{ "bcoid": "GLY_000084", "title": "Human Diseases", "description": "The Human Diseases dataset contains list of human [taxid:9606] diseases as described by OMIM and Monarch ...", "filename": "human_protein_disease.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Diseases", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P30613-1...", "omim..." ], [ "P30613-1...", "omim..." ] ], "headers": [ "uniprotkb_ca...", "database_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_name" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "database_label" } ], [ "P30613-1", "omim", "102900", "" ], [ "P30613-1", "omim", "266200", "" ], [ "P20930-1", "omim", "146700", "" ], [ "P20930-1", "omim", "605803", "" ], [ "P20933-1", "mondo", "0008830", "Aspartylglucosaminuria" ], [ "P20933-1", "omim", "208400", "" ], [ "P20936-1", "omim", "608354", "" ], [ "P20936-1", "omim", "608355", "" ], [ "Q8NHX9-1", "omim", "612267", "" ], [ "Q9NXR8-1", "omim", "275355", "" ], [ "Q9NXR1-2", "omim", "605013", "" ], [ "Q9NXR1-2", "omim", "614019", "" ], [ "Q96J66-1", "omim", "117800", "" ], [ "Q13835-1", "omim", "604536", "" ], [ "P40424-1", "omim", "617641", "" ], [ "Q8WTV0-1", "omim", "610762", "" ], [ "Q9H2I8-1", "omim", "615179", "" ], [ "P08842-1", "omim", "308100", "" ], [ "P03891-1", "omim", "502500", "" ], [ "P03891-1", "omim", "535000", "" ], [ "P03897-1", "omim", "256000", "" ], [ "P03897-1", "omim", "500014", "" ], [ "P02768-1", "omim", "615999", "" ], [ "P02768-1", "omim", "616000", "" ], [ "P08559-1", "omim", "312170", "" ], [ "P02765-1", "omim", "203650", "" ], [ "P02766-1", "omim", "105210", "" ], [ "P02766-1", "omim", "115430", "" ], [ "P02766-1", "omim", "145680", "" ], [ "Q9UJ71-1", "omim", "613393", "" ], [ "P35579-1", "omim", "155100", "" ], [ "P35579-1", "omim", "603622", "" ], [ "Q8N1G0-1", "omim", "616833", "" ], [ "O15259-1", "omim", "256100", "" ], [ "O15259-1", "omim", "266900", "" ], [ "O15259-1", "omim", "609583", "" ], [ "P41180-1", "omim", "145980", "" ], [ "P41180-1", "omim", "239200", "" ], [ "P41180-1", "omim", "601198", "" ], [ "P41180-1", "omim", "612899", "" ], [ "Q86XA0-1", "omim", "615942", "" ], [ "O15072-1", "omim", "618154", "" ], [ "P29401-1", "omim", "617044", "" ], [ "P41181-1", "omim", "125800", "" ], [ "O00330-1", "omim", "245349", "" ], [ "Q7RTW8-1", "omim", "607039", "" ], [ "P12074-1", "omim", "616039", "" ], [ "Q9P219-1", "omim", "236600", "" ], [ "Q9P219-1", "omim", "616053", "" ], [ "Q9UK17-1", "omim", "607346", "" ], [ "Q9UK17-1", "omim", "616399", "" ], [ "Q9P212-1", "omim", "610725", "" ], [ "Q92838-1", "omim", "305100", "" ], [ "Q92838-1", "omim", "313500", "" ], [ "Q9H845-1", "omim", "611126", "" ], [ "Q9BZG2-1", "omim", "617297", "" ], [ "O43933-1", "omim", "214100", "" ], [ "O43933-1", "omim", "234580", "" ], [ "O43933-1", "omim", "601539", "" ], [ "Q9BZG8-1", "omim", "616901", "" ], [ "Q9Y592-1", "omim", "615862", "" ], [ "P19099-1", "omim", "103900", "" ], [ "P19099-1", "omim", "203400", "" ], [ "P19099-1", "omim", "610600", "" ], [ "P09001-1", "omim", "614582", "" ], [ "P53708-1", "omim", "191830", "" ], [ "Q14563-1", "omim", "614897", "" ], [ "Q8WYB5-1", "omim", "603736", "" ], [ "Q8WYB5-1", "omim", "606170", "" ], [ "Q14566-1", "omim", "223100", "" ], [ "O60741-1", "omim", "615871", "" ], [ "Q9UHF7-1", "omim", "150230", "" ], [ "Q9UHF7-1", "omim", "190350", "" ], [ "Q9UHF7-1", "omim", "190351", "" ], [ "Q9UHC6-1", "omim", "610042", "" ], [ "Q9UHC6-1", "omim", "612100", "" ], [ "P41212-1", "omim", "601626", "" ], [ "P41212-1", "omim", "131440", "" ], [ "P41212-1", "omim", "616216", "" ], [ "Q92597-1", "omim", "601455", "" ], [ "Q9BQP7-1", "omim", "615084", "" ], [ "P07202-1", "omim", "274500", "" ], [ "P07204-1", "omim", "612926", "" ], [ "P07204-1", "omim", "614486", "" ] ] }, "readme": "Name\n - Human Diseases\n\nVersion\n - 1.4.5\n\nCreated on\n - 2019-01-23T17:21:05.953432\n\nModified on\n - 2019-09-12T14:43:38.058730\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk], Jean-Philippe Gourdine [gourdine@ohsu.edu], Melissa Haendel [haendel@ohsu.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Human Diseases dataset contains list of human [taxid:9606] diseases as described by OMIM and Monarch Initiave database \n - Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship.\n - The Monarch Initiative is focused primarily on phenotype-related resources and brings in data associated with those phenotypes so that the users can begin to make connections among other biological entities of interest.\n - If you are using this dataset please give proper attribution to OMIM, Monarch Initiative, EMBL-EBI-UniProt and GlyGen\n\nDescription Domain\n Keywords\n - disease\n - HPO\n - OMIM\n - Congenital Disorders of Glycosylation (CDG)\n - Monarch Initiative\n\n Pipeline Steps\n - Step-1: The script extracts the OMIM phenotypes for UniProtKB accessions and disease information from human_glyco-phenotype_disease_curation_list_v12-18-74.csv. The script maps the UniProtKB accessions to the UniprotKB canonical accessions.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: uniprot-proteome-9606-homo-sapiens-2019-05.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/source/uniprot-proteome-9606-homo-sapiens-2019-05.nt\n Name: human_protein_glyco_disease.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/compiled/human_protein_glyco_disease.csv\n Name: human_protein_idmapping.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_idmapping.csv\n Output Subdomain\n Name: human_protein_disease.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_disease.csv\n Name: human_protein_disease.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_disease.stat.csv\n\nFields\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"5432\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"3947\"\n Name: \"database_label\"\n Description: \"Label or name assigned to the corresponding identifier in the source database\"\n Unique Values: \"186\"\n Name: \"database_name\"\n Description: \"The name of the source database\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-1.4.5/reviewed/human_protein_disease.csv" }