From d45b19039903396549367881fc1370e2d267b24b Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 30 Nov 2021 22:43:12 -0500 Subject: [PATCH 01/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 49 ++++++++++++++++++++++++++- 1 file changed, 48 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 1829a6540..c43fd39e3 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -1961,6 +1961,7 @@ "name": "Animal Trait Ontology for Livestock", "prefix": "ATOL" }, + "download_owl": "https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl", "example": "0002233", "mappings": { "bioportal": "ATOL", @@ -2240,6 +2241,7 @@ "name": "Brain-Computer Interaction (BCI) Ontology", "prefix": "BCI-O" }, + "download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl", "example": "040000", "mappings": { "bioportal": "BCI-O", @@ -4428,7 +4430,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.", - "download_obo": "ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo", + "download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo", "example": "0001", "homepage": "https://github.com/calipho-sib/controlled-vocabulary", "name": "CALIPHO Group Ontology of Human Anatomy", @@ -5001,6 +5003,12 @@ "uri_format": "http://identifiers.org/cco/$1" } }, + "ccrid": { + "example": "4201PAT-CCTCC00348", + "homepage": "http://www.cellresource.cn", + "name": "National Experimental Cell Resource Sharing Platform", + "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" + }, "cdao": { "bioportal": { "name": "Comparative Data Analysis Ontology", @@ -5235,6 +5243,13 @@ "uri_format": "http://identifiers.org/cellimage/$1" } }, + "cellopub": { + "description": "Cellosaurus identifeirs for publications, like Pubmed", + "example": "CLPUB00496", + "homepage": "https://web.expasy.org/cellosaurus/", + "name": "Cellosaurus Publication", + "uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1" + }, "cellosaurus": { "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", "example": "CVCL_0440", @@ -5677,6 +5692,14 @@ "uri_format": "https://www.ebi.ac.uk/chembldb/target/inspect/$1" } }, + "chembl.cell": { + "example": "CHEMBL3307800", + "part_of": "chembl", + "synonyms": [ + "ChEMBL-Cells" + ], + "uri_format": "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1" + }, "chembl.compound": { "example": "CHEMBL465070", "mappings": { @@ -13837,6 +13860,12 @@ "uri_format": "http://identifiers.org/fbol/$1" } }, + "fbql": { + "deprecated": true, + "example": "00005254", + "name": "FlyBase Qualifiers", + "pattern": "^\\d+$" + }, "fbrf": { "contributor": { "email": "cthoyt@gmail.com", @@ -21434,6 +21463,12 @@ "uri_format": "http://identifiers.org/jcm/$1" } }, + "jcrb": { + "example": "JCRB1355", + "homepage": "https://cellbank.nibiohn.go.jp", + "name": "JRBC Cell Bank", + "uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1" + }, "jcsd": { "mappings": { "miriam": "jcsd", @@ -21592,6 +21627,12 @@ "uri_format": "https://www.kaggle.com/$1" } }, + "kclb": { + "example": "10020.2", + "homepage": "https://cellbank.snu.ac.kr/english", + "name": "Korean Cell Line Bank", + "uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1" + }, "kegg": { "cheminf": { "description": "Database identifier used by KEGG.", @@ -44734,6 +44775,12 @@ "uri_format": "https://www.xenbase.org/gene/showgene.do?method=display&geneId=$1" } }, + "ximbio": { + "example": "151022", + "homepage": "https://ximbio.com", + "name": "Ximbio", + "uri_format": "https://ximbio.com/reagent/$1" + }, "xl": { "deprecated": true, "mappings": { From 0c7ce3e4b9d5ee00610f6f99860a749ec4b72ae5 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 30 Nov 2021 22:54:32 -0500 Subject: [PATCH 02/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index c43fd39e3..da23ffdce 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -5816,7 +5816,10 @@ "is_obo": false, "prefix": "CHEMBL.TARGET", "uri_format": "http://identifiers.org/chembl.target/$1" - } + }, + "synonyms": [ + "ChEMBL-Targets" + ] }, "chemdb": { "mappings": { From 7afa67e82550a900a5a51e4d1bdaeae08d8ccb1c Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:26:17 -0500 Subject: [PATCH 03/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index da23ffdce..aeec55375 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -2491,6 +2491,15 @@ "uri_format": "http://identifiers.org/begdb/$1" } }, + "beiresources": { + "example": "MRA-253", + "homepage": "https://www.beiresources.org", + "name": "BEI Resources", + "synonyms": [ + "BEI_Resources" + ], + "uri_format": "https://www.beiresources.org/Catalog/cellBanks/$1.aspx" + }, "bel": { "comment": "INDRA uses bel as a catch-all for scomp/sfam", "contributor": { @@ -3981,6 +3990,12 @@ "name": "Bio-Pesticides DataBase", "uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm" }, + "brcr": { + "example": "60316", + "homepage": "https://catalog.bcrc.firdi.org.tw", + "name": "BRCR Strain Collection Catalog", + "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" + }, "brenda": { "go": { "homepage": "http://www.brenda-enzymes.info", @@ -13925,6 +13940,12 @@ "part_of": "flybase", "uri_format": "https://flybase.org/reports/FBtc$1" }, + "fcsfree": { + "example": "240-17-488-3-4-12", + "homepage": "https://fcs-free.org", + "name": "Fetal Calf Serum-Free Database", + "uri_format": "https://fcs-free.org/fcs-database?$1" + }, "fideo": { "bioportal": { "name": "Food Interactions with Drugs Evidence Ontology", @@ -22938,6 +22959,12 @@ "name": "Logical Observation Identifiers Names and Codes", "uri_format": "https://loinc.org/$1" }, + "lonza": { + "example": "968", + "homepage": "https://knowledge.lonza.com", + "name": "Lonza", + "uri_format": "https://knowledge.lonza.com/cell?id=$1" + }, "lotus": { "comment": "IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case.", "contact": { From 856ef7f4da0820cadb590151ff0611fb2faa8538 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:26:52 -0500 Subject: [PATCH 04/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 102 ++++++++++++++++++++++++++ 1 file changed, 102 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index aeec55375..9743d3d55 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -2492,6 +2492,12 @@ } }, "beiresources": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "MRA-253", "homepage": "https://www.beiresources.org", "name": "BEI Resources", @@ -3098,6 +3104,12 @@ "uri_format": "https://thebiogrid.org/interaction/$1" }, "biolegend": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "BioLegend is a life sciences supply vendor.", "example": "3403", "homepage": "https://www.biolegend.com", @@ -3786,6 +3798,12 @@ } }, "biozil": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Redistributor of bilogics and biomedical supplies", "example": "ls-c35719-120", "homepage": "https://www.biozol.de/en", @@ -3991,6 +4009,12 @@ "uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm" }, "brcr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "60316", "homepage": "https://catalog.bcrc.firdi.org.tw", "name": "BRCR Strain Collection Catalog", @@ -5019,6 +5043,12 @@ } }, "ccrid": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "4201PAT-CCTCC00348", "homepage": "http://www.cellresource.cn", "name": "National Experimental Cell Resource Sharing Platform", @@ -5259,6 +5289,12 @@ } }, "cellopub": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Cellosaurus identifeirs for publications, like Pubmed", "example": "CLPUB00496", "homepage": "https://web.expasy.org/cellosaurus/", @@ -5708,6 +5744,12 @@ } }, "chembl.cell": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "CHEMBL3307800", "part_of": "chembl", "synonyms": [ @@ -12855,6 +12897,12 @@ } }, "enzo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Enzo Life Sciences is an antibody vendor.", "example": "ALX-210-175", "homepage": "https://www.enzolifesciences.com", @@ -13879,6 +13927,12 @@ } }, "fbql": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "deprecated": true, "example": "00005254", "name": "FlyBase Qualifiers", @@ -13941,6 +13995,12 @@ "uri_format": "https://flybase.org/reports/FBtc$1" }, "fcsfree": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "240-17-488-3-4-12", "homepage": "https://fcs-free.org", "name": "Fetal Calf Serum-Free Database", @@ -21488,6 +21548,12 @@ } }, "jcrb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "JCRB1355", "homepage": "https://cellbank.nibiohn.go.jp", "name": "JRBC Cell Bank", @@ -21652,6 +21718,12 @@ } }, "kclb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "10020.2", "homepage": "https://cellbank.snu.ac.kr/english", "name": "Korean Cell Line Bank", @@ -22960,6 +23032,12 @@ "uri_format": "https://loinc.org/$1" }, "lonza": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "968", "homepage": "https://knowledge.lonza.com", "name": "Lonza", @@ -29168,6 +29246,12 @@ } }, "novus": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "A vendor of antibodies and other biologics", "example": "nb100-56351", "homepage": "https://www.novusbio.com", @@ -38795,6 +38879,12 @@ "uri_format": "http://sideeffects.embl.de/se/$1" }, "sigmaaldirch": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Sigma Aldrich is a life sciences supply vendor.", "example": "HPA000698", "homepage": "https://www.sigmaaldrich.com", @@ -40936,6 +41026,12 @@ ] }, "thermofisher": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "ThermoFisher is a life sciences supply vendor.", "example": "OSR00185W", "homepage": "https://www.thermofisher.com", @@ -44806,6 +44902,12 @@ } }, "ximbio": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "example": "151022", "homepage": "https://ximbio.com", "name": "Ximbio", From 7495cc7ed3e2a31184aa31b6783624f49a06d218 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:29:28 -0500 Subject: [PATCH 05/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 9743d3d55..99e46c748 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -2308,6 +2308,18 @@ "uri_format": "http://purl.obolibrary.org/obo/BCO_$1" } }, + "bcrc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "example": "60316", + "homepage": "https://catalog.bcrc.firdi.org.tw", + "name": "BCRC Strain Collection Catalog", + "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" + }, "bdgp.est": { "has_canonical": "dbest", "mappings": { @@ -4008,18 +4020,6 @@ "name": "Bio-Pesticides DataBase", "uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm" }, - "brcr": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "example": "60316", - "homepage": "https://catalog.bcrc.firdi.org.tw", - "name": "BRCR Strain Collection Catalog", - "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" - }, "brenda": { "go": { "homepage": "http://www.brenda-enzymes.info", From 43ea80e44ffb5b33995eb7549b7a00d4fa67f5d8 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:38:44 -0500 Subject: [PATCH 06/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 114 ++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 99e46c748..02e56df25 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -2309,6 +2309,13 @@ } }, "bcrc": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://catalog.bcrc.firdi.org.tw/", + "name": "Taiwan Bioresource Collection and Research Center", + "prefix": "BCRC", + "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -2317,6 +2324,9 @@ }, "example": "60316", "homepage": "https://catalog.bcrc.firdi.org.tw", + "mappings": { + "cellosaurus": "BCRC" + }, "name": "BCRC Strain Collection Catalog", "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" }, @@ -2504,6 +2514,13 @@ } }, "beiresources": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.beiresources.org/Home.aspx", + "name": "BEI Resources", + "prefix": "BEI_Resources", + "uri_format": "https://www.beiresources.org/Catalog/cellBanks/$1.aspx" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -2512,6 +2529,9 @@ }, "example": "MRA-253", "homepage": "https://www.beiresources.org", + "mappings": { + "cellosaurus": "BEI_Resources" + }, "name": "BEI Resources", "synonyms": [ "BEI_Resources" @@ -5289,6 +5309,13 @@ } }, "cellopub": { + "cellosaurus": { + "category": "Reference resources", + "homepage": "https://web.expasy.org/cellosaurus/", + "name": "Cellosaurus Publication", + "prefix": "CelloPub", + "uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -5298,6 +5325,9 @@ "description": "Cellosaurus identifeirs for publications, like Pubmed", "example": "CLPUB00496", "homepage": "https://web.expasy.org/cellosaurus/", + "mappings": { + "cellosaurus": "CelloPub" + }, "name": "Cellosaurus Publication", "uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1" }, @@ -5744,6 +5774,13 @@ } }, "chembl.cell": { + "cellosaurus": { + "category": "Chemistry resources", + "homepage": "https://www.ebi.ac.uk/chembldb", + "name": "ChEMBL database of bioactive drug-like small molecules - Cell lines section", + "prefix": "ChEMBL-Cells", + "uri_format": "https://www.ebi.ac.uk/chembldb/cell/inspect/$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -5751,6 +5788,9 @@ "orcid": "0000-0003-4423-4370" }, "example": "CHEMBL3307800", + "mappings": { + "cellosaurus": "ChEMBL-Cells" + }, "part_of": "chembl", "synonyms": [ "ChEMBL-Cells" @@ -5824,7 +5864,15 @@ } }, "chembl.target": { + "cellosaurus": { + "category": "Chemistry resources", + "homepage": "https://www.ebi.ac.uk/chembldb", + "name": "ChEMBL database of bioactive drug-like small molecules - Targets section", + "prefix": "ChEMBL-Targets", + "uri_format": "https://www.ebi.ac.uk/chembldb/target/inspect/$1" + }, "mappings": { + "cellosaurus": "ChEMBL-Targets", "miriam": "chembl.target", "n2t": "chembl.target", "prefixcommons": "CHEMBL.TARGET" @@ -13167,6 +13215,22 @@ "uri_format": "http://identifiers.org/erv/$1" } }, + "estdab": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://www.ebi.ac.uk/ipd/estdab/", + "name": "European Searchable Tumour Line Database", + "prefix": "ESTDAB", + "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1" + }, + "comment": "Website is dead", + "deprecated": true, + "example": "046", + "mappings": { + "cellosaurus": "ESTDAB" + }, + "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1" + }, "eu89h": { "mappings": { "miriam": "eu89h", @@ -13995,6 +14059,13 @@ "uri_format": "https://flybase.org/reports/FBtc$1" }, "fcsfree": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://fcs-free.org/", + "name": "Fetal Calf Serum-Free Database", + "prefix": "FCS-free", + "uri_format": "https://fcs-free.org/fcs-database?$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -14003,6 +14074,9 @@ }, "example": "240-17-488-3-4-12", "homepage": "https://fcs-free.org", + "mappings": { + "cellosaurus": "FCS-free" + }, "name": "Fetal Calf Serum-Free Database", "uri_format": "https://fcs-free.org/fcs-database?$1" }, @@ -21548,6 +21622,13 @@ } }, "jcrb": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "http://cellbank.nibiohn.go.jp/english/", + "name": "Japanese Collection of Research Bioresources Cell Bank", + "prefix": "JCRB", + "uri_format": "http://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -21556,6 +21637,9 @@ }, "example": "JCRB1355", "homepage": "https://cellbank.nibiohn.go.jp", + "mappings": { + "cellosaurus": "JCRB" + }, "name": "JRBC Cell Bank", "uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1" }, @@ -21718,6 +21802,13 @@ } }, "kclb": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://cellbank.snu.ac.kr/main/index.html", + "name": "Korean Cell Line Bank", + "prefix": "KCLB", + "uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?page=detail&CatNo=59&strQ=$1&submit1=Find+it" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -21726,6 +21817,9 @@ }, "example": "10020.2", "homepage": "https://cellbank.snu.ac.kr/english", + "mappings": { + "cellosaurus": "KCLB" + }, "name": "Korean Cell Line Bank", "uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1" }, @@ -23032,6 +23126,13 @@ "uri_format": "https://loinc.org/$1" }, "lonza": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://knowledge.lonza.com", + "name": "Lonza Cell and Transfection Database", + "prefix": "Lonza", + "uri_format": "https://knowledge.lonza.com/cell?id=$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -23040,6 +23141,9 @@ }, "example": "968", "homepage": "https://knowledge.lonza.com", + "mappings": { + "cellosaurus": "Lonza" + }, "name": "Lonza", "uri_format": "https://knowledge.lonza.com/cell?id=$1" }, @@ -44902,6 +45006,13 @@ } }, "ximbio": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://ximbio.com", + "name": "Ximbio reagents online portal", + "prefix": "Ximbio", + "uri_format": "https://ximbio.com/reagent/$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -44910,6 +45021,9 @@ }, "example": "151022", "homepage": "https://ximbio.com", + "mappings": { + "cellosaurus": "Ximbio" + }, "name": "Ximbio", "uri_format": "https://ximbio.com/reagent/$1" }, From c0cf56c42f976aefcceca0eb3fd030f867779d4e Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:38:50 -0500 Subject: [PATCH 07/57] Update curation.tsv --- .../data/external/cellosaurus/curation.tsv | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/src/bioregistry/data/external/cellosaurus/curation.tsv b/src/bioregistry/data/external/cellosaurus/curation.tsv index a9f904072..2ab0142fe 100644 --- a/src/bioregistry/data/external/cellosaurus/curation.tsv +++ b/src/bioregistry/data/external/cellosaurus/curation.tsv @@ -1,25 +1,18 @@ prefix name homepage category uri_format ABM Applied Biological Materials cell line products https://www.abmgood.com/Cell-Biology.html Cell line collections https://www.abmgood.com/catalogsearch/result/?cat=&q=$1 AddexBio AddexBio cell line products https://www.addexbio.com/productshow?id=4 Cell line collections https://www.addexbio.com/productdetail?pid=$1 -BCRC Taiwan Bioresource Collection and Research Center https://catalog.bcrc.firdi.org.tw/ Cell line collections https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 BCRJ Banco de Celulas do Rio de Janeiro http://bcrj.org.br/celula/bcrj Cell line collections http://bcrj.org.br/celula/$1 -BEI_Resources BEI Resources https://www.beiresources.org/Home.aspx Cell line collections https://www.beiresources.org/Catalog/cellBanks/$1.aspx BioSamples BioSamples database https://www.ebi.ac.uk/biosamples/ Biological sample resources https://www.ebi.ac.uk/biosamples/samples/$1 Cell_Biolabs Cell Biolabs cell line products https://www.cellbiolabs.com Cell line collections https://www.cellbiolabs.com/search?keywords=$1 Cell_Model_Passport Sanger Cell Model Passports https://cellmodelpassports.sanger.ac.uk/ Cell line databases/resources https://cellmodelpassports.sanger.ac.uk/passports/$1 -CelloPub Cellosaurus Publication https://web.expasy.org/cellosaurus/ Reference resources https://web.expasy.org/cellosaurus/cellopub/$1 CGH-DB CGH Data Base http://www.cghtmd.jp/CGHDatabase/index_e.jsp Cell line databases/resources http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en -ChEMBL-Cells ChEMBL database of bioactive drug-like small molecules - Cell lines section https://www.ebi.ac.uk/chembldb Chemistry resources https://www.ebi.ac.uk/chembldb/cell/inspect/$1 -ChEMBL-Targets ChEMBL database of bioactive drug-like small molecules - Targets section https://www.ebi.ac.uk/chembldb Chemistry resources https://www.ebi.ac.uk/chembldb/target/inspect/$1 CLS Cell Lines Service https://www.clsgmbh.de Cell line collections https://www.clsgmbh.de/$1.html ColonAtlas Colorectal Cancer Atlas http://www.coloncanceratlas.org Cell line databases/resources http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 Cosmic-CLP COSMIC Cell lines Project https://cancer.sanger.ac.uk/cell_lines Cell line databases/resources https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 DGRC Drosophila Genomics Resource Center https://dgrc.bio.indiana.edu/cells/Catalog Cell line collections https://dgrc.bio.indiana.edu/product/View?product=$1 DiscoverX DiscoverX cell line products https://www.discoverx.com/products-applications/cell-lines Cell line collections https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact EBiSC European Bank for induced pluripotent Stem Cells https://www.ebisc.org Cell line collections https://cells.ebisc.org/$1 -ESTDAB European Searchable Tumour Line Database https://www.ebi.ac.uk/ipd/estdab/ Cell line databases/resources https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1 FCDI FujiFilm Cellular Dynamics, Inc https://fujifilmcdi.com/the-cirm-ipsc-bank Cell line collections -FCS-free Fetal Calf Serum-Free Database https://fcs-free.org/ Cell line databases/resources https://fcs-free.org/fcs-database?$1 HipSci Human Induced Pluripotent Stem Cells Initiative http://www.hipsci.org Cell line databases/resources http://www.hipsci.org/lines/#/lines/$1 HIVReagentProgram NIH HIV Reagent Program https://www.hivreagentprogram.org/Home.aspx Cell line collections https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx Horizon_Discovery Horizon Discovery cell line collection https://horizondiscovery.com/ Cell line collections https://horizondiscovery.com/en/search?searchterm=$1 @@ -31,16 +24,13 @@ IGSR International Genome Sample Resource https://www.internationalgenome.org/ B Imanis Imanis Life Sciences cell line products https://www.imanislife.com/collections/cell-lines/ Cell line collections https://www.imanislife.com/?s=$1 ISCR International Stem Cell Registry https://www.umassmed.edu/iscr/ Cell line databases/resources IZSLER Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna biobank http://www.ibvr.org/Services/CellCultures.aspx Cell line collections -JCRB Japanese Collection of Research Bioresources Cell Bank http://cellbank.nibiohn.go.jp/english/ Cell line collections http://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1 KCB Kunming Cell Bank of Type Culture Collection http://www.kmcellbank.com/ Cell line collections -KCLB Korean Cell Line Bank https://cellbank.snu.ac.kr/main/index.html Cell line collections https://cellbank.snu.ac.kr/english/sub/catalog.php?page=detail&CatNo=59&strQ=$1&submit1=Find+it Kerafast Kerafast cell lines https://www.kerafast.com/ Cell line collections https://www.kerafast.com/Search?SearchTerm="$1" KYinno KYinno cell lines https://www.kyinno.com/ Cell line collections https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf LiGeA Cancer cell LInes GEne fusions portAl http://hpc-bioinformatics.cineca.it/fusion/main Polymorphism and mutation databases http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1 LIMORE Liver Cancer Model Repository https://www.picb.ac.cn/limore/home Cell line databases/resources https://www.picb.ac.cn/limore/cellLines/single?para=$1 LINCS_HMS Harvard Medical School (HMS) LINCS Center http://lincs.hms.harvard.edu/db/cells/ Cell line databases/resources http://lincs.hms.harvard.edu/db/cells/$1 LINCS_LDP LINCS Data Portal http://lincsportal.ccs.miami.edu/cells/ Cell line databases/resources http://lincsportal.ccs.miami.edu/cells/#/view/$1 -Lonza Lonza Cell and Transfection Database https://knowledge.lonza.com Cell line databases/resources https://knowledge.lonza.com/cell?id=$1 MCCL Molecular Connection Cell Line ontology https://bioportal.bioontology.org/ontologies/MCCL Ontologies Millipore Merck Millipore (EMD Millipore) https://www.merckmillipore.com/ Cell line collections https://www.merckmillipore.com/catalogue/item/$1 NCBI_Iran National Cell Bank of Iran http://en.pasteur.ac.ir/pages.aspx?id=823 Cell line collections @@ -56,4 +46,3 @@ TCB Tick Cell Biobank https://www.pirbright.ac.uk/tick-cell-lines-views-page Cel TNGB Telethon Network of Genetic Biobanks http://biobanknetwork.telethon.it/ Cell line collections http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 TOKU-E TOKU-E Cell-culture Database http://cell-lines.toku-e.com Cell line databases/resources http://cell-lines.toku-e.com/Cell-Lines_$1.html WiCell WiCell Research Institute Cell Collection https://www.wicell.org Cell line collections https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true -Ximbio Ximbio reagents online portal https://ximbio.com Cell line collections https://ximbio.com/reagent/$1 From 5b0e3f089a779830a2abc02d42961b2073a3e1c6 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:53:30 -0500 Subject: [PATCH 08/57] Skip cellosaurus entries with no format uri --- src/bioregistry/external/cellosaurus.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/bioregistry/external/cellosaurus.py b/src/bioregistry/external/cellosaurus.py index a80159684..0aefeef2e 100644 --- a/src/bioregistry/external/cellosaurus.py +++ b/src/bioregistry/external/cellosaurus.py @@ -56,6 +56,8 @@ def get_cellosaurus(force_download: bool = False): if value is None: continue d[key] = value + if URI_FORMAT_KEY not in d: + continue rv[d.pop("prefix")] = d with PROCESSED_PATH.open("w") as file: From 198a4193f02686101f7e57182fa67cc6c8df264d Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:53:35 -0500 Subject: [PATCH 09/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 1 + 1 file changed, 1 insertion(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 02e56df25..5e915e39f 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -22782,6 +22782,7 @@ }, "lincs.cell": { "mappings": { + "cellosaurus": "lincs_hms", "miriam": "lincs.cell", "n2t": "lincs.cell", "prefixcommons": "LINCS.CELL" From 20c84d558e4c5b4424e48f8a24b692961d520d17 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:53:43 -0500 Subject: [PATCH 10/57] Update cellosaurus.py --- src/bioregistry/align/cellosaurus.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/bioregistry/align/cellosaurus.py b/src/bioregistry/align/cellosaurus.py index 8e91e79ce..9b0af446b 100644 --- a/src/bioregistry/align/cellosaurus.py +++ b/src/bioregistry/align/cellosaurus.py @@ -24,6 +24,7 @@ def get_skip(self) -> Mapping[str, str]: """Get the skipped Cellosaurus identifiers.""" return { "Biosample": "", + "Biosamples": "", "CCRID": "not in english", "CCTCC": "dead site", "CCLV": "stub website, URL dead", From 30b3c2577285c260fcf9d3e799c9fbb8dc2d3610 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:54:59 -0500 Subject: [PATCH 11/57] Update utils.py --- src/bioregistry/align/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/bioregistry/align/utils.py b/src/bioregistry/align/utils.py index 06baa76e5..b30002695 100644 --- a/src/bioregistry/align/utils.py +++ b/src/bioregistry/align/utils.py @@ -11,7 +11,7 @@ from ..data import EXTERNAL from ..resource_manager import Manager from ..schema import Resource -from ..utils import is_mismatch, read_metaregistry +from ..utils import is_mismatch, norm, read_metaregistry __all__ = [ "Aligner", @@ -77,7 +77,7 @@ def _align(self): # add the identifier from an external resource if it's been marked as high quality if bioregistry_id is None and self.include_new: - bioregistry_id = external_id + bioregistry_id = norm(external_id) self.internal_registry[bioregistry_id] = Resource() if bioregistry_id is not None: # a match was found From da0a80629879478aceea769141c2bf43aac3b6ba Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 10:55:20 -0500 Subject: [PATCH 12/57] Update processed data --- .../data/external/cellosaurus/curation.tsv | 12 --- .../data/external/cellosaurus/processed.json | 85 ------------------- 2 files changed, 97 deletions(-) diff --git a/src/bioregistry/data/external/cellosaurus/curation.tsv b/src/bioregistry/data/external/cellosaurus/curation.tsv index 2ab0142fe..8e9f39868 100644 --- a/src/bioregistry/data/external/cellosaurus/curation.tsv +++ b/src/bioregistry/data/external/cellosaurus/curation.tsv @@ -12,35 +12,23 @@ Cosmic-CLP COSMIC Cell lines Project https://cancer.sanger.ac.uk/cell_lines Cell DGRC Drosophila Genomics Resource Center https://dgrc.bio.indiana.edu/cells/Catalog Cell line collections https://dgrc.bio.indiana.edu/product/View?product=$1 DiscoverX DiscoverX cell line products https://www.discoverx.com/products-applications/cell-lines Cell line collections https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact EBiSC European Bank for induced pluripotent Stem Cells https://www.ebisc.org Cell line collections https://cells.ebisc.org/$1 -FCDI FujiFilm Cellular Dynamics, Inc https://fujifilmcdi.com/the-cirm-ipsc-bank Cell line collections HipSci Human Induced Pluripotent Stem Cells Initiative http://www.hipsci.org Cell line databases/resources http://www.hipsci.org/lines/#/lines/$1 HIVReagentProgram NIH HIV Reagent Program https://www.hivreagentprogram.org/Home.aspx Cell line collections https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx Horizon_Discovery Horizon Discovery cell line collection https://horizondiscovery.com/ Cell line collections https://horizondiscovery.com/en/search?searchterm=$1 -IARC_TP53 IARC TP53 Database http://p53.iarc.fr/CellLines.aspx Polymorphism and mutation databases -IBRC Iranian Biological Research Center cell line collection http://www.en.ibrc.ir/ Cell line collections ICLC Interlab Cell Line Collection http://www.iclc.it Cell line collections http://www.iclc.it/details/det_list.php?line_id=$1 IGRhCellID Integrated Genomic Resources of human Cell Lines for Identification http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi Cell line databases/resources http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1 IGSR International Genome Sample Resource https://www.internationalgenome.org/ Biological sample resources https://www.internationalgenome.org/data-portal/sample/$1 Imanis Imanis Life Sciences cell line products https://www.imanislife.com/collections/cell-lines/ Cell line collections https://www.imanislife.com/?s=$1 -ISCR International Stem Cell Registry https://www.umassmed.edu/iscr/ Cell line databases/resources -IZSLER Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna biobank http://www.ibvr.org/Services/CellCultures.aspx Cell line collections -KCB Kunming Cell Bank of Type Culture Collection http://www.kmcellbank.com/ Cell line collections Kerafast Kerafast cell lines https://www.kerafast.com/ Cell line collections https://www.kerafast.com/Search?SearchTerm="$1" KYinno KYinno cell lines https://www.kyinno.com/ Cell line collections https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf LiGeA Cancer cell LInes GEne fusions portAl http://hpc-bioinformatics.cineca.it/fusion/main Polymorphism and mutation databases http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1 LIMORE Liver Cancer Model Repository https://www.picb.ac.cn/limore/home Cell line databases/resources https://www.picb.ac.cn/limore/cellLines/single?para=$1 LINCS_HMS Harvard Medical School (HMS) LINCS Center http://lincs.hms.harvard.edu/db/cells/ Cell line databases/resources http://lincs.hms.harvard.edu/db/cells/$1 LINCS_LDP LINCS Data Portal http://lincsportal.ccs.miami.edu/cells/ Cell line databases/resources http://lincsportal.ccs.miami.edu/cells/#/view/$1 -MCCL Molecular Connection Cell Line ontology https://bioportal.bioontology.org/ontologies/MCCL Ontologies Millipore Merck Millipore (EMD Millipore) https://www.merckmillipore.com/ Cell line collections https://www.merckmillipore.com/catalogue/item/$1 -NCBI_Iran National Cell Bank of Iran http://en.pasteur.ac.ir/pages.aspx?id=823 Cell line collections -NCI-DTP NCI Development Therapeutics Program https://dtp.cancer.gov/repositories/ Cell line collections NHCDR NINDS Human Cell and Data Repository https://stemcells.nindsgenetics.org Cell line collections https://stemcells.nindsgenetics.org?line=$1 -NISES National Institute of Sericultural and Entomological Science Cell Database https://web.archive.org/web/20160709065305/https://www.gene.affrc.go.jp/ex-nises/NISESCells/CellindexE1.html Cell line collections PerkinElmer PerkinElmer cell line collection https://www.perkinelmer.com/ Cell line collections https://www.perkinelmer.com/searchresult?searchName=$1 Progenetix Cancer genome data @ progenetix.org https://progenetix.org/ Polymorphism and mutation databases https://progenetix.org/biosamples/by-curie/cellosaurus:$1 -RSCB Royan Stem Cell Bank http://www.royaninstitute.org/cmsen/index.php?option=com_content&task=view&id=205&Itemid=40 Cell line collections -SKY/M-FISH/CGH SKY/M-FISH and CGH database https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd136/ Cell line databases/resources SLKBase SUM Breast Cancer Cell Line Knowledge Base https://sumlineknowledgebase.com/ Cell line databases/resources https://sumlineknowledgebase.com/?page_id=$1 TCB Tick Cell Biobank https://www.pirbright.ac.uk/tick-cell-lines-views-page Cell line collections https://www.pirbright.ac.uk/node/$1 TNGB Telethon Network of Genetic Biobanks http://biobanknetwork.telethon.it/ Cell line collections http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 diff --git a/src/bioregistry/data/external/cellosaurus/processed.json b/src/bioregistry/data/external/cellosaurus/processed.json index 67642615f..026e6ba81 100644 --- a/src/bioregistry/data/external/cellosaurus/processed.json +++ b/src/bioregistry/data/external/cellosaurus/processed.json @@ -89,22 +89,12 @@ "name": "Cancer Cell Line Encyclopedia", "uri_format": "https://portals.broadinstitute.org/ccle/page?cell_line=$1" }, - "CCLV": { - "category": "Cell line collections", - "homepage": "https://www.fli.de/en/services/collection-of-cell-lines-in-veterinary-medicine-cclv/", - "name": "Collection of Cell Lines in Veterinary Medicine" - }, "CCRID": { "category": "Cell line databases/resources", "homepage": "http://cellresource.cn/", "name": "Chinese Cell Resource Information Database", "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" }, - "CCTCC": { - "category": "Cell line collections", - "homepage": "http://www.cctcc.org/", - "name": "China Center for Type Culture Collection" - }, "CGH-DB": { "category": "Cell line databases/resources", "homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp", @@ -261,11 +251,6 @@ "name": "European Searchable Tumour Line Database", "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1" }, - "FCDI": { - "category": "Cell line collections", - "homepage": "https://fujifilmcdi.com/the-cirm-ipsc-bank", - "name": "FujiFilm Cellular Dynamics, Inc" - }, "FCS-free": { "category": "Cell line databases/resources", "homepage": "https://fcs-free.org/", @@ -314,16 +299,6 @@ "name": "Horizon Discovery cell line collection", "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" }, - "IARC_TP53": { - "category": "Polymorphism and mutation databases", - "homepage": "http://p53.iarc.fr/CellLines.aspx", - "name": "IARC TP53 Database" - }, - "IBRC": { - "category": "Cell line collections", - "homepage": "http://www.en.ibrc.ir/", - "name": "Iranian Biological Research Center cell line collection" - }, "ICLC": { "category": "Cell line collections", "homepage": "http://www.iclc.it", @@ -342,27 +317,12 @@ "name": "International Genome Sample Resource", "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" }, - "IHW": { - "category": "Cell line databases/resources", - "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", - "name": "International Histocompatibility Workshop cell lines" - }, "IPD-IMGT/HLA": { "category": "Cell line databases/resources", "homepage": "https://www.ebi.ac.uk/ipd/imgt/hla/", "name": "IPD-IMGT/HLA database", "uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/fetch_cell.cgi?$1" }, - "ISCR": { - "category": "Cell line databases/resources", - "homepage": "https://www.umassmed.edu/iscr/", - "name": "International Stem Cell Registry" - }, - "IZSLER": { - "category": "Cell line collections", - "homepage": "http://www.ibvr.org/Services/CellCultures.aspx", - "name": "Istituto Zooprofilattico Sperimentale della Lombardia e dell\u0092Emilia Romagna biobank" - }, "Imanis": { "category": "Cell line collections", "homepage": "https://www.imanislife.com/collections/cell-lines/", @@ -375,11 +335,6 @@ "name": "Japanese Collection of Research Bioresources Cell Bank", "uri_format": "http://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1" }, - "KCB": { - "category": "Cell line collections", - "homepage": "http://www.kmcellbank.com/", - "name": "Kunming Cell Bank of Type Culture Collection" - }, "KCLB": { "category": "Cell line collections", "homepage": "https://cellbank.snu.ac.kr/main/index.html", @@ -428,11 +383,6 @@ "name": "Lonza Cell and Transfection Database", "uri_format": "https://knowledge.lonza.com/cell?id=$1" }, - "MCCL": { - "category": "Ontologies", - "homepage": "https://bioportal.bioontology.org/ontologies/MCCL", - "name": "Molecular Connection Cell Line ontology" - }, "MGI": { "category": "Organism-specific databases", "homepage": "http://www.informatics.jax.org", @@ -463,22 +413,12 @@ "name": "Merck Millipore (EMD Millipore)", "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" }, - "NCBI_Iran": { - "category": "Cell line collections", - "homepage": "http://en.pasteur.ac.ir/pages.aspx?id=823", - "name": "National Cell Bank of Iran" - }, "NCBI_TaxID": { "category": "Taxonomy", "homepage": "https://www.ncbi.nlm.nih.gov/taxonomy", "name": "NCBI taxonomy database", "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1&lvl=3" }, - "NCI-DTP": { - "category": "Cell line collections", - "homepage": "https://dtp.cancer.gov/repositories/", - "name": "NCI Development Therapeutics Program" - }, "NCIt": { "category": "Ontologies", "homepage": "https://ncit.nci.nih.gov/ncitbrowser", @@ -491,11 +431,6 @@ "name": "NINDS Human Cell and Data Repository", "uri_format": "https://stemcells.nindsgenetics.org?line=$1" }, - "NISES": { - "category": "Cell line collections", - "homepage": "https://web.archive.org/web/20160709065305/https://www.gene.affrc.go.jp/ex-nises/NISESCells/CellindexE1.html", - "name": "National Institute of Sericultural and Entomological Science Cell Database" - }, "ORDO": { "category": "Ontologies", "homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo", @@ -556,22 +491,12 @@ "name": "Rat Genome Database", "uri_format": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1" }, - "RSCB": { - "category": "Cell line collections", - "homepage": "http://www.royaninstitute.org/cmsen/index.php?option=com_content&task=view&id=205&Itemid=40", - "name": "Royan Stem Cell Bank" - }, "SKIP": { "category": "Cell line databases/resources", "homepage": "https://www.skip.stemcellinformatics.org/en/", "name": "Stemcell Knowledge and Information Portal", "uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1" }, - "SKY/M-FISH/CGH": { - "category": "Cell line databases/resources", - "homepage": "https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd136/", - "name": "SKY/M-FISH and CGH database" - }, "SLKBase": { "category": "Cell line databases/resources", "homepage": "https://sumlineknowledgebase.com/", @@ -631,22 +556,12 @@ "name": "Ximbio reagents online portal", "uri_format": "https://ximbio.com/reagent/$1" }, - "dbMHC": { - "category": "Cell line databases/resources", - "homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/", - "name": "dbMHC database" - }, "dbSNP": { "category": "Polymorphism and mutation databases", "homepage": "https://www.ncbi.nlm.nih.gov/snp/", "name": "Single Nucleotide Polymorphism database", "uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1" }, - "eagle-i": { - "category": "Biological sample resources", - "homepage": "https://www.eagle-i.net/", - "name": "eagle-i resource discovery tool" - }, "hPSCreg": { "category": "Cell line databases/resources", "homepage": "https://hpscreg.eu", From 984f1ca31fd11366b4acffd331d054db2641709a Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 11:03:54 -0500 Subject: [PATCH 13/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 385 ++++++++++++++++++++++++++ 1 file changed, 385 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 5e915e39f..d017ffec5 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -132,6 +132,18 @@ }, "uri_format": "https://web.expasy.org/abcd/ABCD_$1" }, + "abm": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.abmgood.com/Cell-Biology.html", + "name": "Applied Biological Materials cell line products", + "prefix": "ABM", + "uri_format": "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1" + }, + "mappings": { + "cellosaurus": "ABM" + } + }, "abs": { "mappings": { "miriam": "abs", @@ -215,6 +227,18 @@ "uri_format": "http://identifiers.org/aceview.worm/$1" } }, + "addexbio": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.addexbio.com/productshow?id=4", + "name": "AddexBio cell line products", + "prefix": "AddexBio", + "uri_format": "https://www.addexbio.com/productdetail?pid=$1" + }, + "mappings": { + "cellosaurus": "AddexBio" + } + }, "addgene": { "mappings": { "miriam": "addgene", @@ -2330,6 +2354,18 @@ "name": "BCRC Strain Collection Catalog", "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" }, + "bcrj": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "http://bcrj.org.br/celula/bcrj", + "name": "Banco de Celulas do Rio de Janeiro", + "prefix": "BCRJ", + "uri_format": "http://bcrj.org.br/celula/$1" + }, + "mappings": { + "cellosaurus": "BCRJ" + } + }, "bdgp.est": { "has_canonical": "dbest", "mappings": { @@ -5257,6 +5293,30 @@ "uri_format": "http://identifiers.org/cdpd/$1" } }, + "cell_biolabs": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.cellbiolabs.com", + "name": "Cell Biolabs cell line products", + "prefix": "Cell_Biolabs", + "uri_format": "https://www.cellbiolabs.com/search?keywords=$1" + }, + "mappings": { + "cellosaurus": "Cell_Biolabs" + } + }, + "cell_model_passport": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://cellmodelpassports.sanger.ac.uk/", + "name": "Sanger Cell Model Passports", + "prefix": "Cell_Model_Passport", + "uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1" + }, + "mappings": { + "cellosaurus": "Cell_Model_Passport" + } + }, "cellbank.australia": { "cellosaurus": { "category": "Cell line collections", @@ -5512,6 +5572,18 @@ "uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1" } }, + "cghdb": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp", + "name": "CGH Data Base", + "prefix": "CGH-DB", + "uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en" + }, + "mappings": { + "cellosaurus": "CGH-DB" + } + }, "cgnc": { "contributor": { "email": "cthoyt@gmail.com", @@ -6849,6 +6921,18 @@ "prefix": "P2158" } }, + "cls": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.clsgmbh.de", + "name": "Cell Lines Service", + "prefix": "CLS", + "uri_format": "https://www.clsgmbh.de/$1.html" + }, + "mappings": { + "cellosaurus": "CLS" + } + }, "clyh": { "bioportal": { "name": "Clytia hemisphaerica Development and Anatomy Ontology", @@ -7650,6 +7734,18 @@ "name": "MIMIC III Database", "no_own_terms": true }, + "colonatlas": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "http://www.coloncanceratlas.org", + "name": "Colorectal Cancer Atlas", + "prefix": "ColonAtlas", + "uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1" + }, + "mappings": { + "cellosaurus": "ColonAtlas" + } + }, "combine.specifications": { "mappings": { "miriam": "combine.specifications", @@ -8066,6 +8162,18 @@ "name": "COSMIC Cell Lines", "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" }, + "cosmicclp": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://cancer.sanger.ac.uk/cell_lines", + "name": "COSMIC Cell lines Project", + "prefix": "Cosmic-CLP", + "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" + }, + "mappings": { + "cellosaurus": "Cosmic-CLP" + } + }, "covid19": { "bioportal": { "name": "COVID-19 Ontology", @@ -9821,6 +9929,18 @@ "uri_format": "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1" } }, + "dgrc": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://dgrc.bio.indiana.edu/cells/Catalog", + "name": "Drosophila Genomics Resource Center", + "prefix": "DGRC", + "uri_format": "https://dgrc.bio.indiana.edu/product/View?product=$1" + }, + "mappings": { + "cellosaurus": "DGRC" + } + }, "dicom": { "bioportal": { "name": "DICOM Controlled Terminology", @@ -10115,6 +10235,18 @@ "uri_format": "https://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=$1" } }, + "discoverx": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.discoverx.com/products-applications/cell-lines", + "name": "DiscoverX cell line products", + "prefix": "DiscoverX", + "uri_format": "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact" + }, + "mappings": { + "cellosaurus": "DiscoverX" + } + }, "disdriv": { "example": "0000000", "mappings": { @@ -11147,6 +11279,18 @@ "name": "eagle-i", "uri_format": "http://hawaii.eagle-i.net/i/$1" }, + "ebisc": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.ebisc.org", + "name": "European Bank for induced pluripotent Stem Cells", + "prefix": "EBiSC", + "uri_format": "https://cells.ebisc.org/$1" + }, + "mappings": { + "cellosaurus": "EBiSC" + } + }, "ecacc": { "cellosaurus": { "category": "Cell line collections", @@ -18489,6 +18633,30 @@ "uri_format": "http://identifiers.org/hinv.transcript/$1" } }, + "hipsci": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "http://www.hipsci.org", + "name": "Human Induced Pluripotent Stem Cells Initiative", + "prefix": "HipSci", + "uri_format": "http://www.hipsci.org/lines/#/lines/$1" + }, + "mappings": { + "cellosaurus": "HipSci" + } + }, + "hivreagentprogram": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.hivreagentprogram.org/Home.aspx", + "name": "NIH HIV Reagent Program", + "prefix": "HIVReagentProgram", + "uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx" + }, + "mappings": { + "cellosaurus": "HIVReagentProgram" + } + }, "hmdb": { "cheminf": { "description": "Database identifier used by Human Metabolome Database.", @@ -18794,6 +18962,18 @@ "uri_format": "https://www.ncbi.nlm.nih.gov/homologene?term=$1" } }, + "horizon_discovery": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://horizondiscovery.com/", + "name": "Horizon Discovery cell line collection", + "prefix": "Horizon_Discovery", + "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" + }, + "mappings": { + "cellosaurus": "Horizon_Discovery" + } + }, "hovergen": { "homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php", "mappings": { @@ -19718,6 +19898,18 @@ "prefix": "ICEO" } }, + "iclc": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "http://www.iclc.it", + "name": "Interlab Cell Line Collection", + "prefix": "ICLC", + "uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1" + }, + "mappings": { + "cellosaurus": "ICLC" + } + }, "ico": { "bioportal": { "name": "Informed Consent Ontology", @@ -20113,6 +20305,18 @@ "uri_format": "http://purl.obolibrary.org/obo/IEV_$1" } }, + "igrhcellid": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi", + "name": "Integrated Genomic Resources of human Cell Lines for Identification", + "prefix": "IGRhCellID", + "uri_format": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1" + }, + "mappings": { + "cellosaurus": "IGRhCellID" + } + }, "igsn": { "mappings": { "miriam": "igsn", @@ -20139,6 +20343,18 @@ "uri_format": "hdl.handle.net/10273/$1" } }, + "igsr": { + "cellosaurus": { + "category": "Biological sample resources", + "homepage": "https://www.internationalgenome.org/", + "name": "International Genome Sample Resource", + "prefix": "IGSR", + "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" + }, + "mappings": { + "cellosaurus": "IGSR" + } + }, "ihw": { "cellosaurus": { "category": "Cell line databases/resources", @@ -20155,6 +20371,18 @@ "name": "International Histocompatibility Workshop cell lines", "pattern": "^IHW\\d+$" }, + "imanis": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.imanislife.com/collections/cell-lines/", + "name": "Imanis Life Sciences cell line products", + "prefix": "Imanis", + "uri_format": "https://www.imanislife.com/?s=$1" + }, + "mappings": { + "cellosaurus": "Imanis" + } + }, "imdrf": { "contributor": { "email": "cthoyt@gmail.com", @@ -22431,6 +22659,18 @@ "uri_format": "https://www.kegg.jp/entry/$1" } }, + "kerafast": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.kerafast.com/", + "name": "Kerafast cell lines", + "prefix": "Kerafast", + "uri_format": "https://www.kerafast.com/Search?SearchTerm="$1"" + }, + "mappings": { + "cellosaurus": "Kerafast" + } + }, "knapsack": { "mappings": { "miriam": "knapsack", @@ -22494,6 +22734,18 @@ "https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7" ] }, + "kyinno": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.kyinno.com/", + "name": "KYinno cell lines", + "prefix": "KYinno", + "uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf" + }, + "mappings": { + "cellosaurus": "KYinno" + } + }, "labo": { "bioportal": { "name": "clinical LABoratory Ontology", @@ -22780,6 +23032,30 @@ "uri_format": "http://identifiers.org/ligandexpo/$1" } }, + "ligea": { + "cellosaurus": { + "category": "Polymorphism and mutation databases", + "homepage": "http://hpc-bioinformatics.cineca.it/fusion/main", + "name": "Cancer cell LInes GEne fusions portAl", + "prefix": "LiGeA", + "uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1" + }, + "mappings": { + "cellosaurus": "LiGeA" + } + }, + "limore": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://www.picb.ac.cn/limore/home", + "name": "Liver Cancer Model Repository", + "prefix": "LIMORE", + "uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1" + }, + "mappings": { + "cellosaurus": "LIMORE" + } + }, "lincs.cell": { "mappings": { "cellosaurus": "lincs_hms", @@ -25300,6 +25576,18 @@ "uri_format": "http://identifiers.org/microsporidia/$1" } }, + "millipore": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.merckmillipore.com/", + "name": "Merck Millipore (EMD Millipore)", + "prefix": "Millipore", + "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" + }, + "mappings": { + "cellosaurus": "Millipore" + } + }, "mim": { "bioportal": { "name": "Molecular Interaction Map", @@ -28872,6 +29160,18 @@ "uri_format": "http://identifiers.org/ngl/$1" } }, + "nhcdr": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://stemcells.nindsgenetics.org", + "name": "NINDS Human Cell and Data Repository", + "prefix": "NHCDR", + "uri_format": "https://stemcells.nindsgenetics.org?line=$1" + }, + "mappings": { + "cellosaurus": "NHCDR" + } + }, "niaest": { "mappings": { "miriam": "niaest", @@ -33097,6 +33397,18 @@ "uri_format": "http://www.peptideatlas.org/PASS/$1" } }, + "perkinelmer": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.perkinelmer.com/", + "name": "PerkinElmer cell line collection", + "prefix": "PerkinElmer", + "uri_format": "https://www.perkinelmer.com/searchresult?searchName=$1" + }, + "mappings": { + "cellosaurus": "PerkinElmer" + } + }, "peroxibase": { "mappings": { "miriam": "peroxibase", @@ -35199,6 +35511,18 @@ "uri_format": "http://identifiers.org/prodom/$1" } }, + "progenetix": { + "cellosaurus": { + "category": "Polymorphism and mutation databases", + "homepage": "https://progenetix.org/", + "name": "Cancer genome data @ progenetix.org", + "prefix": "Progenetix", + "uri_format": "https://progenetix.org/biosamples/by-curie/cellosaurus:$1" + }, + "mappings": { + "cellosaurus": "Progenetix" + } + }, "proglyc": { "mappings": { "miriam": "proglyc", @@ -39241,6 +39565,18 @@ }, "uri_format": "http://www.w3.org/2004/02/skos/core#$1" }, + "slkbase": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://sumlineknowledgebase.com/", + "name": "SUM Breast Cancer Cell Line Knowledge Base", + "prefix": "SLKBase", + "uri_format": "https://sumlineknowledgebase.com/?page_id=$1" + }, + "mappings": { + "cellosaurus": "SLKBase" + } + }, "smart": { "go": { "homepage": "http://smart.embl-heidelberg.de/", @@ -40927,6 +41263,18 @@ "uri_format": "http://purl.obolibrary.org/obo/TAXRANK_$1" } }, + "tcb": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.pirbright.ac.uk/tick-cell-lines-views-page", + "name": "Tick Cell Biobank", + "prefix": "TCB", + "uri_format": "https://www.pirbright.ac.uk/node/$1" + }, + "mappings": { + "cellosaurus": "TCB" + } + }, "tcdb": { "go": { "homepage": "http://www.tcdb.org/", @@ -41208,6 +41556,18 @@ "pattern": "^\\d+$", "uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html" }, + "tngb": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "http://biobanknetwork.telethon.it/", + "name": "Telethon Network of Genetic Biobanks", + "prefix": "TNGB", + "uri_format": "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1" + }, + "mappings": { + "cellosaurus": "TNGB" + } + }, "to": { "bioportal": { "name": "Plant Trait Ontology", @@ -41259,6 +41619,19 @@ "uri_format": "http://purl.obolibrary.org/obo/TO_$1" } }, + "tokue": { + "deprecated": true, + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "http://cell-lines.toku-e.com", + "name": "TOKU-E Cell-culture Database", + "prefix": "TOKU-E", + "uri_format": "http://cell-lines.toku-e.com/Cell-Lines_$1.html" + }, + "mappings": { + "cellosaurus": "TOKU-E" + } + }, "tol": { "mappings": { "miriam": "tol", @@ -44360,6 +44733,18 @@ "name": "WGS84 Geo Positioning", "uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1" }, + "wicell": { + "cellosaurus": { + "category": "Cell line collections", + "homepage": "https://www.wicell.org", + "name": "WiCell Research Institute Cell Collection", + "prefix": "WiCell", + "uri_format": "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true" + }, + "mappings": { + "cellosaurus": "WiCell" + } + }, "wikidata": { "biolink": { "is_identifiers": false, From 51f3b23342cb966ae6a957c422a6e023ba32f182 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 11:04:32 -0500 Subject: [PATCH 14/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index d017ffec5..a440c27d9 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -41620,7 +41620,6 @@ } }, "tokue": { - "deprecated": true, "cellosaurus": { "category": "Cell line databases/resources", "homepage": "http://cell-lines.toku-e.com", @@ -41628,6 +41627,7 @@ "prefix": "TOKU-E", "uri_format": "http://cell-lines.toku-e.com/Cell-Lines_$1.html" }, + "deprecated": true, "mappings": { "cellosaurus": "TOKU-E" } From cae440e47836dd6406b55caf46e7dfc129144c4a Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 11:04:35 -0500 Subject: [PATCH 15/57] Update curation.tsv --- .../data/external/cellosaurus/curation.tsv | 32 ------------------- 1 file changed, 32 deletions(-) diff --git a/src/bioregistry/data/external/cellosaurus/curation.tsv b/src/bioregistry/data/external/cellosaurus/curation.tsv index 8e9f39868..0b551cc7f 100644 --- a/src/bioregistry/data/external/cellosaurus/curation.tsv +++ b/src/bioregistry/data/external/cellosaurus/curation.tsv @@ -1,36 +1,4 @@ prefix name homepage category uri_format -ABM Applied Biological Materials cell line products https://www.abmgood.com/Cell-Biology.html Cell line collections https://www.abmgood.com/catalogsearch/result/?cat=&q=$1 -AddexBio AddexBio cell line products https://www.addexbio.com/productshow?id=4 Cell line collections https://www.addexbio.com/productdetail?pid=$1 -BCRJ Banco de Celulas do Rio de Janeiro http://bcrj.org.br/celula/bcrj Cell line collections http://bcrj.org.br/celula/$1 BioSamples BioSamples database https://www.ebi.ac.uk/biosamples/ Biological sample resources https://www.ebi.ac.uk/biosamples/samples/$1 -Cell_Biolabs Cell Biolabs cell line products https://www.cellbiolabs.com Cell line collections https://www.cellbiolabs.com/search?keywords=$1 -Cell_Model_Passport Sanger Cell Model Passports https://cellmodelpassports.sanger.ac.uk/ Cell line databases/resources https://cellmodelpassports.sanger.ac.uk/passports/$1 -CGH-DB CGH Data Base http://www.cghtmd.jp/CGHDatabase/index_e.jsp Cell line databases/resources http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en -CLS Cell Lines Service https://www.clsgmbh.de Cell line collections https://www.clsgmbh.de/$1.html -ColonAtlas Colorectal Cancer Atlas http://www.coloncanceratlas.org Cell line databases/resources http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 -Cosmic-CLP COSMIC Cell lines Project https://cancer.sanger.ac.uk/cell_lines Cell line databases/resources https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 -DGRC Drosophila Genomics Resource Center https://dgrc.bio.indiana.edu/cells/Catalog Cell line collections https://dgrc.bio.indiana.edu/product/View?product=$1 -DiscoverX DiscoverX cell line products https://www.discoverx.com/products-applications/cell-lines Cell line collections https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact -EBiSC European Bank for induced pluripotent Stem Cells https://www.ebisc.org Cell line collections https://cells.ebisc.org/$1 -HipSci Human Induced Pluripotent Stem Cells Initiative http://www.hipsci.org Cell line databases/resources http://www.hipsci.org/lines/#/lines/$1 -HIVReagentProgram NIH HIV Reagent Program https://www.hivreagentprogram.org/Home.aspx Cell line collections https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx -Horizon_Discovery Horizon Discovery cell line collection https://horizondiscovery.com/ Cell line collections https://horizondiscovery.com/en/search?searchterm=$1 -ICLC Interlab Cell Line Collection http://www.iclc.it Cell line collections http://www.iclc.it/details/det_list.php?line_id=$1 -IGRhCellID Integrated Genomic Resources of human Cell Lines for Identification http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi Cell line databases/resources http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1 -IGSR International Genome Sample Resource https://www.internationalgenome.org/ Biological sample resources https://www.internationalgenome.org/data-portal/sample/$1 -Imanis Imanis Life Sciences cell line products https://www.imanislife.com/collections/cell-lines/ Cell line collections https://www.imanislife.com/?s=$1 -Kerafast Kerafast cell lines https://www.kerafast.com/ Cell line collections https://www.kerafast.com/Search?SearchTerm="$1" -KYinno KYinno cell lines https://www.kyinno.com/ Cell line collections https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf -LiGeA Cancer cell LInes GEne fusions portAl http://hpc-bioinformatics.cineca.it/fusion/main Polymorphism and mutation databases http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1 -LIMORE Liver Cancer Model Repository https://www.picb.ac.cn/limore/home Cell line databases/resources https://www.picb.ac.cn/limore/cellLines/single?para=$1 LINCS_HMS Harvard Medical School (HMS) LINCS Center http://lincs.hms.harvard.edu/db/cells/ Cell line databases/resources http://lincs.hms.harvard.edu/db/cells/$1 LINCS_LDP LINCS Data Portal http://lincsportal.ccs.miami.edu/cells/ Cell line databases/resources http://lincsportal.ccs.miami.edu/cells/#/view/$1 -Millipore Merck Millipore (EMD Millipore) https://www.merckmillipore.com/ Cell line collections https://www.merckmillipore.com/catalogue/item/$1 -NHCDR NINDS Human Cell and Data Repository https://stemcells.nindsgenetics.org Cell line collections https://stemcells.nindsgenetics.org?line=$1 -PerkinElmer PerkinElmer cell line collection https://www.perkinelmer.com/ Cell line collections https://www.perkinelmer.com/searchresult?searchName=$1 -Progenetix Cancer genome data @ progenetix.org https://progenetix.org/ Polymorphism and mutation databases https://progenetix.org/biosamples/by-curie/cellosaurus:$1 -SLKBase SUM Breast Cancer Cell Line Knowledge Base https://sumlineknowledgebase.com/ Cell line databases/resources https://sumlineknowledgebase.com/?page_id=$1 -TCB Tick Cell Biobank https://www.pirbright.ac.uk/tick-cell-lines-views-page Cell line collections https://www.pirbright.ac.uk/node/$1 -TNGB Telethon Network of Genetic Biobanks http://biobanknetwork.telethon.it/ Cell line collections http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 -TOKU-E TOKU-E Cell-culture Database http://cell-lines.toku-e.com Cell line databases/resources http://cell-lines.toku-e.com/Cell-Lines_$1.html -WiCell WiCell Research Institute Cell Collection https://www.wicell.org Cell line collections https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true From 5631c8253d0cdfc8e4b4f5c7ea6b38e468854f8c Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 11:05:54 -0500 Subject: [PATCH 16/57] Add back filtered missing URI formatter --- .../data/external/cellosaurus/curation.tsv | 12 +++ .../data/external/cellosaurus/processed.json | 85 +++++++++++++++++++ src/bioregistry/external/cellosaurus.py | 4 +- 3 files changed, 99 insertions(+), 2 deletions(-) diff --git a/src/bioregistry/data/external/cellosaurus/curation.tsv b/src/bioregistry/data/external/cellosaurus/curation.tsv index 0b551cc7f..7c8e58059 100644 --- a/src/bioregistry/data/external/cellosaurus/curation.tsv +++ b/src/bioregistry/data/external/cellosaurus/curation.tsv @@ -1,4 +1,16 @@ prefix name homepage category uri_format BioSamples BioSamples database https://www.ebi.ac.uk/biosamples/ Biological sample resources https://www.ebi.ac.uk/biosamples/samples/$1 +FCDI FujiFilm Cellular Dynamics, Inc https://fujifilmcdi.com/the-cirm-ipsc-bank Cell line collections +IARC_TP53 IARC TP53 Database http://p53.iarc.fr/CellLines.aspx Polymorphism and mutation databases +IBRC Iranian Biological Research Center cell line collection http://www.en.ibrc.ir/ Cell line collections +ISCR International Stem Cell Registry https://www.umassmed.edu/iscr/ Cell line databases/resources +IZSLER Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna biobank http://www.ibvr.org/Services/CellCultures.aspx Cell line collections +KCB Kunming Cell Bank of Type Culture Collection http://www.kmcellbank.com/ Cell line collections LINCS_HMS Harvard Medical School (HMS) LINCS Center http://lincs.hms.harvard.edu/db/cells/ Cell line databases/resources http://lincs.hms.harvard.edu/db/cells/$1 LINCS_LDP LINCS Data Portal http://lincsportal.ccs.miami.edu/cells/ Cell line databases/resources http://lincsportal.ccs.miami.edu/cells/#/view/$1 +MCCL Molecular Connection Cell Line ontology https://bioportal.bioontology.org/ontologies/MCCL Ontologies +NCBI_Iran National Cell Bank of Iran http://en.pasteur.ac.ir/pages.aspx?id=823 Cell line collections +NCI-DTP NCI Development Therapeutics Program https://dtp.cancer.gov/repositories/ Cell line collections +NISES National Institute of Sericultural and Entomological Science Cell Database https://web.archive.org/web/20160709065305/https://www.gene.affrc.go.jp/ex-nises/NISESCells/CellindexE1.html Cell line collections +RSCB Royan Stem Cell Bank http://www.royaninstitute.org/cmsen/index.php?option=com_content&task=view&id=205&Itemid=40 Cell line collections +SKY/M-FISH/CGH SKY/M-FISH and CGH database https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd136/ Cell line databases/resources diff --git a/src/bioregistry/data/external/cellosaurus/processed.json b/src/bioregistry/data/external/cellosaurus/processed.json index 026e6ba81..67642615f 100644 --- a/src/bioregistry/data/external/cellosaurus/processed.json +++ b/src/bioregistry/data/external/cellosaurus/processed.json @@ -89,12 +89,22 @@ "name": "Cancer Cell Line Encyclopedia", "uri_format": "https://portals.broadinstitute.org/ccle/page?cell_line=$1" }, + "CCLV": { + "category": "Cell line collections", + "homepage": "https://www.fli.de/en/services/collection-of-cell-lines-in-veterinary-medicine-cclv/", + "name": "Collection of Cell Lines in Veterinary Medicine" + }, "CCRID": { "category": "Cell line databases/resources", "homepage": "http://cellresource.cn/", "name": "Chinese Cell Resource Information Database", "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" }, + "CCTCC": { + "category": "Cell line collections", + "homepage": "http://www.cctcc.org/", + "name": "China Center for Type Culture Collection" + }, "CGH-DB": { "category": "Cell line databases/resources", "homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp", @@ -251,6 +261,11 @@ "name": "European Searchable Tumour Line Database", "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1" }, + "FCDI": { + "category": "Cell line collections", + "homepage": "https://fujifilmcdi.com/the-cirm-ipsc-bank", + "name": "FujiFilm Cellular Dynamics, Inc" + }, "FCS-free": { "category": "Cell line databases/resources", "homepage": "https://fcs-free.org/", @@ -299,6 +314,16 @@ "name": "Horizon Discovery cell line collection", "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" }, + "IARC_TP53": { + "category": "Polymorphism and mutation databases", + "homepage": "http://p53.iarc.fr/CellLines.aspx", + "name": "IARC TP53 Database" + }, + "IBRC": { + "category": "Cell line collections", + "homepage": "http://www.en.ibrc.ir/", + "name": "Iranian Biological Research Center cell line collection" + }, "ICLC": { "category": "Cell line collections", "homepage": "http://www.iclc.it", @@ -317,12 +342,27 @@ "name": "International Genome Sample Resource", "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" }, + "IHW": { + "category": "Cell line databases/resources", + "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", + "name": "International Histocompatibility Workshop cell lines" + }, "IPD-IMGT/HLA": { "category": "Cell line databases/resources", "homepage": "https://www.ebi.ac.uk/ipd/imgt/hla/", "name": "IPD-IMGT/HLA database", "uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/fetch_cell.cgi?$1" }, + "ISCR": { + "category": "Cell line databases/resources", + "homepage": "https://www.umassmed.edu/iscr/", + "name": "International Stem Cell Registry" + }, + "IZSLER": { + "category": "Cell line collections", + "homepage": "http://www.ibvr.org/Services/CellCultures.aspx", + "name": "Istituto Zooprofilattico Sperimentale della Lombardia e dell\u0092Emilia Romagna biobank" + }, "Imanis": { "category": "Cell line collections", "homepage": "https://www.imanislife.com/collections/cell-lines/", @@ -335,6 +375,11 @@ "name": "Japanese Collection of Research Bioresources Cell Bank", "uri_format": "http://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1" }, + "KCB": { + "category": "Cell line collections", + "homepage": "http://www.kmcellbank.com/", + "name": "Kunming Cell Bank of Type Culture Collection" + }, "KCLB": { "category": "Cell line collections", "homepage": "https://cellbank.snu.ac.kr/main/index.html", @@ -383,6 +428,11 @@ "name": "Lonza Cell and Transfection Database", "uri_format": "https://knowledge.lonza.com/cell?id=$1" }, + "MCCL": { + "category": "Ontologies", + "homepage": "https://bioportal.bioontology.org/ontologies/MCCL", + "name": "Molecular Connection Cell Line ontology" + }, "MGI": { "category": "Organism-specific databases", "homepage": "http://www.informatics.jax.org", @@ -413,12 +463,22 @@ "name": "Merck Millipore (EMD Millipore)", "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" }, + "NCBI_Iran": { + "category": "Cell line collections", + "homepage": "http://en.pasteur.ac.ir/pages.aspx?id=823", + "name": "National Cell Bank of Iran" + }, "NCBI_TaxID": { "category": "Taxonomy", "homepage": "https://www.ncbi.nlm.nih.gov/taxonomy", "name": "NCBI taxonomy database", "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1&lvl=3" }, + "NCI-DTP": { + "category": "Cell line collections", + "homepage": "https://dtp.cancer.gov/repositories/", + "name": "NCI Development Therapeutics Program" + }, "NCIt": { "category": "Ontologies", "homepage": "https://ncit.nci.nih.gov/ncitbrowser", @@ -431,6 +491,11 @@ "name": "NINDS Human Cell and Data Repository", "uri_format": "https://stemcells.nindsgenetics.org?line=$1" }, + "NISES": { + "category": "Cell line collections", + "homepage": "https://web.archive.org/web/20160709065305/https://www.gene.affrc.go.jp/ex-nises/NISESCells/CellindexE1.html", + "name": "National Institute of Sericultural and Entomological Science Cell Database" + }, "ORDO": { "category": "Ontologies", "homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo", @@ -491,12 +556,22 @@ "name": "Rat Genome Database", "uri_format": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1" }, + "RSCB": { + "category": "Cell line collections", + "homepage": "http://www.royaninstitute.org/cmsen/index.php?option=com_content&task=view&id=205&Itemid=40", + "name": "Royan Stem Cell Bank" + }, "SKIP": { "category": "Cell line databases/resources", "homepage": "https://www.skip.stemcellinformatics.org/en/", "name": "Stemcell Knowledge and Information Portal", "uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1" }, + "SKY/M-FISH/CGH": { + "category": "Cell line databases/resources", + "homepage": "https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd136/", + "name": "SKY/M-FISH and CGH database" + }, "SLKBase": { "category": "Cell line databases/resources", "homepage": "https://sumlineknowledgebase.com/", @@ -556,12 +631,22 @@ "name": "Ximbio reagents online portal", "uri_format": "https://ximbio.com/reagent/$1" }, + "dbMHC": { + "category": "Cell line databases/resources", + "homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/", + "name": "dbMHC database" + }, "dbSNP": { "category": "Polymorphism and mutation databases", "homepage": "https://www.ncbi.nlm.nih.gov/snp/", "name": "Single Nucleotide Polymorphism database", "uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1" }, + "eagle-i": { + "category": "Biological sample resources", + "homepage": "https://www.eagle-i.net/", + "name": "eagle-i resource discovery tool" + }, "hPSCreg": { "category": "Cell line databases/resources", "homepage": "https://hpscreg.eu", diff --git a/src/bioregistry/external/cellosaurus.py b/src/bioregistry/external/cellosaurus.py index 0aefeef2e..8576e2dc8 100644 --- a/src/bioregistry/external/cellosaurus.py +++ b/src/bioregistry/external/cellosaurus.py @@ -26,7 +26,7 @@ } -def get_cellosaurus(force_download: bool = False): +def get_cellosaurus(force_download: bool = False, keep_missing_uri: bool = True): """Get the Cellosaurus registry.""" if PROCESSED_PATH.exists() and not force_download: with PROCESSED_PATH.open() as file: @@ -56,7 +56,7 @@ def get_cellosaurus(force_download: bool = False): if value is None: continue d[key] = value - if URI_FORMAT_KEY not in d: + if not keep_missing_uri and URI_FORMAT_KEY not in d: continue rv[d.pop("prefix")] = d From a3165b4842551c4d9e37f82f7703683644b9371e Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 11:26:49 -0500 Subject: [PATCH 17/57] Update lincs link --- src/bioregistry/data/bioregistry.json | 9 ++++++++- src/bioregistry/data/external/cellosaurus/curation.tsv | 1 - 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index a440c27d9..8aed02118 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -23057,8 +23057,15 @@ } }, "lincs.cell": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "http://lincsportal.ccs.miami.edu/cells/", + "name": "LINCS Data Portal", + "prefix": "LINCS_LDP", + "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" + }, "mappings": { - "cellosaurus": "lincs_hms", + "cellosaurus": "LINCS_LDP", "miriam": "lincs.cell", "n2t": "lincs.cell", "prefixcommons": "LINCS.CELL" diff --git a/src/bioregistry/data/external/cellosaurus/curation.tsv b/src/bioregistry/data/external/cellosaurus/curation.tsv index 7c8e58059..98f6dc884 100644 --- a/src/bioregistry/data/external/cellosaurus/curation.tsv +++ b/src/bioregistry/data/external/cellosaurus/curation.tsv @@ -7,7 +7,6 @@ ISCR International Stem Cell Registry https://www.umassmed.edu/iscr/ Cell line d IZSLER Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna biobank http://www.ibvr.org/Services/CellCultures.aspx Cell line collections KCB Kunming Cell Bank of Type Culture Collection http://www.kmcellbank.com/ Cell line collections LINCS_HMS Harvard Medical School (HMS) LINCS Center http://lincs.hms.harvard.edu/db/cells/ Cell line databases/resources http://lincs.hms.harvard.edu/db/cells/$1 -LINCS_LDP LINCS Data Portal http://lincsportal.ccs.miami.edu/cells/ Cell line databases/resources http://lincsportal.ccs.miami.edu/cells/#/view/$1 MCCL Molecular Connection Cell Line ontology https://bioportal.bioontology.org/ontologies/MCCL Ontologies NCBI_Iran National Cell Bank of Iran http://en.pasteur.ac.ir/pages.aspx?id=823 Cell line collections NCI-DTP NCI Development Therapeutics Program https://dtp.cancer.gov/repositories/ Cell line collections From 006a8dcc5c931e055dae0866535820b75230af10 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 11:30:02 -0500 Subject: [PATCH 18/57] Update cellosaurus alignment --- src/bioregistry/align/cellosaurus.py | 3 --- src/bioregistry/data/bioregistry.json | 18 +++++++++++++++++- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/src/bioregistry/align/cellosaurus.py b/src/bioregistry/align/cellosaurus.py index 9b0af446b..dd8d2c0be 100644 --- a/src/bioregistry/align/cellosaurus.py +++ b/src/bioregistry/align/cellosaurus.py @@ -23,9 +23,6 @@ class CellosaurusAligner(Aligner): def get_skip(self) -> Mapping[str, str]: """Get the skipped Cellosaurus identifiers.""" return { - "Biosample": "", - "Biosamples": "", - "CCRID": "not in english", "CCTCC": "dead site", "CCLV": "stub website, URL dead", } diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 8aed02118..9c9a2d841 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -3712,6 +3712,9 @@ } ], "sampleId": "SAMEA2397676", + "synonyms": [ + "biosamples" + ], "uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1" }, "n2t": { @@ -5099,6 +5102,13 @@ } }, "ccrid": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "http://cellresource.cn/", + "name": "Chinese Cell Resource Information Database", + "prefix": "CCRID", + "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -5107,6 +5117,9 @@ }, "example": "4201PAT-CCTCC00348", "homepage": "http://www.cellresource.cn", + "mappings": { + "cellosaurus": "CCRID" + }, "name": "National Experimental Cell Resource Sharing Platform", "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" }, @@ -23098,7 +23111,10 @@ "is_obo": false, "prefix": "LINCS.CELL", "uri_format": "http://identifiers.org/lincs.cell/$1" - } + }, + "synonyms": [ + "LINCS_LDP" + ] }, "lincs.data": { "mappings": { From 19f909f6b09fef4c66c29f0009d23d4a1e4c71ef Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 11:51:55 -0500 Subject: [PATCH 19/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 9c9a2d841..9a31283ff 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -3712,9 +3712,6 @@ } ], "sampleId": "SAMEA2397676", - "synonyms": [ - "biosamples" - ], "uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1" }, "n2t": { @@ -3732,7 +3729,10 @@ "is_obo": false, "prefix": "BIOSAMPLE", "uri_format": "http://identifiers.org/biosample/$1" - } + }, + "synonyms": [ + "biosamples" + ] }, "biosimulations": { "mappings": { From 5013827c47c93f8e5962c9de2df18a69366518d9 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 12:03:48 -0500 Subject: [PATCH 20/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 46a21f4a0..3b8b04348 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -8294,6 +8294,10 @@ "prefix": "gro" } }, + "credit": { + "homepage": "https://casrai.org/credit/", + "name": "CASRAI Contributor Roles Taxonomy" + }, "crisprdb": { "mappings": { "miriam": "crisprdb", @@ -39811,7 +39815,9 @@ "SNOMEDCTCT_2019_03_01", "SNOMEDCT_US_2019_09_01", "SNOMEDCT_US_2020_03_01", - "SNOMEDCT_US_2020_09_01" + "SNOMEDCT_US_2020_09_01", + "SNOMEDCT_US_2021_03_01", + "SNOMEDCT_US_2021_09_01" ], "wikidata": { "database": "Q1753883", From 277a0d627c42078cf74c23b7f804f6f9265f4fba Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 12:38:49 -0500 Subject: [PATCH 21/57] Add NPO --- src/bioregistry/data/bioregistry.json | 14 ++++++++++++++ .../data/external/bioportal/curation.tsv | 1 - 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 3b8b04348..8cccb9ebf 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -29702,6 +29702,20 @@ "name": "Natural Product Activity and Species Source Database", "pattern": "^NPC\\d+$" }, + "npo": { + "bioportal": { + "name": "NanoParticle Ontology", + "prefix": "NPO" + }, + "example": "1731", + "mappings": { + "bioportal": "NPO" + }, + "name": "NanoParticle Ontology", + "contact": { + "name":"Nathan Baker", "email": "nathan.baker@pnl.gov" + } + }, "nuclearbd": { "mappings": { "miriam": "nuclearbd", diff --git a/src/bioregistry/data/external/bioportal/curation.tsv b/src/bioregistry/data/external/bioportal/curation.tsv index 65deaa0b6..e6e20b305 100644 --- a/src/bioregistry/data/external/bioportal/curation.tsv +++ b/src/bioregistry/data/external/bioportal/curation.tsv @@ -418,7 +418,6 @@ NMOBR NeuroMorpho.Org brain region ontologies NMOSP NeuroMorpho.Org species ontology NONRCTO Non-Randomized Controlled Trials Ontology NPI Non-Pharmacological Interventions (NPIs) -NPO NanoParticle Ontology NPOKB Neuron Phenotype Ontology NTIY nexus_test NXDX Test NXDX From 9ae306f0aba5aab89a83c2a35a964e73079f437b Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:37:41 -0500 Subject: [PATCH 22/57] Add FTT (used in ENVO) References https://github.com/EnvironmentOntology/envo/issues/1130 --- src/bioregistry/data/bioregistry.json | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 8cccb9ebf..0db41c5cc 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -14958,6 +14958,16 @@ "uri_format": "http://identifiers.org/fsnp/$1" } }, + "ftt": { + "example": "273", + "homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3", + "name": "Feature Type Thesaurus", + "references": [ + "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200", + "https://github.com/EnvironmentOntology/envo/issues/1130" + ], + "uri_format": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1" + }, "funcbase.fly": { "mappings": { "miriam": "funcbase.fly", From 7ac656259861d2f55e1a341b9dffc6eb6e268faf Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:38:13 -0500 Subject: [PATCH 23/57] Add GeoNames (used in ENVO) --- src/bioregistry/data/bioregistry.json | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 0db41c5cc..c1b17d92d 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -16191,6 +16191,17 @@ }, "uri_format": "http://purl.obolibrary.org/obo/GEO_$1" }, + "geonames": { + "description": "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.", + "example": "ADM1", + "homepage": "https://www.geonames.org", + "name": "GeoNames", + "synonyms": [ + "Geomames", + "Geonamaes" + ], + "uri_format": "https://www.geonames.org/recent-changes/featurecode/$1/" + }, "gexo": { "bioportal": { "name": "Gene Expression Ontology", From bfe1e654a777ff9f970daa822a59c83a616f44df Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:38:21 -0500 Subject: [PATCH 24/57] Add GEMET (used in ENVO) --- src/bioregistry/data/bioregistry.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index c1b17d92d..c96c843d1 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -15592,6 +15592,12 @@ "prefix": "GECKO" } }, + "gemet": { + "example": "627", + "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", + "name": "General Multilingual Environmental Thesaurus", + "uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1" + }, "genatlas": { "mappings": { "miriam": "genatlas", From 394e9298d85637719af6644323ca26edf7dba1bd Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:38:29 -0500 Subject: [PATCH 25/57] Add LTER (used in ENVO) --- src/bioregistry/data/bioregistry.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index c96c843d1..6df8774ec 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -23583,6 +23583,12 @@ "pattern": "^\\d+$", "uri_format": "https://labsyspharm.github.io/lspci/$1" }, + "lter": { + "example": "182", + "homepage": "https://vocab.lternet.edu/vocab/vocab/index.php", + "name": "Long Term Ecological Research Controlled Vocabulary", + "uri_format": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1" + }, "ma": { "bioportal": { "name": "Mouse Adult Gross Anatomy Ontology", From 9be766d43e2bca0abf0cbd21f0a3ab7f53117650 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:38:37 -0500 Subject: [PATCH 26/57] Reformat --- src/bioregistry/data/bioregistry.json | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 6df8774ec..70fcd7853 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -29740,14 +29740,15 @@ "name": "NanoParticle Ontology", "prefix": "NPO" }, + "contact": { + "email": "nathan.baker@pnl.gov", + "name": "Nathan Baker" + }, "example": "1731", "mappings": { "bioportal": "NPO" }, - "name": "NanoParticle Ontology", - "contact": { - "name":"Nathan Baker", "email": "nathan.baker@pnl.gov" - } + "name": "NanoParticle Ontology" }, "nuclearbd": { "mappings": { From 7e118fad2b27188e45f1e8a1afc43331ac4c1125 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:38:56 -0500 Subject: [PATCH 27/57] Add CMECS (used in ENVO) --- src/bioregistry/data/bioregistry.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 70fcd7853..e98f6b599 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -6990,6 +6990,11 @@ "prefix": "CLYH" } }, + "cmecs": { + "example": "595", + "name": "Costal and Marine Ecological Classification Standard", + "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" + }, "cmf": { "deprecated": true, "description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain", From e06dc84b8ff82b4fbfd721954ac1b538aeca434c Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:39:04 -0500 Subject: [PATCH 28/57] Add ExoLexicon (used in ENVO) --- src/bioregistry/data/bioregistry.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index e98f6b599..aa9019c97 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -11747,6 +11747,12 @@ "uri_format": "http://ecogene.org/gene/$1" } }, + "ecolexicon": { + "comment": "No resolution - everything is in a single page app", + "example": "canal", + "homepage": "http://ecolexicon.ugr.es/en/index.htm", + "name": "EcoLexicon" + }, "ecoliwiki": { "go": { "description": "EcoliHub\\'s subsystem for community annotation of E. coli K-12", From 3b2c21e15f0f77487687bfc5fd2e80e0304f76c6 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:39:11 -0500 Subject: [PATCH 29/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index aa9019c97..11a5d5b64 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -13137,6 +13137,7 @@ "name": "Environment Ontology for Livestock", "prefix": "EOL" }, + "download_owl": "https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl", "example": "0001927", "mappings": { "bioportal": "EOL", @@ -13222,6 +13223,7 @@ "name": "Early Pregnancy Ontology", "prefix": "EPO" }, + "download_owl": "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl", "mappings": { "bioportal": "EPO", "obofoundry": "epo", From 829abe76596e1695be6006896b0b980cea1b8045 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:39:31 -0500 Subject: [PATCH 30/57] Add SWEET Ontology (used in ENVO) --- src/bioregistry/data/bioregistry.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 11a5d5b64..6fff07c1c 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -40688,6 +40688,10 @@ "uri_format": "https://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1" } }, + "sweetrealm": { + "download_obo": "https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo", + "name": "SWEET Ontology" + }, "swh": { "banana": "swh", "mappings": { From 33fed1d547acfa30b104126e57e02ce4d3ae9cf6 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 17:40:41 -0500 Subject: [PATCH 31/57] Add synonym for WWF (for ENVO) --- src/bioregistry/data/bioregistry.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 6fff07c1c..8dcecfb58 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -45308,6 +45308,9 @@ "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, + "synonyms": [ + "WWF" + ], "uri_format": "https://www.worldwildlife.org/ecoregions/$1", "wikidata": { "database": "Q929975", From ea7c17c6d5c6b1385f5f0a81620fef77151058cd Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 19:19:58 -0500 Subject: [PATCH 32/57] Update SABIO-RK for GO --- src/bioregistry/data/bioregistry.json | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 8dcecfb58..5698eff5b 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -38399,7 +38399,11 @@ "is_obo": false, "prefix": "SABIORK.REACTION", "uri_format": "http://identifiers.org/sabiork.reaction/$1" - } + }, + "synonyms": [ + "SABIO-RK" + ], + "uri_format": "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1" }, "sael": { "contributor": { From 854e155f3253f21f3a254367fd6b7cc6c1421f06 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 19:20:03 -0500 Subject: [PATCH 33/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 5698eff5b..1d22410c1 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -38321,7 +38321,8 @@ "is_obo": false, "prefix": "SABIORK.EC", "uri_format": "http://identifiers.org/sabiork.ec/$1" - } + }, + "provides": "eccode" }, "sabiork.kineticrecord": { "go": { From 41266aaa88c712c79106f2a1ef7e3ec2cfdd651e Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 19:20:17 -0500 Subject: [PATCH 34/57] Add FlyBrain Neuron Database --- src/bioregistry/data/bioregistry.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 1d22410c1..22556ab44 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -14562,6 +14562,12 @@ "uri_format": "http://flybase.org/reports/$1" } }, + "flybrain.ndb": { + "example": "10531", + "homepage": "https://flybrain-ndb.virtualflybrain.org", + "name": "FlyBrain Neuron Database", + "uri_format": "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html" + }, "fma": { "bioportal": { "name": "Foundational Model of Anatomy", From 69968514734bc907ac141220a1828014222340a0 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 20:07:12 -0500 Subject: [PATCH 35/57] Add VSP (for MAXO) --- src/bioregistry/data/bioregistry.json | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 22556ab44..7208b591c 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -44452,6 +44452,15 @@ "name": "Veterinary Substances DataBase", "uri_format": "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm" }, + "vso": { + "bioportal": { + "name": "Vital Sign Ontology", + "prefix": "VSO" + }, + "mappings": { + "bioportal": "VSO" + } + }, "vt": { "bioportal": { "name": "Vertebrate Trait Ontology", From 9f1e01083a9755b3cf040d3f6479de0687147240 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 20:07:23 -0500 Subject: [PATCH 36/57] Add inhand (for HPATH) --- src/bioregistry/data/bioregistry.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 7208b591c..43643cda8 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -20822,6 +20822,12 @@ "prefix": "P235" } }, + "inhand": { + "comment": "This nomenclature is available via email. Truly a disgrace.", + "homepage": "https://www.goreni.org/gr3_nomenclature.php", + "name": "The International Harmonization of Nomenclature and Diagnostic criteria", + "proprietary": true + }, "inn": { "comment": "can not find a place to resolve to", "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", From f7af6ff0026f6ee27c3440d8a38b8ec932094ead Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 20:07:30 -0500 Subject: [PATCH 37/57] Add synonym for HPATH --- src/bioregistry/data/bioregistry.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 43643cda8..801d5334b 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -19226,7 +19226,10 @@ "name": "Histopathology Ontology", "prefix": "hpath", "version": "2019-07-05" - } + }, + "synonyms": [ + "MC" + ] }, "hpm.peptide": { "mappings": { From 73b04587debc26e2afada1f954b6aba1b43cd01f Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 20:07:38 -0500 Subject: [PATCH 38/57] Add NCBI book (for MAXO) --- src/bioregistry/data/bioregistry.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 801d5334b..d20661c3e 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -28308,6 +28308,10 @@ "name": "NCATS Drugs", "uri_format": "https://drugs.ncats.io/drug/$1" }, + "ncbibook": { + "example": "NBK331", + "uri_format": "https://www.ncbi.nlm.nih.gov/books/$1" + }, "ncbigene": { "biolink": { "is_identifiers": true, From ec4457022377747b78263aa6970a35e17fe7ffe7 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 1 Dec 2021 20:07:55 -0500 Subject: [PATCH 39/57] Update curation.tsv --- src/bioregistry/data/external/bioportal/curation.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/src/bioregistry/data/external/bioportal/curation.tsv b/src/bioregistry/data/external/bioportal/curation.tsv index e6e20b305..bdfd30e07 100644 --- a/src/bioregistry/data/external/bioportal/curation.tsv +++ b/src/bioregistry/data/external/bioportal/curation.tsv @@ -636,7 +636,6 @@ VODANAKENYA VODANA KENYA VODANAMFLCODE VODANAFACILITIESLIST VODANAUGANDA VODANAUGANDA VODANETHIOPIA_OR ETHIOPIA_OUTPATIENT -VSO Vital Sign Ontology WC Whole-cell modeling ontology WEAR WEAR: Wind Energy mAteRials Taxonomy WEAVE WEAVE: Wind Energy ActiVitiEs From 189a9bb662c7a0ab58c7ded40ddd2496ff9f2735 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 2 Dec 2021 08:53:22 -0500 Subject: [PATCH 40/57] Collapse cosmicclp inco cosmic.cell --- src/bioregistry/data/bioregistry.json | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index d20661c3e..b997be0f0 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -8178,9 +8178,7 @@ "example": "906801", "homepage": "https://cancer.sanger.ac.uk/cell_lines/", "name": "COSMIC Cell Lines", - "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" - }, - "cosmicclp": { + "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1", "cellosaurus": { "category": "Cell line databases/resources", "homepage": "https://cancer.sanger.ac.uk/cell_lines", @@ -41582,6 +41580,12 @@ "uri_format": "http://purl.obolibrary.org/obo/TGMA_$1" } }, + "tgn": { + "deprecated": true, + "references": [ + "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200" + ] + }, "th": { "contributor": { "email": "cthoyt@gmail.com", From ed2b2cfc48bcc9054de77ab7e8a0e2917298ecbc Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 2 Dec 2021 14:00:44 -0500 Subject: [PATCH 41/57] Add REO information Big thanks to James for pointing this out! Co-Authored-By: James A. Overton --- src/bioregistry/data/bioregistry.json | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index b997be0f0..3da6456d2 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -37105,6 +37105,22 @@ "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" } }, + "reo": { + "comment": "From James O.: It was an ontology for \"reagents\" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.", + "contact": { + "email": "matt@tislab.org", + "github": "mbrush", + "name": "Matthew Brush" + }, + "example": "0000079", + "homepage": "https://github.com/tis-lab/reagent-ontology", + "name": "Reagent Ontology", + "references": [ + "https://github.com/obi-ontology/obi/issues/1015", + "https://code.google.com/archive/p/reagent-ontology/", + "https://github.com/obi-ontology/obi/issues/1135" + ] + }, "repeatsdb.protein": { "mappings": { "miriam": "repeatsdb.protein" From b9a3a24743c508ea280d31cc170bf917465a2541 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 2 Dec 2021 14:03:50 -0500 Subject: [PATCH 42/57] Merge cosmicclp and cosmic.cell --- src/bioregistry/data/bioregistry.json | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 3da6456d2..e72c392b1 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -8169,6 +8169,13 @@ } }, "cosmic.cell": { + "cellosaurus": { + "category": "Cell line databases/resources", + "homepage": "https://cancer.sanger.ac.uk/cell_lines", + "name": "COSMIC Cell lines Project", + "prefix": "Cosmic-CLP", + "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" + }, "contributor": { "email": "cthoyt@gmail.com", "name": "Charles Tapley Hoyt", @@ -8177,18 +8184,11 @@ "description": "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer", "example": "906801", "homepage": "https://cancer.sanger.ac.uk/cell_lines/", - "name": "COSMIC Cell Lines", - "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1", - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "https://cancer.sanger.ac.uk/cell_lines", - "name": "COSMIC Cell lines Project", - "prefix": "Cosmic-CLP", - "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" - }, "mappings": { "cellosaurus": "Cosmic-CLP" - } + }, + "name": "COSMIC Cell Lines", + "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" }, "covid19": { "bioportal": { From 9b445d06053e33d2a991de7252bec6c0388f5298 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 2 Dec 2021 14:26:21 -0500 Subject: [PATCH 43/57] Update NCRO downloads --- src/bioregistry/data/bioregistry.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index e72c392b1..55a8f10bf 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -28743,6 +28743,8 @@ "name": "Non-coding RNA Ontology", "prefix": "NCRO" }, + "download_obo": "https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo", + "download_owl": "http://purl.obolibrary.org/obo/ncro.owl", "example": "0002927", "mappings": { "bioportal": "NCRO", From 996c60b8a36fffba16463825e8c971b3845e8c32 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 2 Dec 2021 14:27:52 -0500 Subject: [PATCH 44/57] Add GO Chemicals Big thanks to Jim for the help tracking some of this information down Co-Authored-By: Jim Balhoff <210210+balhoff@users.noreply.github.com> --- src/bioregistry/data/bioregistry.json | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 55a8f10bf..ab10192bb 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -16942,6 +16942,21 @@ "prefix": "P686" } }, + "go.chemical": { + "description": "Represent chemical entities having particular CHEBI roles", + "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", + "example": "25512", + "name": "GO Chemicals", + "references": [ + "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", + "https://github.com/geneontology/go-ontology/issues/19535" + ], + "synonyms": [ + "go.chemicals", + "go.chebi", + "goche" + ] + }, "go.model": { "description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.", "example": "5fce9b7300001250", From 279ee932dd56a33faa44df8783daa39dc123152f Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 7 Dec 2021 22:05:54 -0500 Subject: [PATCH 45/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 59 +++++++++++++++++++-------- 1 file changed, 41 insertions(+), 18 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index ab10192bb..9dbd20c7c 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -16942,21 +16942,6 @@ "prefix": "P686" } }, - "go.chemical": { - "description": "Represent chemical entities having particular CHEBI roles", - "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", - "example": "25512", - "name": "GO Chemicals", - "references": [ - "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", - "https://github.com/geneontology/go-ontology/issues/19535" - ], - "synonyms": [ - "go.chemicals", - "go.chebi", - "goche" - ] - }, "go.model": { "description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.", "example": "5fce9b7300001250", @@ -17057,6 +17042,22 @@ "uri_format": "http://identifiers.org/goa/$1" } }, + "goche": { + "description": "Represent chemical entities having particular CHEBI roles", + "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", + "example": "25512", + "name": "GO Chemicals", + "preferred_prefix": "GOCHE", + "references": [ + "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", + "https://github.com/geneontology/go-ontology/issues/19535" + ], + "synonyms": [ + "go.chemicals", + "go.chebi", + "go.chemical" + ] + }, "goeco": { "contributor": { "email": "cthoyt@gmail.com", @@ -23790,7 +23791,10 @@ "is_obo": false, "prefix": "MAIZEGDB.LOCUS", "uri_format": "http://identifiers.org/maizegdb.locus/$1" - } + }, + "synonyms": [ + "MaizeGDB" + ] }, "mamo": { "bioportal": { @@ -30219,6 +30223,11 @@ "uri_format": "http://purl.obolibrary.org/obo/$1" } }, + "oboformat": { + "description": "Related to the OBO in OWL meta-model", + "name": "OBO Format", + "preferred_prefix": "oboFormat" + }, "oboinowl": { "description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties", "download_obo": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo", @@ -30498,7 +30507,9 @@ "name": "Ontology for Genetic Interval", "prefix": "OGI" }, + "deprecated": true, "example": "0000019", + "homepage": "https://code.google.com/archive/p/ontology-for-genetic-interval/", "mappings": { "bioportal": "OGI", "obofoundry": "ogi", @@ -30533,7 +30544,10 @@ "is_obo": true, "prefix": "OGI", "uri_format": "http://purl.obolibrary.org/obo/OGI_$1" - } + }, + "synonyms": [ + "OGI.owl" + ] }, "ogms": { "bioportal": { @@ -31965,6 +31979,7 @@ "prefix": "ORDO", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http://www.orpha.net/ORDO/$1" }, + "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", "mappings": { "biolink": "ORPHA", "bioportal": "ORDO", @@ -32021,7 +32036,9 @@ "name": "Orthology Ontology", "prefix": "ORTH" }, + "download_owl": "https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl", "example": "HomologyRelation", + "homepage": "https://github.com/qfo/OrthologyOntology", "mappings": { "bioportal": "ORTH", "ols": "orth" @@ -36518,7 +36535,7 @@ "name": "Pathway Ontology", "prefix": "PW" }, - "download_obo": "ftp://ftp.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo", + "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo", "example": "0000423", "mappings": { "bioportal": "PW", @@ -42273,6 +42290,12 @@ "database": "Q81661821" } }, + "tuberculist": { + "example": "Rv2879c", + "homepage": "http://genolist.pasteur.fr/TubercuList", + "name": "TubercuList", + "uri_format": "http://genolist.pasteur.fr/TubercuList/genome.cgi?external_query+$1" + }, "txpo": { "bioportal": { "name": "Toxic Process Ontology", From 3276916f340a6333e56b7dcefe6305e70b3013db Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 7 Dec 2021 22:27:36 -0500 Subject: [PATCH 46/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 9dbd20c7c..fa8d83e94 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -8513,7 +8513,8 @@ "synonyms": [ "CRISP Thesaurus, 2006", "CRISP Thesaurus", - "CSP2005" + "CSP2005", + "CRISP" ] }, "cst": { @@ -34020,6 +34021,13 @@ "uri_format": "http://identifiers.org/phenolexplorer/$1" } }, + "phenx": { + "description": "A Web-based catalog of recommended measurement protocols", + "example": "130502", + "homepage": "https://www.phenxtoolkit.org/", + "name": "PhenX Toolkit", + "uri_format": "https://www.phenxtoolkit.org/protocols/view/$1" + }, "phipo": { "bioportal": { "name": "Pathogen Host Interaction Phenotype Ontology", @@ -36894,7 +36902,8 @@ "prefix": "RDO" }, "description": "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.", - "download_obo": "https://ratmine.mcw.edu/ontology/disease/RDO.obo", + "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo", + "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl", "example": "9002859", "homepage": "https://ratmine.mcw.edu/ontology/disease/", "mappings": { @@ -38170,6 +38179,8 @@ "name": "Rat Strain Ontology", "prefix": "RS" }, + "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo", + "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl", "example": "0001807", "mappings": { "bioportal": "RS", From b8a1c70d0852322d02e6997b323472200f23d18f Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 7 Dec 2021 22:32:27 -0500 Subject: [PATCH 47/57] Add apaonto --- src/bioregistry/data/bioregistry.json | 16 ++++++++++++++++ .../data/external/bioportal/curation.tsv | 2 -- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index fa8d83e94..9bff950cf 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -1002,6 +1002,15 @@ "uri_format": "http://identifiers.org/aop.stressor/$1" } }, + "apaonto": { + "bioportal": { + "name": "Psychology Ontology", + "prefix": "APAONTO" + }, + "mappings": { + "bioportal": "APAONTO" + } + }, "apd": { "mappings": { "miriam": "apd", @@ -34022,9 +34031,16 @@ } }, "phenx": { + "bioportal": { + "name": "PhenX Phenotypic Terms", + "prefix": "PHENX" + }, "description": "A Web-based catalog of recommended measurement protocols", "example": "130502", "homepage": "https://www.phenxtoolkit.org/", + "mappings": { + "bioportal": "PHENX" + }, "name": "PhenX Toolkit", "uri_format": "https://www.phenxtoolkit.org/protocols/view/$1" }, diff --git a/src/bioregistry/data/external/bioportal/curation.tsv b/src/bioregistry/data/external/bioportal/curation.tsv index bdfd30e07..aac265707 100644 --- a/src/bioregistry/data/external/bioportal/curation.tsv +++ b/src/bioregistry/data/external/bioportal/curation.tsv @@ -29,7 +29,6 @@ APADISORDERS Disorders cluster APAEDUCLUSTER Educational Cluster APANEUROCLUSTER APA Neuro Cluster APAOCUEMPLOY APA Occupational and Employment cluster -APAONTO Psychology Ontology APASTATISTICAL APA Statistical Cluster APATANDT APA Tests and Testing cluster APATREATMENT APA Treatment Cluster @@ -506,7 +505,6 @@ PGXO PGxO PHAGE Phylogenetics Ontology PHARE Pharmacogenomic Relationships Ontology PHENOMEBLAST PhenomeBLAST Ontology -PHENX PhenX Phenotypic Terms PHFUMIADO Phallusia fumigata Anatomy and Development Ontology PHMAMMADO Phallusia mammillata Anatomy and Development Ontology PHYLONT Phylogenetic Ontology From 007db0acc7e6fa635d0b2d32e7c0e243907538f9 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 11:33:56 -0500 Subject: [PATCH 48/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 9bff950cf..fb5b38dab 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -12042,6 +12042,11 @@ }, "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1" }, + "edda": { + "bioportal": { + "prefix": "EDDA" + } + }, "efo": { "biolink": { "is_identifiers": false, @@ -13752,6 +13757,12 @@ "ExO" ] }, + "fabio": { + "example": "d4e2515", + "homepage": "https://github.com/sparontologies/fabio", + "name": "FaBiO, the FRBR-aligned Bibliographic Ontology", + "uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1" + }, "facebase": { "mappings": { "miriam": "facebase", @@ -23506,6 +23517,9 @@ "bioportal": "LOINC" }, "name": "Logical Observation Identifiers Names and Codes", + "synonyms": [ + "LNC" + ], "uri_format": "https://loinc.org/$1" }, "lonza": { @@ -38876,6 +38890,7 @@ } }, "sdgio": { + "download_owl": "https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl", "example": "00020134", "mappings": { "ols": "sdgio", @@ -38894,7 +38909,10 @@ "library": "Not Specified/No", "name": "Sustainable Development Goals Interface Ontology", "prefix": "SDGIO" - } + }, + "references": [ + "https://github.com/SDG-InterfaceOntology/sdgio/issues/233" + ] }, "sdis": { "contributor": { From 852bcc5c6c11a523f8403eff904b6ec8bbded875 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 13:04:44 -0500 Subject: [PATCH 49/57] Update getters.py --- src/bioregistry/external/getters.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/external/getters.py b/src/bioregistry/external/getters.py index 45a113c0a..794e3c9ad 100644 --- a/src/bioregistry/external/getters.py +++ b/src/bioregistry/external/getters.py @@ -2,6 +2,8 @@ """List of getters.""" +from typing import Callable, List, Tuple + from .biolink import get_biolink # noqa:F401 from .bioportal import get_bioportal # noqa:F401 from .cellosaurus import get_cellosaurus # noqa:F401 @@ -21,7 +23,7 @@ "GETTERS", ] -GETTERS = [ +GETTERS: List[Tuple[str, str, Callable]] = [ ("obofoundry", "OBO", get_obofoundry), ("ols", "OLS", get_ols), ("miriam", "MIRIAM", get_miriam), From 2bc22dd1f857059ca7c0f3646e75949a4a94c033 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 13:14:14 -0500 Subject: [PATCH 50/57] Add examples --- src/bioregistry/data/bioregistry.json | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 061a94c43..b547a786b 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -140,6 +140,7 @@ "prefix": "ABM", "uri_format": "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1" }, + "example": "T0599", "mappings": { "cellosaurus": "ABM" } @@ -235,6 +236,7 @@ "prefix": "AddexBio", "uri_format": "https://www.addexbio.com/productdetail?pid=$1" }, + "example": "C0020004/4992", "mappings": { "cellosaurus": "AddexBio" } @@ -1007,9 +1009,11 @@ "name": "Psychology Ontology", "prefix": "APAONTO" }, + "example": "Abdomen", "mappings": { "bioportal": "APAONTO" - } + }, + "uri_format": "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1" }, "apd": { "mappings": { @@ -2371,6 +2375,7 @@ "prefix": "BCRJ", "uri_format": "http://bcrj.org.br/celula/$1" }, + "example": "0278", "mappings": { "cellosaurus": "BCRJ" } @@ -5323,6 +5328,7 @@ "prefix": "Cell_Biolabs", "uri_format": "https://www.cellbiolabs.com/search?keywords=$1" }, + "example": "AKR-270", "mappings": { "cellosaurus": "Cell_Biolabs" } @@ -5335,6 +5341,7 @@ "prefix": "Cell_Model_Passport", "uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1" }, + "example": "SIDM01262", "mappings": { "cellosaurus": "Cell_Model_Passport" } @@ -5602,6 +5609,7 @@ "prefix": "CGH-DB", "uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en" }, + "example": "300165/p13898_2106T", "mappings": { "cellosaurus": "CGH-DB" } @@ -7769,6 +7777,7 @@ "prefix": "ColonAtlas", "uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1" }, + "example": "ALA", "mappings": { "cellosaurus": "ColonAtlas" } @@ -8307,6 +8316,7 @@ } }, "credit": { + "example": "Software", "homepage": "https://casrai.org/credit/", "name": "CASRAI Contributor Roles Taxonomy" }, @@ -10273,6 +10283,7 @@ "prefix": "DiscoverX", "uri_format": "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact" }, + "example": "95-0166C6", "mappings": { "cellosaurus": "DiscoverX" } @@ -11317,6 +11328,7 @@ "prefix": "EBiSC", "uri_format": "https://cells.ebisc.org/$1" }, + "example": "ESi007-A", "mappings": { "cellosaurus": "EBiSC" } @@ -31446,6 +31458,7 @@ } }, "ontoavida": { + "example": "00000001", "mappings": { "obofoundry": "ontoavida" }, From 261ca938a9d6cc8ec9d0095462a074277ffde789 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 14:19:21 -0500 Subject: [PATCH 51/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 53 +++++++++++++++++++-------- 1 file changed, 37 insertions(+), 16 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index b547a786b..e3d677377 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -9977,6 +9977,7 @@ "prefix": "DGRC", "uri_format": "https://dgrc.bio.indiana.edu/product/View?product=$1" }, + "example": "215", "mappings": { "cellosaurus": "DGRC" } @@ -12057,7 +12058,8 @@ "edda": { "bioportal": { "prefix": "EDDA" - } + }, + "example": "health_care_quality_assessment" }, "efo": { "biolink": { @@ -18751,6 +18753,7 @@ "prefix": "HipSci", "uri_format": "http://www.hipsci.org/lines/#/lines/$1" }, + "example": "HPSI0114i-bezi_1", "mappings": { "cellosaurus": "HipSci" } @@ -19080,6 +19083,7 @@ "prefix": "Horizon_Discovery", "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" }, + "example": "HD+118-001", "mappings": { "cellosaurus": "Horizon_Discovery" } @@ -20019,6 +20023,7 @@ "prefix": "ICLC", "uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1" }, + "example": "ATL98012", "mappings": { "cellosaurus": "ICLC" } @@ -20426,6 +20431,7 @@ "prefix": "IGRhCellID", "uri_format": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1" }, + "example": "ACHN", "mappings": { "cellosaurus": "IGRhCellID" } @@ -20464,6 +20470,7 @@ "prefix": "IGSR", "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" }, + "example": "NA06985", "mappings": { "cellosaurus": "IGSR" } @@ -20492,6 +20499,7 @@ "prefix": "Imanis", "uri_format": "https://www.imanislife.com/?s=$1" }, + "example": "CL070", "mappings": { "cellosaurus": "Imanis" } @@ -22786,6 +22794,7 @@ "prefix": "Kerafast", "uri_format": "https://www.kerafast.com/Search?SearchTerm="$1"" }, + "example": "EJH014", "mappings": { "cellosaurus": "Kerafast" } @@ -23171,6 +23180,7 @@ "prefix": "LIMORE", "uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1" }, + "example": "Li7", "mappings": { "cellosaurus": "LIMORE" } @@ -29315,6 +29325,7 @@ "prefix": "NHCDR", "uri_format": "https://stemcells.nindsgenetics.org?line=$1" }, + "example": "ND50028", "mappings": { "cellosaurus": "NHCDR" } @@ -33807,7 +33818,15 @@ "uri_format": "https://www.pgscatalog.org/pgs/$1" }, "pgx": { + "cellosaurus": { + "category": "Polymorphism and mutation databases", + "homepage": "https://progenetix.org/", + "name": "Cancer genome data @ progenetix.org", + "prefix": "Progenetix", + "uri_format": "https://progenetix.org/biosamples/by-curie/cellosaurus:$1" + }, "mappings": { + "cellosaurus": "Progenetix", "miriam": "pgx", "n2t": "pgx", "prefixcommons": "PGX" @@ -33839,7 +33858,10 @@ "is_obo": false, "prefix": "PGX", "uri_format": "http://identifiers.org/pgx/$1" - } + }, + "synonyms": [ + "Progenetix" + ] }, "pharmacodb.cell": { "cellosaurus": { @@ -35725,18 +35747,6 @@ "uri_format": "http://identifiers.org/prodom/$1" } }, - "progenetix": { - "cellosaurus": { - "category": "Polymorphism and mutation databases", - "homepage": "https://progenetix.org/", - "name": "Cancer genome data @ progenetix.org", - "prefix": "Progenetix", - "uri_format": "https://progenetix.org/biosamples/by-curie/cellosaurus:$1" - }, - "mappings": { - "cellosaurus": "Progenetix" - } - }, "proglyc": { "mappings": { "miriam": "proglyc", @@ -39815,6 +39825,7 @@ "prefix": "SLKBase", "uri_format": "https://sumlineknowledgebase.com/?page_id=$1" }, + "example": "3618", "mappings": { "cellosaurus": "SLKBase" } @@ -40843,8 +40854,13 @@ } }, "sweetrealm": { + "bioportal": { + "prefix": "SWEET" + }, + "description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).", "download_obo": "https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo", - "name": "SWEET Ontology" + "example": "ANOVA", + "name": "Semantic Web for Earth and Environment Technology Ontology" }, "swh": { "banana": "swh", @@ -41519,6 +41535,7 @@ "prefix": "TCB", "uri_format": "https://www.pirbright.ac.uk/node/$1" }, + "example": "2966", "mappings": { "cellosaurus": "TCB" } @@ -41818,6 +41835,7 @@ "prefix": "TNGB", "uri_format": "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1" }, + "example": "67035", "mappings": { "cellosaurus": "TNGB" } @@ -44612,9 +44630,11 @@ "name": "Vital Sign Ontology", "prefix": "VSO" }, + "example": "0000041", "mappings": { "bioportal": "VSO" - } + }, + "uri_format": "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1" }, "vt": { "bioportal": { @@ -45010,6 +45030,7 @@ "prefix": "WiCell", "uri_format": "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true" }, + "example": "ai10e-kctd13b", "mappings": { "cellosaurus": "WiCell" } From 5c71fa1cab88aa1db0605f3a2ab7e5de1abe3114 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 14:24:22 -0500 Subject: [PATCH 52/57] Add remaining examples --- src/bioregistry/data/bioregistry.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index e3d677377..c9646be1b 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -6959,6 +6959,7 @@ "prefix": "CLS", "uri_format": "https://www.clsgmbh.de/$1.html" }, + "example": "300108/p3934_A-172", "mappings": { "cellosaurus": "CLS" } @@ -18766,6 +18767,7 @@ "prefix": "HIVReagentProgram", "uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx" }, + "example": "ARP-1513", "mappings": { "cellosaurus": "HIVReagentProgram" } @@ -22870,6 +22872,7 @@ "prefix": "KYinno", "uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf" }, + "example": "KC-0979", "mappings": { "cellosaurus": "KYinno" } @@ -23168,6 +23171,8 @@ "prefix": "LiGeA", "uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1" }, + "comment": "This might just be a provider for CCLE", + "example": "CCLE_867", "mappings": { "cellosaurus": "LiGeA" } @@ -25735,6 +25740,7 @@ "prefix": "Millipore", "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" }, + "example": "SCC111", "mappings": { "cellosaurus": "Millipore" } @@ -30274,6 +30280,7 @@ }, "oboformat": { "description": "Related to the OBO in OWL meta-model", + "example": "alt_id", "name": "OBO Format", "preferred_prefix": "oboFormat" }, @@ -33616,6 +33623,7 @@ "prefix": "PerkinElmer", "uri_format": "https://www.perkinelmer.com/searchresult?searchName=$1" }, + "example": "SCC111", "mappings": { "cellosaurus": "PerkinElmer" } From d4df0cafb9ae258641efc6a780b36817e1b8ecbd Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 14:25:20 -0500 Subject: [PATCH 53/57] Align bioportal --- src/bioregistry/data/bioregistry.json | 10 +++++++++- src/bioregistry/data/external/bioportal/curation.tsv | 2 -- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index c9646be1b..f63de3742 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -12058,9 +12058,13 @@ }, "edda": { "bioportal": { + "name": "EDDA Study Designs Taxonomy", "prefix": "EDDA" }, - "example": "health_care_quality_assessment" + "example": "health_care_quality_assessment", + "mappings": { + "bioportal": "EDDA" + } }, "efo": { "biolink": { @@ -40863,11 +40867,15 @@ }, "sweetrealm": { "bioportal": { + "name": "Semantic Web for Earth and Environment Technology Ontology", "prefix": "SWEET" }, "description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).", "download_obo": "https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo", "example": "ANOVA", + "mappings": { + "bioportal": "SWEET" + }, "name": "Semantic Web for Earth and Environment Technology Ontology" }, "swh": { diff --git a/src/bioregistry/data/external/bioportal/curation.tsv b/src/bioregistry/data/external/bioportal/curation.tsv index 2278ea0fd..171d86d1c 100644 --- a/src/bioregistry/data/external/bioportal/curation.tsv +++ b/src/bioregistry/data/external/bioportal/curation.tsv @@ -159,7 +159,6 @@ EBP EmpowerBP ECP Electronic Care Plan ECSO The Ecosystem Ontology EDAM-BIOIMAGING EDAM Bioimaging Ontology -EDDA EDDA Study Designs Taxonomy EDDA_PT EDDA Publication Types Taxonomy EGO Epigenome Ontology ELD EthiopianListOfDiseases @@ -585,7 +584,6 @@ SSO Syndromic Surveillance Ontology STO-DRAFT The Stroke Ontology suicideo suicideonto SURGICAL Nurse Surgical -SWEET Semantic Web for Earth and Environment Technology Ontology SYN Sage Bionetworks Synapse Ontology TCDO Traditional Chinese Drug Ontology TCO Thyroid Cancer Ontology From cfa9b0f908026a3cafee0eb9a9944e66705866ad Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 14:29:53 -0500 Subject: [PATCH 54/57] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index f63de3742..bb3ba3ff4 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -28382,7 +28382,10 @@ "uri_format": "https://drugs.ncats.io/drug/$1" }, "ncbibook": { + "description": "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ", "example": "NBK331", + "homepage": "https://www.ncbi.nlm.nih.gov/books", + "name": "NCBI Bookshelf", "uri_format": "https://www.ncbi.nlm.nih.gov/books/$1" }, "ncbigene": { @@ -41747,9 +41750,13 @@ }, "tgn": { "deprecated": true, + "example": "1023371", + "homepage": "https://www.getty.edu/research/tools/vocabularies/tgn/", + "name": "Getty Thesaurus of Geographic Names", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200" - ] + ], + "uri_format": "http://vocab.getty.edu/page/tgn/$1" }, "th": { "contributor": { From cecc4d87aa1ce2345048b7ba3e87cc8bf79adbc2 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 14:35:44 -0500 Subject: [PATCH 55/57] Add homepages --- src/bioregistry/data/bioregistry.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index bb3ba3ff4..cc3f36d75 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -1010,6 +1010,7 @@ "prefix": "APAONTO" }, "example": "Abdomen", + "homepage": "https://bioportal.bioontology.org/ontologies/APAONTO", "mappings": { "bioportal": "APAONTO" }, @@ -7010,6 +7011,7 @@ }, "cmecs": { "example": "595", + "homepage": "https://cmecscatalog.org/cmecs", "name": "Costal and Marine Ecological Classification Standard", "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" }, @@ -12062,6 +12064,7 @@ "prefix": "EDDA" }, "example": "health_care_quality_assessment", + "homepage": "https://bioportal.bioontology.org/ontologies/EDDA", "mappings": { "bioportal": "EDDA" } @@ -17086,6 +17089,7 @@ "description": "Represent chemical entities having particular CHEBI roles", "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", "example": "25512", + "homepage": "https://github.com/geneontology/go-ontology/", "name": "GO Chemicals", "preferred_prefix": "GOCHE", "references": [ @@ -29856,6 +29860,7 @@ "name": "Nathan Baker" }, "example": "1731", + "homepage": "https://bioportal.bioontology.org/ontologies/NPO", "mappings": { "bioportal": "NPO" }, @@ -30288,6 +30293,7 @@ "oboformat": { "description": "Related to the OBO in OWL meta-model", "example": "alt_id", + "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", "name": "OBO Format", "preferred_prefix": "oboFormat" }, @@ -40876,6 +40882,7 @@ "description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).", "download_obo": "https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo", "example": "ANOVA", + "homepage": "https://bioportal.bioontology.org/ontologies/SWEET", "mappings": { "bioportal": "SWEET" }, @@ -44654,6 +44661,7 @@ "prefix": "VSO" }, "example": "0000041", + "homepage": "https://bioportal.bioontology.org/ontologies/VSO", "mappings": { "bioportal": "VSO" }, From 68628bb0551261a5b3673bc7525bafb22c54a089 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 15:36:36 -0500 Subject: [PATCH 56/57] Finish descriptions --- src/bioregistry/data/bioregistry.json | 30 ++++++++++++++++++++------- src/bioregistry/schema/struct.py | 7 ++++++- 2 files changed, 29 insertions(+), 8 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index cc3f36d75..7b87dc7c4 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -1009,6 +1009,7 @@ "name": "Psychology Ontology", "prefix": "APAONTO" }, + "description": "Ontology from the APA", "example": "Abdomen", "homepage": "https://bioportal.bioontology.org/ontologies/APAONTO", "mappings": { @@ -7010,9 +7011,13 @@ } }, "cmecs": { + "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", "example": "595", "homepage": "https://cmecscatalog.org/cmecs", "name": "Costal and Marine Ecological Classification Standard", + "references": [ + "http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf" + ], "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" }, "cmf": { @@ -8319,6 +8324,7 @@ } }, "credit": { + "description": "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.", "example": "Software", "homepage": "https://casrai.org/credit/", "name": "CASRAI Contributor Roles Taxonomy" @@ -11773,6 +11779,7 @@ }, "ecolexicon": { "comment": "No resolution - everything is in a single page app", + "description": "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.", "example": "canal", "homepage": "http://ecolexicon.ugr.es/en/index.htm", "name": "EcoLexicon" @@ -12063,6 +12070,7 @@ "name": "EDDA Study Designs Taxonomy", "prefix": "EDDA" }, + "description": "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.", "example": "health_care_quality_assessment", "homepage": "https://bioportal.bioontology.org/ontologies/EDDA", "mappings": { @@ -13780,6 +13788,7 @@ ] }, "fabio": { + "description": "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.", "example": "d4e2515", "homepage": "https://github.com/sparontologies/fabio", "name": "FaBiO, the FRBR-aligned Bibliographic Ontology", @@ -14604,6 +14613,7 @@ } }, "flybrain.ndb": { + "description": "A database of fly neurons and pathways with an associated 3D viewer.", "example": "10531", "homepage": "https://flybrain-ndb.virtualflybrain.org", "name": "FlyBrain Neuron Database", @@ -15019,6 +15029,7 @@ } }, "ftt": { + "description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.", "example": "273", "homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3", "name": "Feature Type Thesaurus", @@ -15653,6 +15664,7 @@ } }, "gemet": { + "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.", "example": "627", "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", "name": "General Multilingual Environmental Thesaurus", @@ -20892,6 +20904,7 @@ }, "inhand": { "comment": "This nomenclature is available via email. Truly a disgrace.", + "description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", "homepage": "https://www.goreni.org/gr3_nomenclature.php", "name": "The International Harmonization of Nomenclature and Diagnostic criteria", "proprietary": true @@ -23571,6 +23584,7 @@ "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, + "description": "Contains information about cells and data sheets related to transfection.", "example": "968", "homepage": "https://knowledge.lonza.com", "mappings": { @@ -23685,6 +23699,7 @@ "uri_format": "https://labsyspharm.github.io/lspci/$1" }, "lter": { + "description": "Ecological terms", "example": "182", "homepage": "https://vocab.lternet.edu/vocab/vocab/index.php", "name": "Long Term Ecological Research Controlled Vocabulary", @@ -27993,7 +28008,10 @@ "is_obo": false, "prefix": "MYCO.TUBER", "uri_format": "http://identifiers.org/myco.tuber/$1" - } + }, + "synonyms": [ + "TubercuList" + ] }, "mycobank": { "mappings": { @@ -29859,6 +29877,7 @@ "email": "nathan.baker@pnl.gov", "name": "Nathan Baker" }, + "description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.", "example": "1731", "homepage": "https://bioportal.bioontology.org/ontologies/NPO", "mappings": { @@ -37253,6 +37272,8 @@ "github": "mbrush", "name": "Matthew Brush" }, + "description": "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.", + "download_owl": "https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl", "example": "0000079", "homepage": "https://github.com/tis-lab/reagent-ontology", "name": "Reagent Ontology", @@ -42420,12 +42441,6 @@ "database": "Q81661821" } }, - "tuberculist": { - "example": "Rv2879c", - "homepage": "http://genolist.pasteur.fr/TubercuList", - "name": "TubercuList", - "uri_format": "http://genolist.pasteur.fr/TubercuList/genome.cgi?external_query+$1" - }, "txpo": { "bioportal": { "name": "Toxic Process Ontology", @@ -44660,6 +44675,7 @@ "name": "Vital Sign Ontology", "prefix": "VSO" }, + "description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ", "example": "0000041", "homepage": "https://bioportal.bioontology.org/ontologies/VSO", "mappings": { diff --git a/src/bioregistry/schema/struct.py b/src/bioregistry/schema/struct.py index 304ae863e..31ed94416 100644 --- a/src/bioregistry/schema/struct.py +++ b/src/bioregistry/schema/struct.py @@ -508,7 +508,12 @@ def get_name(self) -> Optional[str]: def get_description(self) -> Optional[str]: """Get the description for the given prefix, if available.""" - return self.get_prefix_key("description", ("miriam", "ols", "obofoundry", "wikidata")) + rv = self.get_prefix_key("description", ("miriam", "ols", "obofoundry", "wikidata")) + if rv is not None: + return rv + if self.cellosaurus and "category" in self.cellosaurus: + return self.cellosaurus["category"] + return None def get_pattern(self) -> Optional[str]: """Get the pattern for the given prefix, if it's available. From 6dc4f30b01cf92e408abef1bc7a2f787f3c03745 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 8 Dec 2021 15:39:52 -0500 Subject: [PATCH 57/57] Add missing contributor information --- src/bioregistry/data/bioregistry.json | 90 +++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 7b87dc7c4..49cc92e25 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -7011,6 +7011,12 @@ } }, "cmecs": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", "example": "595", "homepage": "https://cmecscatalog.org/cmecs", @@ -8324,6 +8330,12 @@ } }, "credit": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.", "example": "Software", "homepage": "https://casrai.org/credit/", @@ -11779,6 +11791,12 @@ }, "ecolexicon": { "comment": "No resolution - everything is in a single page app", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.", "example": "canal", "homepage": "http://ecolexicon.ugr.es/en/index.htm", @@ -13788,6 +13806,12 @@ ] }, "fabio": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.", "example": "d4e2515", "homepage": "https://github.com/sparontologies/fabio", @@ -14613,6 +14637,12 @@ } }, "flybrain.ndb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "A database of fly neurons and pathways with an associated 3D viewer.", "example": "10531", "homepage": "https://flybrain-ndb.virtualflybrain.org", @@ -15029,6 +15059,12 @@ } }, "ftt": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.", "example": "273", "homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3", @@ -15664,6 +15700,12 @@ } }, "gemet": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.", "example": "627", "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", @@ -16270,6 +16312,12 @@ "uri_format": "http://purl.obolibrary.org/obo/GEO_$1" }, "geonames": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.", "example": "ADM1", "homepage": "https://www.geonames.org", @@ -17098,6 +17146,12 @@ } }, "goche": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Represent chemical entities having particular CHEBI roles", "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", "example": "25512", @@ -20904,6 +20958,12 @@ }, "inhand": { "comment": "This nomenclature is available via email. Truly a disgrace.", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", "homepage": "https://www.goreni.org/gr3_nomenclature.php", "name": "The International Harmonization of Nomenclature and Diagnostic criteria", @@ -23699,6 +23759,12 @@ "uri_format": "https://labsyspharm.github.io/lspci/$1" }, "lter": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Ecological terms", "example": "182", "homepage": "https://vocab.lternet.edu/vocab/vocab/index.php", @@ -28404,6 +28470,12 @@ "uri_format": "https://drugs.ncats.io/drug/$1" }, "ncbibook": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ", "example": "NBK331", "homepage": "https://www.ncbi.nlm.nih.gov/books", @@ -30310,6 +30382,12 @@ } }, "oboformat": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "Related to the OBO in OWL meta-model", "example": "alt_id", "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", @@ -37272,6 +37350,12 @@ "github": "mbrush", "name": "Matthew Brush" }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "description": "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.", "download_owl": "https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl", "example": "0000079", @@ -41777,6 +41861,12 @@ } }, "tgn": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "deprecated": true, "example": "1023371", "homepage": "https://www.getty.edu/research/tools/vocabularies/tgn/",