprecated": false, "deprecationDate": null, - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", - "id": 1437, - "mirId": "MIR:00000508", - "modified": "2019-06-11T14:17:36.384+0000", - "name": "Gramene Growth Stage Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^GRO\\:\\d+$", - "prefix": "gramene.growthstage", + "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).", + "id": 1621, + "mirId": "MIR:00000582", + "modified": "2019-06-11T14:17:54.753+0000", + "name": "MultiCellDS collection", + "namespaceEmbeddedInLui": false, + "pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$", + "prefix": "multicellds.collection", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Gramene Growth Stage Ontology at Cold Spring Harbor", - "id": 1438, + "description": "MultiCellDScollection at Keck School of Medicine", + "id": 1623, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 556, + "id": 1622, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Cold Spring Harbor Laboratory, New York", + "name": "Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00100649", - "name": "Gramene Growth Stage Ontology at Cold Spring Harbor", + "mirId": "MIR:00100779", + "name": "MultiCellDScollection at Keck School of Medicine", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.gramene.org/", - "sampleId": "0007133", - "urlPattern": "http://www.gramene.org/db/ontology/search?id=GRO:{$id}" + "resourceHomeUrl": "http://multicellds.org/MultiCellDB.php", + "sampleId": "MCDS_C_0000000001", + "urlPattern": "http://multicellds.org/MultiCellDB/{$id}" } ], - "sampleId": "0007133" + "sampleId": "MCDS_C_0000000001" }, { - "created": "2019-06-11T14:17:36.594+0000", + "created": "2019-06-11T14:17:55.012+0000", "deprecated": false, "deprecationDate": null, - "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", - "id": 1439, - "mirId": "MIR:00000510", - "modified": "2019-06-11T14:17:36.594+0000", - "name": "MGnify Sample", + "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.", + "id": 1624, + "mirId": "MIR:00000583", + "modified": "2019-06-11T14:17:55.012+0000", + "name": "MultiCellDS Digital snapshot", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z]+[0-9]+$", - "prefix": "mgnify.samp", + "pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$", + "prefix": "multicellds.snapshot", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "MGnify Sample", - "id": 1440, + "description": "MultiCellDS snapshot at Keck School of Medicine", + "id": 1625, "institution": { - "description": "At EMBL-EBI, we make the world’s 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.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 1622, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "US", + "countryName": "United States" }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" + "name": "Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California", + "rorId": null }, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100656", - "name": "MGnify Sample", + "mirId": "MIR:00100780", + "name": "MultiCellDS snapshot at Keck School of Medicine", "official": false, - "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/metagenomics", - "sampleId": "SRS086444", - "urlPattern": "https://www.ebi.ac.uk/metagenomics/samples/{$id}" + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://multicellds.org/MultiCellDB.php", + "sampleId": "MCDS_S_0000000001", + "urlPattern": "http://multicellds.org/MultiCellDB/{$id}" } ], - "sampleId": "SRS086444" + "sampleId": "MCDS_S_0000000001" }, { - "created": "2019-06-11T14:17:36.823+0000", + "created": "2019-06-11T14:18:10.677+0000", "deprecated": false, "deprecationDate": null, - "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", - "id": 1441, - "mirId": "MIR:00000511", - "modified": "2019-06-11T14:17:36.823+0000", - "name": "European Genome-phenome Archive Study", + "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", + "id": 1796, + "mirId": "MIR:00000647", + "modified": "2019-06-11T14:18:10.677+0000", + "name": "Metabolomics Workbench Project", "namespaceEmbeddedInLui": false, - "pattern": "^EGAS\\d{11}$", - "prefix": "ega.study", + "pattern": "^PR[0-9]{6}$", + "prefix": "mw.project", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "EGA Study at European Bioinformatics Institute", - "id": 1442, + "description": "Metabolomics Workbench Project", + "id": 1797, "institution": { - "description": "At EMBL-EBI, we make the world’s 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.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, + "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", + "homeUrl": "https://ucsd.edu/", + "id": 190, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "US", + "countryName": "United States" }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" + "name": "University of California, San Diego", + "rorId": "https://ror.org/0168r3w48" }, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100657", - "name": "EGA Study at European Bioinformatics Institute", + "mirId": "MIR:00100861", + "name": "Metabolomics Workbench Project", "official": true, - "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/ega/studies", - "sampleId": "EGAS00000000001", - "urlPattern": "https://www.ebi.ac.uk/ega/studies/{$id}" - }, - { - "deprecated": false, - "deprecationDate": null, - "description": "EGA Study through OmicsDI", - "id": 1443, - "institution": { - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100851", - "name": "EGA Study through OmicsDI", - "official": false, - "providerCode": "omicsdi", - "resourceHomeUrl": "https://www.omicsdi.org/", - "sampleId": "EGAS00000000001", - "urlPattern": "https://www.omicsdi.org/dataset/ega/{$id}" + "providerCode": "ucsd", + "resourceHomeUrl": "http://www.metabolomicsworkbench.org/", + "sampleId": "PR000001", + "urlPattern": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID={$id}" } ], - "sampleId": "EGAS00000000001" + "sampleId": "PR000001" }, { - "created": "2019-06-11T14:17:37.233+0000", + "created": "2019-06-11T14:18:10.316+0000", "deprecated": false, "deprecationDate": null, - "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", - "id": 1444, - "mirId": "MIR:00000512", - "modified": "2019-06-11T14:17:37.233+0000", - "name": "European Genome-phenome Archive Dataset", + "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", + "id": 1792, + "mirId": "MIR:00000646", + "modified": "2019-06-11T14:18:10.316+0000", + "name": "Metabolomics Workbench Study", "namespaceEmbeddedInLui": false, - "pattern": "^EGAD\\d{11}$", - "prefix": "ega.dataset", + "pattern": "^ST[0-9]{6}$", + "prefix": "mw.study", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "EGA Dataset at European Bioinformatics Institute", - "id": 1445, + "description": "Metabolomics Workbench Study through OmicsDI", + "id": 1795, "institution": { "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", "homeUrl": "https://www.ebi.ac.uk", @@ -24852,835 +25124,807 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00100658", - "name": "EGA Dataset at European Bioinformatics Institute", - "official": true, - "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/ega/dataset", - "sampleId": "EGAD00000000001", - "urlPattern": "https://www.ebi.ac.uk/ega/datasets/{$id}" + "mirId": "MIR:00100860", + "name": "Metabolomics Workbench Study through OmicsDI", + "official": false, + "providerCode": "omicsdi", + "resourceHomeUrl": "https://www.omicsdi.org/", + "sampleId": "ST000900", + "urlPattern": "https://www.omicsdi.org/dataset/metabolomics_workbench/{$id}" }, { "deprecated": false, "deprecationDate": null, - "description": "EGA Dataset through OmicsDI", - "id": 1446, + "description": "Metabolomics Workbench Study", + "id": 1794, "institution": { - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, + "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", + "homeUrl": "https://ucsd.edu/", + "id": 190, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "US", + "countryName": "United States" }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" + "name": "University of California, San Diego", + "rorId": "https://ror.org/0168r3w48" }, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100852", - "name": "EGA Dataset through OmicsDI", - "official": false, - "providerCode": "omicsdi", - "resourceHomeUrl": "https://www.omicsdi.org/", - "sampleId": "EGAD00000000001", - "urlPattern": "https://www.omicsdi.org/dataset/ega/{$id}" + "mirId": "MIR:00100859", + "name": "Metabolomics Workbench Study", + "official": true, + "providerCode": "ucsd", + "resourceHomeUrl": "http://www.metabolomicsworkbench.org/", + "sampleId": "ST000900", + "urlPattern": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID={$id}" } ], - "sampleId": "EGAD00000000001" + "sampleId": "ST000900" }, { - "created": "2019-06-11T14:17:38.030+0000", + "created": "2019-06-11T14:16:28.887+0000", "deprecated": false, "deprecationDate": null, - "description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. 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This collection references Mycobacteria leprae information.", + "id": 647, + "mirId": "MIR:00000217", + "modified": "2019-06-11T14:16:28.887+0000", + "name": "MycoBrowser leprae", "namespaceEmbeddedInLui": false, - "pattern": "^P(X|R)D\\d{6}$", - "prefix": "pride.project", + "pattern": "^ML\\w+$", + "prefix": "myco.lepra", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "PRIDE Project at EBI", - "id": 1454, - "institution": { - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100662", - "name": "PRIDE Project at EBI", - "official": true, - "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/pride/", - "sampleId": "PXD000440", - "urlPattern": "https://www.ebi.ac.uk/pride/archive/projects/{$id}" - }, - { - "deprecated": false, - "deprecationDate": null, - "description": "PRIDE Project through OmicsDI", - "id": 1455, + "description": "MycoBrowser leprae at Global Health Institute", + "id": 648, "institution": { - "description": "At EMBL-EBI, we make the world’s 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.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 645, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "CH", + "countryName": "Switzerland" }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" + "name": "Global Health Institute, Lausanne", + "rorId": null }, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "CH", + "countryName": "Switzerland" }, - "mirId": "MIR:00100858", - "name": "PRIDE Project through OmicsDI", + "mirId": "MIR:00100276", + "name": "MycoBrowser leprae at Global Health Institute", "official": false, - "providerCode": "omicsdi", - "resourceHomeUrl": "https://www.omicsdi.org/", - "sampleId": "PXD000440", - "urlPattern": "https://www.omicsdi.org/dataset/pride/{$id}" + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://mycobrowser.epfl.ch/leprosy.html", + "sampleId": "ML0224", + "urlPattern": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name={$id}" } ], - "sampleId": "PXD000440" + "sampleId": "ML0224" }, { - "created": "2019-06-11T14:17:38.379+0000", + "created": "2019-06-11T14:16:29.087+0000", "deprecated": false, "deprecationDate": null, - "description": "The Antibody Registry provides identifiers for antibodies used in publications. 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This collection references Mycobacteria marinum information.", + "id": 649, + "mirId": "MIR:00000218", + "modified": "2019-06-11T14:16:29.087+0000", + "name": "MycoBrowser marinum", "namespaceEmbeddedInLui": false, - "pattern": "^\\d{6}$", - "prefix": "antibodyregistry", + "pattern": "^MMAR\\_\\d+$", + "prefix": "myco.marinum", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Antibody Registry at University of California", - "id": 1458, + "description": "MycoBrowser marinum at Global Health Institute", + "id": 650, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1457, + "id": 645, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CH", + "countryName": "Switzerland" }, - "name": "Neuroscience Information Framework, University of California, San Diego, California", + "name": "Global Health Institute, Lausanne", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CH", + "countryName": "Switzerland" }, - "mirId": "MIR:00100664", - "name": "Antibody Registry at University of California", + "mirId": "MIR:00100277", + "name": "MycoBrowser marinum at Global Health Institute", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://antibodyregistry.org/", - "sampleId": "493771", - "urlPattern": "http://antibodyregistry.org/AB_{$id}" + "resourceHomeUrl": "http://mycobrowser.epfl.ch/marinolist.html", + "sampleId": "MMAR_2462", + "urlPattern": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name={$id}" } ], - "sampleId": "493771" + "sampleId": "MMAR_2462" }, { - "created": "2019-06-11T14:17:38.625+0000", + "created": "2019-06-11T14:16:29.310+0000", "deprecated": false, "deprecationDate": null, - "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", - "id": 1459, - "mirId": "MIR:00000517", - "modified": "2019-06-11T14:17:38.625+0000", - "name": "Mathematical Modelling Ontology", + "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", + "id": 651, + "mirId": "MIR:00000219", + "modified": "2019-06-11T14:16:29.310+0000", + "name": "MycoBrowser smegmatis", "namespaceEmbeddedInLui": false, - "pattern": "^MAMO_\\d{7}$", - "prefix": "mamo", + "pattern": "^MSMEG\\w+$", + "prefix": "myco.smeg", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "MAMO through BioPortal", - "id": 1460, + "description": "MycoBrowser smegmatis at Global Health Institute", + "id": 652, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 5, + "id": 645, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CH", + "countryName": "Switzerland" }, - "name": "National Center for Biomedical Ontology, Stanford", + "name": "Global Health Institute, Lausanne", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CH", + "countryName": "Switzerland" }, - "mirId": "MIR:00100665", - "name": "MAMO through BioPortal", + "mirId": "MIR:00100278", + "name": "MycoBrowser smegmatis at Global Health Institute", "official": false, - "providerCode": "bptl", - "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/MAMO", - "sampleId": "MAMO_0000026", - "urlPattern": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/{$id}" - }, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://mycobrowser.epfl.ch/smegmalist.html", + "sampleId": "MSMEG_3769", + "urlPattern": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name={$id}" + } + ], + "sampleId": "MSMEG_3769" + }, + { + "created": "2019-06-11T14:16:28.639+0000", + "deprecated": false, + "deprecationDate": null, + "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. 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"id": 556, + "id": 547, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "NL", + "countryName": "Netherlands" }, - "name": "Cold Spring Harbor Laboratory, New York", + "name": "CBS-KNAW Fungal Biodiversity Centre, Utrecht", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "NL", + "countryName": "Netherlands" }, - "mirId": "MIR:00100667", - "name": "Plant Environment Ontology through Gramene", + "mirId": "MIR:00100224", + "name": "MycoBank at Fungal Biodiversity Centre", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://archive.gramene.org/db/ontology/search_term?id=EO:0007359", - "sampleId": "0007404", - "urlPattern": "http://archive.gramene.org/db/ontology/search?query=EO:{$id}" - }, + "resourceHomeUrl": "http://www.mycobank.org/", + "sampleId": "349124", + "urlPattern": "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_={$id}" + } + ], + "sampleId": "349124" + }, + { + "created": "2019-06-11T14:18:05.468+0000", + "deprecated": false, + "deprecationDate": null, + "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.", + "id": 1735, + "mirId": "MIR:00000625", + "modified": "2019-06-11T14:18:05.468+0000", + "name": "Universal Spectrum Identifier", + "namespaceEmbeddedInLui": true, + "pattern": "^mzspec:.+$", + "prefix": "mzspec", + "resources": [ { "deprecated": false, "deprecationDate": null, - 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This collection references phosphoprotein information.", + "id": 1118, + "mirId": "MIR:00000386", + "modified": "2019-06-11T14:17:08.458+0000", + "name": "PhosphoPoint Phosphoprotein", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9]+$", - "prefix": "gnpis", + "pattern": "^\\w+$", + "prefix": "phosphopoint.protein", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "GnpIS", - "id": 1743, + "description": "PhosphoPoint Phosphoprotein at National Taiwan University", + "id": 1119, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1742, + "id": 1116, "location": { - "countryCode": "FR", - "countryName": "France" + "countryCode": "CN", + "countryName": "China" }, - "name": "URGI (Research Unit in Genomics-Info), INRA de Versailles, Route de Saint-Cyr, Versailles", + "name": "Department of Computer Science and Information Engineering, National Taiwan University", "rorId": null }, "location": { - "countryCode": "FR", - "countryName": "France" + "countryCode": "CN", + "countryName": "China" }, - "mirId": "MIR:00100831", - "name": "GnpIS", + "mirId": "MIR:00100500", + "name": "PhosphoPoint Phosphoprotein at National Taiwan University", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://urgi.versailles.inra.fr/gnpis/", - "sampleId": "AY109603", - "urlPattern": "https://urgi.versailles.inra.fr/gnpis/#result/term={$id}" + "resourceHomeUrl": "http://kinase.bioinformatics.tw/", + "sampleId": "AURKA", + "urlPattern": "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name={$id}&drawing=0&sorting=0&kinome=0" } ], - "sampleId": "AY109603" + "sampleId": "AURKA" }, { - "created": "2019-06-11T14:18:06.185+0000", + "created": "2019-06-11T14:16:00.712+0000", "deprecated": false, "deprecationDate": null, - "description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.", - "id": 1744, - "mirId": "MIR:00000628", - "modified": "2019-06-11T14:18:06.185+0000", - "name": "LiceBase", + "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.", + "id": 338, + "mirId": "MIR:00000105", + "modified": "2019-06-11T14:16:00.712+0000", + "name": "PhosphoSite Protein", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9\\-\\/]+$", - "prefix": "licebase", + "pattern": "^\\d{5}$", + "prefix": "phosphosite.protein", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "LiceBase", - "id": 1746, + "description": "PhosphoSite", + "id": 340, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1745, + "id": 339, "location": { - "countryCode": "NO", - "countryName": "Norway" + "countryCode": "US", + "countryName": "United States" }, - "name": "Sea Lice Research Centre (SLRC), University of Bergen", + "name": "Cell Signaling Technology, Inc.", "rorId": null }, "location": { - "countryCode": "NO", - "countryName": "Norway" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100832", - "name": "LiceBase", + "mirId": "MIR:00100138", + "name": "PhosphoSite", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://licebase.org", - "sampleId": "EMLSAT00000003403", - "urlPattern": "https://licebase.org/?q={$id}" + "resourceHomeUrl": "http://www.phosphosite.org/homeAction.do", + "sampleId": "12300", + "urlPattern": "http://www.phosphosite.org/proteinAction.do?id={$id}" } ], - "sampleId": "EMLSAT00000003403" + "sampleId": "12300" }, { - "created": "2019-06-11T14:18:06.412+0000", + "created": "2019-06-11T14:16:06.208+0000", "deprecated": false, "deprecationDate": null, - "description": "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands.", - "id": 1747, - "mirId": "MIR:00000629", - "modified": "2019-06-11T14:18:06.412+0000", - "name": "SugarBind", + "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.", + "id": 396, + "mirId": "MIR:00000125", + "modified": "2019-06-11T14:16:06.208+0000", + "name": "PhosphoSite Residue", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z]+\\/[0-9]+$", - "prefix": "sugarbind", + "pattern": "^\\d+$", + "prefix": "phosphosite.residue", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "SugarBind", - "id": 1749, + "description": "PhosphoSite Residue", + "id": 397, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1748, + "id": 339, "location": { - "countryCode": "CH", - "countryName": "Switzerland" + "countryCode": "US", + "countryName": "United States" }, - "name": "Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva", + "name": "Cell Signaling Technology, Inc.", "rorId": null }, "location": { - "countryCode": "CH", - "countryName": "Switzerland" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100833", - "name": "SugarBind", + "mirId": "MIR:00100159", + "name": "PhosphoSite Residue", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://sugarbind.expasy.org/", - "sampleId": "lectins/172", - "urlPattern": "http://sugarbind.expasy.org/{$id}" + "resourceHomeUrl": "http://www.phosphosite.org/homeAction.do", + "sampleId": "2842", + "urlPattern": "http://www.phosphosite.org/siteAction.do?id={$id}" } ], - "sampleId": "lectins/172" + "sampleId": "2842" }, { - "created": "2019-06-11T14:18:06.653+0000", + "created": "2019-06-11T14:16:30.326+0000", "deprecated": false, "deprecationDate": null, - "description": "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.", - "id": 1750, - "mirId": "MIR:00000630", - "modified": "2019-06-11T14:18:06.653+0000", - "name": "RNAcentral", + "description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.", + "id": 663, + "mirId": "MIR:00000223", + "modified": "2019-06-11T14:16:30.326+0000", + "name": "PhylomeDB", "namespaceEmbeddedInLui": false, - "pattern": "^URS[0-9A-F]{10}(\\_\\d+)?$", - "prefix": "rnacentral", + "pattern": "^\\w+$", + "prefix": "phylomedb", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "RNAcentral through EMBL-EBI", - "id": 1751, + "description": "PhylomeDB at Centro de Investigación Príncipe Felipe", + "id": 665, "institution": { - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, + "description": "The Centre for Genomic Regulation (CRG) is an international biomedical research institute of excellence, created in December 2000. It is a non-profit foundation funded by the Catalan Government through the Departments of Business & Knowledge, the Spanish Ministry of Science, Innovation & Universities, the \"la Caixa\" Banking Foundation, and includes the participation of Pompeu Fabra University.", + "homeUrl": "https://www.crg.eu", + "id": 664, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "ES", + "countryName": "Spain" }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" + "name": "Centre for Genomic Regulation", + "rorId": "https://ror.org/03wyzt892" }, "location": { - "countryCode": "GB", - "countryName": "United Kingdom" + "countryCode": "ES", + "countryName": "Spain" }, - "mirId": "MIR:00100834", - "name": "RNAcentral through EMBL-EBI", + "mirId": "MIR:00100282", + "name": "PhylomeDB at Centro de Investigación Príncipe Felipe", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://rnacentral.org/", - "sampleId": "URS0000759CF4", - "urlPattern": "https://rnacentral.org/rna/{$id}" + "resourceHomeUrl": "http://phylomedb.org/", + "sampleId": "Phy000CLXM_RAT", + "urlPattern": "http://phylomedb.org/?seqid={$id}" } ], - "sampleId": "URS0000759CF4" + "sampleId": "Phy000CLXM_RAT" }, { - "created": "2019-06-11T14:18:06.853+0000", + "created": "2019-06-11T14:17:19.049+0000", "deprecated": false, "deprecationDate": null, - "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", - "id": 1752, - "mirId": "MIR:00000631", - "modified": "2019-06-11T14:18:06.853+0000", - "name": "MicroScope", + "description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.", + "id": 1241, + "mirId": "MIR:00000432", + "modified": "2019-06-11T14:17:19.049+0000", + "name": "Phytozome Locus", "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "microscope", + "pattern": "^[A-Za-z0-9]+$", + "prefix": "phytozome.locus", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "MicroScope", - "id": 1754, + "description": "Phytozome Locus at Joint Genome Institute", + "id": 1243, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1753, + "id": 1242, "location": { - "countryCode": "FR", - "countryName": "France" + "countryCode": "US", + "countryName": "United States" }, - "name": "Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Evry", + "name": "Joint Genome Institute, California, and the Center for Integrative Genomics, Lausanne", "rorId": null }, "location": { - "countryCode": "FR", - "countryName": "France" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100836", - "name": "MicroScope", + "mirId": "MIR:00100556", + "name": "Phytozome Locus at Joint Genome Institute", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.genoscope.cns.fr/agc/microscope", - "sampleId": "5601141", - "urlPattern": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id={$id}" + "resourceHomeUrl": "http://www.phytozome.net/", + "sampleId": "Glyma0021s00410", + "urlPattern": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:{$id}" } ], - "sampleId": "5601141" + "sampleId": "Glyma0021s00410" }, { - "created": "2019-06-11T14:18:07.113+0000", + "created": "2019-06-11T14:16:08.872+0000", "deprecated": false, "deprecationDate": null, - "description": "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form.", - "id": 1755, - "mirId": "MIR:00000632", - "modified": "2019-06-11T14:18:07.113+0000", - "name": "SwissRegulon", + "description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.", + "id": 424, + "mirId": "MIR:00000133", + "modified": "2019-06-11T14:16:08.872+0000", + "name": "NCI Pathway Interaction Database: Pathway", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9]+$", - "prefix": "swissregulon", + "pattern": "^\\w+$", + "prefix": "pid.pathway", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "SwissRegulon", - "id": 1756, + "description": "NCI Pathway Interaction Database (Pathway)", + "id": 426, "institution": { - "description": "SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide.", - "homeUrl": "https://www.sib.swiss", - "id": 1730, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 425, "location": { - "countryCode": "CH", - "countryName": "Switzerland" + "countryCode": "US", + "countryName": "United States" }, - "name": "SIB Swiss Institute of Bioinformatics", - "rorId": "https://ror.org/002n09z45" + "name": "National Cancer Institute, Rockville, Maryland", + "rorId": null }, "location": { - "countryCode": "CH", - "countryName": "Switzerland" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100837", - "name": "SwissRegulon", + "mirId": "MIR:00100173", + "name": "NCI Pathway Interaction Database (Pathway)", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://swissregulon.unibas.ch", - "sampleId": "AHR", - "urlPattern": "http://swissregulon.unibas.ch/query/{$id}" + "resourceHomeUrl": "http://pid.nci.nih.gov/", + "sampleId": "pi3kcipathway", + "urlPattern": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id={$id}" } ], - "sampleId": "AHR" + "sampleId": "pi3kcipathway" }, { - "created": "2019-06-11T14:18:07.321+0000", + "created": "2019-06-11T14:17:35.969+0000", "deprecated": false, "deprecationDate": null, - "description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.", - "id": 1757, - "mirId": "MIR:00000633", - "modified": "2019-06-11T14:18:07.321+0000", - "name": "ValidatorDB", + "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.", + "id": 1433, + "mirId": "MIR:00000506", + "modified": "2019-06-11T14:17:35.969+0000", + "name": "Animal Genome Pig QTL", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9\\/]+$", - "prefix": "validatordb", + "pattern": "^\\d+$", + "prefix": "pigqtldb", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ValidatorDB", - "id": 1759, + "description": "Animal QTL Pig at Iowa State University", + "id": 1434, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1758, + "id": 1429, "location": { - "countryCode": "CZ", - "countryName": "Czech Republic" + "countryCode": "US", + "countryName": "United States" }, - "name": "Central European Institute of Technology", + "name": "Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa", "rorId": null }, "location": { - "countryCode": "CZ", - "countryName": "Czech Republic" + "countryCode": "US", + "countryName": "United States" }, - "mirId": "MIR:00100838", - "name": "ValidatorDB", + "mirId": "MIR:00100647", + "name": "Animal QTL Pig at Iowa State University", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/", - "sampleId": "ByStructure/2h6o", - "urlPattern": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/{$id}" + "resourceHomeUrl": "https://www.animalgenome.org/QTLdb", + "sampleId": "14", + "urlPattern": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id}" } ], - "sampleId": "ByStructure/2h6o" + "sampleId": "14" }, { - "created": "2019-06-11T14:18:07.548+0000", + "created": "2019-06-11T14:17:01.276+0000", "deprecated": false, "deprecationDate": null, - "description": "Database of the dielectric properties of biological tissues.", - "id": 1760, - "mirId": "MIR:00000634", - "modified": "2019-06-11T14:18:07.548+0000", - "name": "Bio-MINDER Tissue Database", + "description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.", + "id": 1030, + "mirId": "MIR:00000359", + "modified": "2019-06-11T14:17:01.276+0000", + "name": "PINA", "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9\\-]+$", - "prefix": "biominder", + "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", + "prefix": "pina", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Bio-MINDER Tissue Database", - "id": 1762, + "description": "Protein Interaction Network Analysis (PINA) at Garvan Institute", + "id": 1032, "institution": { "description": "CURATOR_REVIEW", "homeUrl": "CURATOR_REVIEW", - "id": 1761, + "id": 1031, "location": { - "countryCode": "IE", - "countryName": "Ireland" + "countryCode": "AU", + "countryName": "Australia" }, - "name": "RWTH Aachen University / NUIG Galway", + "name": "Garvan Institute of Medical Research, Sydney", "rorId": null }, "location": { - "countryCode": "IE", - "countryName": "Ireland" + "countryCode": "AU", + "countryName": "Australia" }, - "mirId": "MIR:00100839", - "name": "Bio-MINDER Tissue Database", + "mirId": "MIR:00100456", + "name": "Protein Interaction Network Analysis (PINA) at Garvan Institute", "official": false, "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://datalab.rwth-aachen.de/MINDER", - "sampleId": "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3", - "urlPattern": "https://datalab.rwth-aachen.de/MINDER/resource/{$id}" + "resourceHomeUrl": "http://cbg.garvan.unsw.edu.au/pina/", + "sampleId": "Q13485", + "urlPattern": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac={$id}&showExtend=null" } ], - "sampleId": "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3" + "sampleId": "Q13485" }, { - "created": "2019-06-11T14:18:07.777+0000", + "created": "2019-06-11T14:16:59.494+0000", "deprecated": false, "deprecationDate": null, - "description": "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images.", - "id": 1763, - "mirId": "MIR:00000635", - "modified": "2019-06-11T14:18:07.777+0000", - "name": "NeuroVault Collection", + "description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. 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SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.", + "id": 1593, + "mirId": "MIR:00000572", + "modified": "2019-06-11T14:17:51.650+0000", + "name": "SASBDB", "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9]+$", - "prefix": "minid", + "pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$", + "prefix": "sasbdb", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "FAIR Research is a collaboration of the Informatics Systems Research Division at the Information Sciences Institute of University of Southern California and the Computational Systems Division at the University of Chicago.", - "id": 1791, + "description": "SASBDB at European Molecular Biology Laboratory", + "id": 1595, "institution": { - "description": "The University of Southern California is a leading private research university located in Los Angeles — a global center for arts, technology and international business. 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The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. 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Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.", + "id": 1146, + "mirId": "MIR:00000395", + "modified": "2019-06-11T14:17:10.973+0000", + "name": "TreeFam", "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "civic.eid", + "pattern": "^\\w{1,2}\\d+$", + "prefix": "treefam", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", - "id": 2785, + "description": "TreeFam database", + "id": 1148, "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", - "homeUrl": "https://wustl.edu/", - "id": 2750, + "description": "BGI Genomics is a publicly listed commercial genomics company, providing a wide range of next generation sequencing services and a broad portfolio of genetic tests for medical institutions, research institutions and other public and private partners.\nEstablished in 1999, we have almost 20 years of genomics experience. Our mission is to leverage our genomics expertise in order to advance life science research and improve human health for the benefit of mankind.", + "homeUrl": "https://www.bgi.com", + "id": 1147, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CN", + "countryName": "China" }, - "name": "Washington University in St. Louis", - "rorId": null + "name": "Beijing Genomics Institute", + "rorId": "https://ror.org/045pn2j94" }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "CN", + "countryName": "China" }, - "mirId": "MIR:00000838", - "name": "Clinical Interpretation of Variants in Cancer (CIViC)", - "official": true, - "providerCode": "civicdb", - "resourceHomeUrl": "https://civicdb.org/", - "sampleId": "1199", - "urlPattern": "https://civicdb.org/links/evidence/{$id}" + "mirId": "MIR:00100515", + "name": "TreeFam database", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://www.treefam.org/", + "sampleId": "TF101014", + "urlPattern": "http://www.treefam.org/family/{$id}" } ], - "sampleId": "1199" + "sampleId": "TF101014" }, { - "created": "2021-08-08T09:33:59.109+0000", + "created": "2019-06-11T14:16:14.019+0000", "deprecated": false, "deprecationDate": null, - "description": "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).", - "id": 2789, - "mirId": "MIR:00000841", - "modified": "2021-08-08T09:33:59.109+0000", - "name": "SED-ML data format", + "description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "id": 479, + "mirId": "MIR:00000154", + "modified": "2019-06-11T14:16:14.019+0000", + "name": "TrichDB", "namespaceEmbeddedInLui": false, - "pattern": "^[a-z]+(\\..*?)?$", - "prefix": "sedml.format", + "pattern": "^\\w+$", + "prefix": "trichdb", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Editorial board responsible for defining the Simulation Experimental Description Markup Language (SED-ML).", - "id": 2790, + "description": "TrichDB at EuPathDB", + "id": 480, "institution": { - "description": "Editorial board responsible for defining the Simulation Experimental Description Markup Language (SED-ML).", - "homeUrl": "http://sed-ml.org/", - "id": 2788, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 467, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "SED-ML Editors", + "name": "Center for Tropical & Emerging Global Diseases, University of Georgia", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00000840", - "name": "SED-ML Editors", - "official": true, - "providerCode": "sedml", - "resourceHomeUrl": "http://sed-ml.org/", - "sampleId": "csv", - "urlPattern": "https://sed-ml.org/urns.html#format:{$id}" + "mirId": "MIR:00100199", + "name": "TrichDB at EuPathDB", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://trichdb.org/trichdb/", + "sampleId": "TVAG_386080", + "urlPattern": "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id}" } ], - "sampleId": "csv" + "sampleId": "TVAG_386080" }, { - "created": "2021-08-08T09:34:23.184+0000", + "created": "2019-06-11T14:16:14.213+0000", "deprecated": false, "deprecationDate": null, - "description": "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).", - "id": 2792, - "mirId": "MIR:00000843", - "modified": "2021-08-08T09:34:23.184+0000", - "name": "SED-ML model format", + "description": "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "id": 481, + "mirId": "MIR:00000155", + "modified": "2019-06-11T14:16:14.213+0000", + "name": "TriTrypDB", "namespaceEmbeddedInLui": false, - "pattern": "^[a-z]+(\\..*?)?$", - "prefix": "sedml.language", + "pattern": "^\\w+(\\.)?\\w+(\\.)?\\w+", + "prefix": "tritrypdb", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Editorial board responsible for defining the Simulation Experimental Description Markup Language (SED-ML).", - "id": 2793, + "description": "TriTrypDB at EuPathDB", + "id": 483, "institution": { - "description": "Editorial board responsible for defining the Simulation Experimental Description Markup Language (SED-ML).", - "homeUrl": "http://sed-ml.org/", - "id": 2788, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 482, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "name": "SED-ML Editors", + "name": "Wellcome Trust Sanger Institute, Hinxton", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "GB", + "countryName": "United Kingdom" }, - "mirId": "MIR:00000842", - "name": "SED-ML Editors", - "official": true, - "providerCode": "sedml", - "resourceHomeUrl": "http://sed-ml.org/", - "sampleId": "sbml.level-3.version-2", - "urlPattern": "https://sed-ml.org/urns.html#language:{$id}" + "mirId": "MIR:00100200", + "name": "TriTrypDB at EuPathDB", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://tritrypdb.org/tritrypdb/", + "sampleId": "Tb927.8.620", + "urlPattern": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id}" } ], - "sampleId": "sbml.level-3.version-2" + "sampleId": "Tb927.8.620" }, { - "created": "2021-08-08T09:39:33.533+0000", + "created": "2019-06-11T14:15:57.654+0000", "deprecated": false, "deprecationDate": null, - "description": "Resource for the community to store, retrieve, search, reference, and reuse CellML models.", - "id": 2796, - "mirId": "MIR:00000845", - "modified": "2021-08-08T09:39:33.533+0000", - "name": "Physiome Model Repository", + "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", + "id": 304, + "mirId": "MIR:00000092", + "modified": "2019-06-11T14:15:57.654+0000", + "name": "TTD Drug", "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9]{32,32}$", - "prefix": "pmr", + "pattern": "^DAP\\d+$", + "prefix": "ttd.drug", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03b94tp07' with Wikidata IDs [Q492467], and ISNI IDs [0000 0004 0372 3343]", - "id": 2797, + "description": "Therapeutic Target Database Drug", + "id": 306, "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03b94tp07' with Wikidata IDs [Q492467], and ISNI IDs [0000 0004 0372 3343]", - "homeUrl": "https://www.auckland.ac.nz/en.html", - "id": 2795, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 305, "location": { - "countryCode": "NZ", - "countryName": "New Zealand" + "countryCode": "SG", + "countryName": "Singapore" }, - "name": "University of Auckland", + "name": "Computational Science Department, National University of Singapore", "rorId": null }, "location": { - "countryCode": "NZ", - "countryName": "New Zealand" + "countryCode": "SG", + "countryName": "Singapore" }, - "mirId": "MIR:00000844", - "name": "University of Auckland", - "official": true, - "providerCode": "abi", - "resourceHomeUrl": "https://www.auckland.ac.nz/en.html", - "sampleId": "ebf69ca24298b28b2361e7d43eb52d6c", - "urlPattern": "https://models.physiomeproject.org/exposure/{$id}" + "mirId": "MIR:00100123", + "name": "Therapeutic Target Database Drug", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", + "sampleId": "DAP000773", + "urlPattern": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID={$id}" } ], - "sampleId": "ebf69ca24298b28b2361e7d43eb52d6c" + "sampleId": "DAP000773" }, { - "created": "2021-08-08T09:41:19.080+0000", + "created": "2019-06-11T14:15:57.896+0000", "deprecated": false, "deprecationDate": null, - "description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.", - "id": 2800, - "mirId": "MIR:00000847", - "modified": "2021-08-08T09:41:19.080+0000", - "name": "FunderRegistry", + "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", + "id": 307, + "mirId": "MIR:00000093", + "modified": "2019-06-11T14:15:57.896+0000", + "name": "TTD Target", "namespaceEmbeddedInLui": false, - "pattern": "^\\d{9,9}$", - "prefix": "funderregistry", + "pattern": "^TTDS\\d+$", + "prefix": "ttd.target", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/02twcfp32' with Wikidata IDs [Q5188229], and ISNI IDs [0000 0004 0506 2673]", - "id": 2801, + "description": "Therapeutic Target Database Target", + "id": 308, "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/02twcfp32' with Wikidata IDs [Q5188229], and ISNI IDs [0000 0004 0506 2673]", - "homeUrl": "https://www.crossref.org/", - "id": 2799, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 305, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "SG", + "countryName": "Singapore" }, - "name": "Crossref", + "name": "Computational Science Department, National University of Singapore", "rorId": null }, "location": { - "countryCode": "US", - "countryName": "United States" + "countryCode": "SG", + "countryName": "Singapore" }, - "mirId": "MIR:00000846", - "name": "Crossref", - "official": true, - "providerCode": "crossref", - "resourceHomeUrl": "https://www.crossref.org/", - "sampleId": "100000001", - "urlPattern": "http://data.crossref.org/fundingdata/funder/10.13039/{$id}" + "mirId": "MIR:00100124", + "name": "Therapeutic Target Database Target", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", + "sampleId": "TTDS00056", + "urlPattern": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID={$id}" } ], - "sampleId": "100000001" + "sampleId": "TTDS00056" }, { - "created": "2021-08-08T09:42:52.720+0000", + "created": "2019-06-11T14:17:22.433+0000", "deprecated": false, "deprecationDate": null, - "description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.", - "id": 2804, - "mirId": "MIR:00000849", - "modified": "2021-08-08T09:42:52.720+0000", - "name": "Linguist", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-zA-Z0-9 +#'*]+$", - "prefix": "linguist", + "description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", + "id": 1280, + "mirId": "MIR:00000446", + "modified": "2021-02-27T10:19:43.666+0000", + "name": "UBERON", + "namespaceEmbeddedInLui": true, + "pattern": "^UBERON:\\d+$", + "prefix": "uberon", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "GitHub, Inc. is a provider of Internet hosting for software development and version control using Git.", - "id": 2805, + "description": "UBERON through bioPortal", + "id": 1281, "institution": { - "description": "GitHub, Inc. is a provider of Internet hosting for software development and version control using Git.", - "homeUrl": "https://github.com/", - "id": 2803, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 5, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "GitHub, Inc.", + "name": "National Center for Biomedical Ontology, Stanford", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00000848", - "name": "GitHub, Inc.", - "official": true, - "providerCode": "github", - "resourceHomeUrl": "https://github.com/", - "sampleId": "Python", - "urlPattern": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#{$id}" - } - ], - "sampleId": "Python" - }, - { - "created": "2021-08-08T09:47:01.408+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.", - "id": 2807, - "mirId": "MIR:00000851", - "modified": "2021-08-08T09:47:01.408+0000", - "name": "Semanticscience Integrated Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^SIO_\\d{6,6}$", - "prefix": "sio", - "resources": [ + "mirId": "MIR:00100579", + "name": "UBERON through bioPortal", + "official": false, + "providerCode": "bptl", + "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/UBERON", + "sampleId": "0008203", + "urlPattern": "http://purl.bioontology.org/ontology/UBERON/UBERON:{$id}" + }, { "deprecated": false, "deprecationDate": null, - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "id": 2808, + "description": "UBERON through OLS", + "id": 1282, "institution": { "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", "homeUrl": "https://www.ebi.ac.uk", @@ -37188,519 +37292,503 @@ "countryCode": "GB", "countryName": "United Kingdom" }, - "mirId": "MIR:00000850", - "name": "European Bioinformatics Institute", + "mirId": "MIR:00100580", + "name": "UBERON through OLS", "official": true, "providerCode": "ols", - "resourceHomeUrl": "https://www.ebi.ac.uk", - "sampleId": "SIO_000276", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form={$id}" + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/uberon", + "sampleId": "0008203", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=UBERON:{$id}" } ], - "sampleId": "SIO_000276" + "sampleId": "0008203" }, { - "created": "2021-08-08T09:49:13.100+0000", + "created": "2019-06-11T14:16:56.122+0000", "deprecated": false, "deprecationDate": null, - "description": "GitHub is an online host of Git source code repositories.", - "id": 2810, - "mirId": "MIR:00000853", - "modified": "2021-08-08T09:49:13.100+0000", - "name": "github", + "description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.", + "id": 970, + "mirId": "MIR:00000338", + "modified": "2019-06-11T14:16:56.122+0000", + "name": "uBio NameBank", "namespaceEmbeddedInLui": false, - "pattern": "^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$", - "prefix": "github", + "pattern": "^\\d+$", + "prefix": "ubio.namebank", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "GitHub, Inc. is a provider of Internet hosting for software development and version control using Git.", - "id": 2811, + "description": "uBio NameBank at The Marine Biological Laboratory", + "id": 972, "institution": { - "description": "GitHub, Inc. is a provider of Internet hosting for software development and version control using Git.", - "homeUrl": "https://github.com/", - "id": 2803, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 971, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "GitHub, Inc.", + "name": "Marine Biological Laboratory, Woods Hole, Massachusetts", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00000852", - "name": "GitHub, Inc.", - "official": true, - "providerCode": "github", - "resourceHomeUrl": "https://github.com/", - "sampleId": "identifiers-org/registry", - "urlPattern": "https://github.com/{$id}" + "mirId": "MIR:00100433", + "name": "uBio NameBank at The Marine Biological Laboratory", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://www.ubio.org", + "sampleId": "2555646", + "urlPattern": "http://www.ubio.org/browser/details.php?namebankID={$id}" } ], - "sampleId": "identifiers-org/registry" + "sampleId": "2555646" }, { - "created": "2021-08-08T09:56:43.759+0000", + "created": "2019-06-11T14:16:42.994+0000", "deprecated": false, "deprecationDate": null, - "description": "\tDatanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. 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The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", - "id": 3258, - "mirId": "MIR:00000957", - "modified": "2022-08-08T18:34:15.882+0000", - "name": "CIViC Disease", + "description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.", + "id": 130, + "mirId": "MIR:00000031", + "modified": "2019-06-11T14:15:40.709+0000", + "name": "Wormpep", "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "civic.did", + "pattern": "^CE\\d{5}$", + "prefix": "wormpep", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.https://civicdb.org/\n", - "id": 3259, + "description": "Wormpep (Master)", + "id": 132, "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", - "homeUrl": "https://wustl.edu/", - "id": 2750, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 131, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Washington University in St. Louis", + "name": "Cold Spring Harbor Laboratory", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00000956", - "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "mirId": "MIR:00100051", + "name": "Wormpep (Master)", "official": true, - "providerCode": "civicdb", - "resourceHomeUrl": "https://civicdb.org/", - "sampleId": "46", - "urlPattern": "https://civicdb.org/links/diseases/{$id}" + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "https://www.wormbase.org/db/seq/protein", + "sampleId": "CE28239", + "urlPattern": "https://www.wormbase.org/db/seq/protein?name={$id}" } ], - "sampleId": "46" + "sampleId": "CE28239" }, { - "created": "2022-08-08T18:36:40.981+0000", + "created": "2019-06-11T14:17:54.476+0000", "deprecated": false, "deprecationDate": null, - "description": "Metabolic Atlas facilitates metabolic modelling by presenting open source genome-scale metabolic models for easy browsing and analysis.", - "id": 3263, - "mirId": "MIR:00000959", - "modified": "2022-08-08T18:36:40.981+0000", - "name": "Metabolic Atlas", + "description": "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.", + "id": 1618, + "mirId": "MIR:00000581", + "modified": "2019-06-11T14:17:54.476+0000", + "name": "World Register of Marine Species", "namespaceEmbeddedInLui": false, - "pattern": "^MA[MR]\\d{5}[a-z]?$", - "prefix": "metatlas", + "pattern": "^\\d+$", + "prefix": "worms", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. The goal is to collect curated GEMs, and to bring these models closer to FAIR principles. The website provides visualisations and comparisons of the GEMs, and links to resources, algorithms, other databases, and more general software applications.", - "id": 3264, + "description": "World Register of Marine Species", + "id": 1620, "institution": { - "description": "NBIS (National Bioinformatics Infrastructure Sweden) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities and the Knut and Alice Wallenberg Foundation, providing state-of-the-art bioinformatics to the Swedish life science researchers community. NBIS is also the Swedish contact point to the European infrastructure for biological information ELIXIR.\n\nPresent NBIS staff has expertise in protein bioinformatics, mass spectrometry (MS), next generation sequencing (NGS), large-scale data handling and integration, metagenomics, systems biology, biostatistics and RNAseq.\n\nNBIS is predominantly offering bioinformatics support in various projects, depending on the user needs. In the projects, the NBIS persons are working close to the research group, and they spend part of their time to teach the users in order to propagate the bioinformatics knowledge. Furthermore, NBIS provides infrastructure and tools for bioinformatics analyses in order to facilitate these analyses for the users.\n\nNBIS forms the bioinformatics platform at the Science for Life Laboratory.", - "homeUrl": "https://nbis.se", - "id": 3262, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 1619, "location": { - "countryCode": "SE", - "countryName": "Sweden" + "countryCode": "BE", + "countryName": "Belgium" }, - "name": "National Bioinformatics Infrastructure Sweden", + "name": "Flanders Marine Institute, Ostend", "rorId": null }, "location": { - "countryCode": "SE", - "countryName": "Sweden" + "countryCode": "BE", + "countryName": "Belgium" }, - "mirId": "MIR:00000958", - "name": "Metabolic Atlas", - "official": true, - "providerCode": "metatlas", - "resourceHomeUrl": "https://metabolicatlas.org", - "sampleId": "MAR01234", - "urlPattern": "https://metabolicatlas.org/identifier/MetabolicAtlas/{$id}" + "mirId": "MIR:00100778", + "name": "World Register of Marine Species", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://www.marinespecies.org/", + "sampleId": "146421", + "urlPattern": "http://www.marinespecies.org/aphia.php?p=taxdetails&id={$id}" + } + ], + "sampleId": "146421" + }, + { + "created": "2019-06-11T14:16:21.651+0000", + "deprecated": false, + "deprecationDate": null, + "description": "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.", + "id": 567, + "mirId": "MIR:00000186", + "modified": "2020-06-09T19:30:57.158+0000", + "name": "Xenbase", + "namespaceEmbeddedInLui": false, + "pattern": "^XB\\-\\w+\\-\\d+$", + "prefix": "xenbase", + "resources": [ + { + "deprecated": false, + "deprecationDate": null, + "description": "Xenbase at University of Calgary", + "id": 569, + "institution": { + "description": "The University of Calgary is one of Canada’s top comprehensive research universities, combining the best of university tradition with the city of Calgary’s vibrant energy and diversity.", + "homeUrl": "https://www.ucalgary.ca/", + "id": 568, + "location": { + "countryCode": "CA", + "countryName": "Canada" + }, + "name": "University of Calgary", + "rorId": "https://ror.org/03yjb2x39" + }, + "location": { + "countryCode": "CA", + "countryName": "Canada" + }, + "mirId": "MIR:00100232", + "name": "Xenbase at University of Calgary", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "https://www.xenbase.org/", + "sampleId": "XB-GENE-922462", + "urlPattern": "https://www.xenbase.org/entry/{$id}" } ], - "sampleId": "MAR01234" + "sampleId": "XB-GENE-922462" }, { - "created": "2020-03-24T05:11:19.658+0000", + "created": "2019-06-11T14:17:26.654+0000", "deprecated": false, "deprecationDate": null, - "description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.", - "id": 2168, - "mirId": "MIR:00000786", - "modified": "2021-10-18T12:32:14.264+0000", - "name": "DANDI: Distributed Archives for Neurophysiology Data Integration", + "description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.", + "id": 1330, + "mirId": "MIR:00000465", + "modified": "2019-06-11T14:17:26.654+0000", + "name": "YDPM", "namespaceEmbeddedInLui": false, - "pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$", - "prefix": "dandi", + "pattern": "^Y[A-Z]{2}\\d+[CW]$", + "prefix": "ydpm", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "DANDI is a Web platform for scientists to share, collaborate, and process data from cellular neurophysiology experiments. DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI will store electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. DANDI will provide: 1) A cloud platform for neurophysiology data storage for the purposes of collaboration and dissemination of data; 2) Easy to use tools for neurophysiology data submission, visualization, and access in the archive; and 3) Standardized applications for data ingestion, visualization and processing, which facilitate adoption of NWB and other standards. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.", - "id": 2169, + "description": "YDPM at Stanford University School of Medicine", + "id": 1332, "institution": { - "description": "Founded to accelerate the nation’s industrial revolution, MIT is profoundly American. With ingenuity and drive, our graduates have invented fundamental technologies, launched new industries, and created millions of American jobs. At the same time, and without the slightest sense of contradiction, MIT is profoundly global(opens in new window). Our community gains tremendous strength as a magnet for talent from around the world. Through teaching, research, and innovation, MIT’s exceptional community pursues its mission of service to the nation and the world.", - "homeUrl": "http://web.mit.edu/", - "id": 2167, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 1331, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "Massachusetts Institute of Technology", + "name": "Stanford University School of Medicine, Stanford, California", "rorId": null }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00000750", - "name": "DANDI: Distributed Archives for Neurophysiology Data Integration", - "official": true, - "providerCode": "dandi", - "resourceHomeUrl": "https://dandiarchive.org/", - "sampleId": "000017", - "urlPattern": "https://dandiarchive.org/dandiset/{$id}" + "mirId": "MIR:00100600", + "name": "YDPM at Stanford University School of Medicine", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://www-deletion.stanford.edu/YDPM/", + "sampleId": "YAL001C", + "urlPattern": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id}" } ], - "sampleId": "000017" + "sampleId": "YAL001C" }, { - "created": "2022-08-15T19:28:35.707+0000", + "created": "2019-06-11T14:17:39.906+0000", "deprecated": false, "deprecationDate": null, - "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.", - "id": 3271, - "mirId": "MIR:00000961", - "modified": "2022-08-18T13:14:34.725+0000", - "name": "ROR", + "description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].", + "id": 1470, + "mirId": "MIR:00000521", + "modified": "2019-06-11T14:17:39.906+0000", + "name": "Yeast Intron Database v4.3", "namespaceEmbeddedInLui": false, - "pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$", - "prefix": "ror", + "pattern": "^[A-Z0-9]+$", + "prefix": "yeastintron", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ", - "id": 3272, + "description": "Yeast Intron Database version 4.3 at Baskin School of Engineering", + "id": 1471, "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03yrm5c26' with Wikidata IDs [Q5020447], and ISNI IDs [0000 0001 1957 5136]", - "homeUrl": "https://www.cdlib.org/", - "id": 3270, + "description": "UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n", + "homeUrl": "https://www.ucsc.edu", + "id": 1319, "location": { "countryCode": "US", "countryName": "United States" }, - "name": "California Digital Library", - "rorId": null + "name": "University of California, Santa Cruz", + "rorId": "https://ror.org/03s65by71" }, "location": { "countryCode": "US", "countryName": "United States" }, - "mirId": "MIR:00001056", - "name": "ROR", - "official": true, - "providerCode": "ror", - "resourceHomeUrl": "https://ror.org", - "sampleId": "03yrm5c26", - "urlPattern": "https://ror.org/{$id}" + "mirId": "MIR:00100673", + "name": "Yeast Intron Database version 4.3 at Baskin School of Engineering", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://intron.ucsc.edu/yeast4.3/", + "sampleId": "SNR17A", + "urlPattern": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName={$id}" } ], - "sampleId": "03yrm5c26" + "sampleId": "SNR17A" }, { - "created": "2022-11-03T14:17:05.019+0000", + "created": "2019-06-11T14:16:56.366+0000", "deprecated": false, "deprecationDate": null, - "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", - "id": 3292, - "mirId": "MIR:00000964", - "modified": "2022-11-03T14:17:05.019+0000", - "name": "ChecklistBank", + "description": "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.", + "id": 973, + "mirId": "MIR:00000339", + "modified": "2019-06-11T14:16:56.366+0000", + "name": "YeTFasCo", "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+(LR)?$", - "prefix": "clb", + "pattern": "^\\w+\\_\\d+(\\.\\d+)?$", + "prefix": "yetfasco", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "ChecklistBank at GBIF. Codeveloped with the Catalogue of Life", - "id": 3293, + "description": "YeTFasCo at University of Toronto", + "id": 975, "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fjyn938' with Wikidata IDs [Q1531570], and no ISNI information", - "homeUrl": "https://www.gbif.org/", - "id": 3291, + "description": "CURATOR_REVIEW", + "homeUrl": "CURATOR_REVIEW", + "id": 974, "location": { - "countryCode": "DK", - "countryName": "Denmark" + "countryCode": "CA", + "countryName": "Canada" }, - "name": "Global Biodiversity Information Facility", + "name": "Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto", "rorId": null }, "location": { - "countryCode": "DK", - "countryName": "Denmark" + "countryCode": "CA", + "countryName": "Canada" }, - "mirId": "MIR:00000963", - "name": "ChecklistBank", - "official": true, - "providerCode": "clb", - "resourceHomeUrl": "https://www.checklistbank.org", - "sampleId": "1010", - "urlPattern": "https://www.checklistbank.org/dataset/{$id}" + "mirId": "MIR:00100434", + "name": "YeTFasCo at University of Toronto", + "official": false, + "providerCode": "CURATOR_REVIEW", + "resourceHomeUrl": "http://yetfasco.ccbr.utoronto.ca/", + "sampleId": "YOR172W_571.0", + "urlPattern": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot={$id}" } ], - "sampleId": "1010" + "sampleId": "YOR172W_571.0" }, { - "created": "2022-11-04T09:54:32.976+0000", + "created": "2019-06-11T14:17:25.610+0000", "deprecated": false, "deprecationDate": null, - "description": "DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.", - "id": 3298, - "mirId": "MIR:00000966", - "modified": "2022-11-04T09:54:32.976+0000", - "name": "DrugCentral", + "description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].", + "id": 1318, + "mirId": "MIR:00000460", + "modified": "2019-06-11T14:17:25.610+0000", + "name": "Yeast Intron Database v3", "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "drugcentral", + "pattern": "^[A-Z0-9]+$", + "prefix": "yid", "resources": [ { "deprecated": false, "deprecationDate": null, - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", - "id": 3299, + "description": "Yeast Intron Database version 3 at Baskin School of Engineering", + "id": 1320, "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", - "homeUrl": "http://www.unm.edu/", - "id": 3297, + "description": "UC Santa Cruz opened in 1965 with 650 students. 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