{ "bcoid": "GLY_000258", "title": "Homolog Clusters", "description": "The Homolog Clusters dataset contains homologs of human [taxid: 9606], mouse [taxid:10090] and rat [taxid:10116] ...", "filename": "protein_homolog_clusters.csv", "filetype": "csv", "categories": { "molecule": "Protein", "tags": "Homologs", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "35234...", "Q8BFQ8-1..." ], [ "35234...", "Q8NB37-1..." ] ], "headers": [ "homolog_clus...", "uniprotkb_ca..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "homolog_cluster_id" }, { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "tax_id" }, { "type": "string", "label": "tax_name" }, { "type": "string", "label": "database" } ], [ "35234", "Q8BFQ8-1", "10090", "Mus musculus", "mgi" ], [ "35234", "Q8NB37-1", "9606", "Homo sapiens", "mgi" ], [ "35234", "D3ZVI9-1", "10116", "Rattus norvegicus", "mgi" ], [ "110555", "Q7TR16-1", "10090", "Mus musculus", "mgi" ], [ "110555", "D3ZW68-1", "10116", "Rattus norvegicus", "mgi" ], [ "110555", "A0A0G2K1C2-1", "10116", "Rattus norvegicus", "mgi" ], [ "110555", "A0A0G2K6E1-1", "10116", "Rattus norvegicus", "mgi" ], [ "110550", "Q7TQZ0-1", "10090", "Mus musculus", "mgi" ], [ "110550", "Q8NGF8-1", "9606", "Homo sapiens", "mgi" ], [ "110550", "A0A0G2JZJ2-1", "10116", "Rattus norvegicus", "mgi" ], [ "73393", "B9EJV3-1", "10090", "Mus musculus", "mgi" ], [ "73393", "Q9C091-1", "9606", "Homo sapiens", "mgi" ], [ "73463", "A7L9Z8-1", "10090", "Mus musculus", "mgi" ], [ "73463", "O75185-1", "9606", "Homo sapiens", "mgi" ], [ "73463", "Q8R4C1-1", "10116", "Rattus norvegicus", "mgi" ], [ "35542", "E9QAE1-1", "10090", "Mus musculus", "mgi" ], [ "35542", "O14513-1", "9606", "Homo sapiens", "mgi" ], [ "35238", "Q8C4S8-1", "10090", "Mus musculus", "mgi" ], [ "35238", "Q9ULE3-1", "9606", "Homo sapiens", "mgi" ], [ "35238", "D3ZLQ1-1", "10116", "Rattus norvegicus", "mgi" ], [ "35239", "Q8CCH2-1", "10090", "Mus musculus", "mgi" ], [ "35239", "Q5JS37-1", "9606", "Homo sapiens", "mgi" ], [ "11542", "Q99P68-1", "10090", "Mus musculus", "mgi" ], [ "11542", "Q9BQB4-1", "9606", "Homo sapiens", "mgi" ], [ "11542", "Q99P67-1", "10116", "Rattus norvegicus", "mgi" ], [ "32238", "Q8K2H6-1", "10090", "Mus musculus", "mgi" ], [ "32238", "Q9UM13-1", "9606", "Homo sapiens", "mgi" ], [ "32238", "B5DEP3-1", "10116", "Rattus norvegicus", "mgi" ], [ "11546", "Q99LQ4-1", "10090", "Mus musculus", "mgi" ], [ "11546", "Q8N300-1", "9606", "Homo sapiens", "mgi" ], [ "11546", "Q4KLG3-1", "10116", "Rattus norvegicus", "mgi" ], [ "11875", "Q925I7-1", "10090", "Mus musculus", "mgi" ], [ "11875", "Q9GZP0-1", "9606", "Homo sapiens", "mgi" ], [ "11875", "Q9EQT1-1", "10116", "Rattus norvegicus", "mgi" ], [ "11544", "Q9D666-1", "10090", "Mus musculus", "mgi" ], [ "11544", "O94901-1", "9606", "Homo sapiens", "mgi" ], [ "11544", "A0A0G2K016-1", "10116", "Rattus norvegicus", "mgi" ], [ "11545", "Q8R4U7-1", "10090", "Mus musculus", "mgi" ], [ "11545", "Q86V48-1", "9606", "Homo sapiens", "mgi" ], [ "131539", "A0A140LHH9-1", "10090", "Mus musculus", "mgi" ], [ "131539", "F1LYQ6-1", "10116", "Rattus norvegicus", "mgi" ], [ "11548", "Q9ERR8-1", "10090", "Mus musculus", "mgi" ], [ "11548", "Q9P2F9-1", "9606", "Homo sapiens", "mgi" ], [ "11548", "D4AEC6-1", "10116", "Rattus norvegicus", "mgi" ], [ "103894", "P62257-1", "10090", "Mus musculus", "mgi" ], [ "103894", "P62256-1", "9606", "Homo sapiens", "mgi" ], [ "73902", "Q99N19-1", "10090", "Mus musculus", "mgi" ], [ "73902", "Q08477-1", "9606", "Homo sapiens", "mgi" ], [ "73902", "P51871-1", "10116", "Rattus norvegicus", "mgi" ], [ "5982", "Q9DAM5-1", "10090", "Mus musculus", "mgi" ], [ "5982", "Q9HC21-1", "9606", "Homo sapiens", "mgi" ], [ "5982", "Q6AYL0-1", "10116", "Rattus norvegicus", "mgi" ], [ "19396", "Q80T54-1", "10090", "Mus musculus", "mgi" ], [ "19396", "D3ZQ49-1", "10116", "Rattus norvegicus", "mgi" ], [ "5980", "Q8CCF0-1", "10090", "Mus musculus", "mgi" ], [ "5980", "Q8WWY3-1", "9606", "Homo sapiens", "mgi" ], [ "5980", "D3ZI68-1", "10116", "Rattus norvegicus", "mgi" ], [ "5981", "Q9CRA8-1", "10090", "Mus musculus", "mgi" ], [ "5981", "Q9NQT4-1", "9606", "Homo sapiens", "mgi" ], [ "5981", "F1LSX7-1", "10116", "Rattus norvegicus", "mgi" ], [ "5984", "Q9EQ61-1", "10090", "Mus musculus", "mgi" ], [ "5984", "O00541-1", "9606", "Homo sapiens", "mgi" ], [ "5984", "Q3B8N8-1", "10116", "Rattus norvegicus", "mgi" ], [ "19390", "Q5GH64-1", "10090", "Mus musculus", "mgi" ], [ "19390", "Q5GH72-1", "9606", "Homo sapiens", "mgi" ], [ "19390", "Q5GH56-1", "10116", "Rattus norvegicus", "mgi" ], [ "134867", "P58252-1", "10090", "Mus musculus", "mgi" ], [ "134867", "P13639-1", "9606", "Homo sapiens", "mgi" ], [ "134867", "P05197-1", "10116", "Rattus norvegicus", "mgi" ], [ "55616", "P18242-1", "10090", "Mus musculus", "mgi" ], [ "55616", "P07339-1", "9606", "Homo sapiens", "mgi" ], [ "123852", "Q9CZA5-1", "10090", "Mus musculus", "mgi" ], [ "123852", "Q6PEW1-1", "9606", "Homo sapiens", "mgi" ], [ "123852", "Q5HZA3-1", "10116", "Rattus norvegicus", "mgi" ], [ "32484", "Q8VHR5-1", "10090", "Mus musculus", "mgi" ], [ "32484", "Q8WXI9-1", "9606", "Homo sapiens", "mgi" ], [ "32484", "Q4V8E1-1", "10116", "Rattus norvegicus", "mgi" ], [ "32507", "Q99MZ3-1", "10090", "Mus musculus", "mgi" ], [ "32507", "Q9NP71-1", "9606", "Homo sapiens", "mgi" ], [ "32507", "Q8VIP2-1", "10116", "Rattus norvegicus", "mgi" ], [ "82192", "Q8BVK9-1", "10090", "Mus musculus", "mgi" ], [ "82192", "Q9HB58-1", "9606", "Homo sapiens", "mgi" ], [ "82192", "Q3KRF1-1", "10116", "Rattus norvegicus", "mgi" ], [ "82444", "D3YVV6-1", "10090", "Mus musculus", "mgi" ] ] }, "readme": "Name\n - Homolog Clusters\n\nVersion\n - 1.5.18\n\nCreated on\n - 2019-09-06T14:06:38.985197\n\nModified on\n - 2019-12-02T15:18:16.853702\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 - \n\nChecksum\n - \n\nUsability Domain\n - The Homolog Clusters dataset contains homologs of human [taxid: 9606], mouse [taxid:10090] and rat [taxid:10116] species mapped to UniProtKB canonical accessions. The homologs data is downloaded from OMA browser and MGI. If you use this dataset please provide proper attribution to MGI, OMA Browser and GlyGen\n\nDescription Domain\n Keywords\n - homologs\n - orthologs\n - MGI\n - OMA\n\n Pipeline Steps\n - Step-1: The script extracts the human, mouse and rat homologs from the input files and using xref files maps the identifiers to UniProtKB canonical accessions\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-species-agnostic-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: mgi_orthologs_hom_allorganism_release6.14_060419_12-33pm.csv\n URI: https://data.glygen.org/ln2wwwdata/source/mgi_orthologs_hom_allorganism_release6.14_060419_12-33pm.csv\n Name: mouse_human_orthologs_oma_release-24_061319_03-45pm.csv\n URI: https://data.glygen.org/ln2wwwdata/source/mouse_human_orthologs_oma_release-24_061319_03-45pm.csv\n Name: rat_human_orthologs_oma_release-24_061319_12-24pm.csv\n URI: https://data.glygen.org/ln2wwwdata/source/rat_human_orthologs_oma_release-24_061319_12-24pm.csv\n Name: mgi_homologs.csv\n URI: https://data.glygen.org/ln2wwwdata/source/mgi_homologs.csv\n Name: mouse_protein_xref_mgi.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_mgi.csv\n Name: human_protein_xref_hgnc.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_xref_hgnc.csv\n Name: human_protein_xref_oma.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_xref_oma.csv\n Name: mouse_protein_xref_oma.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_oma.csv\n Name: mouse_protein_xref_geneid.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_geneid.csv\n Name: rat_protein_xref_geneid.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/rat_protein_xref_geneid.csv\n Name: human_protein_xref_geneid.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_xref_geneid.csv\n Name: rat_protein_xref_oma.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/rat_protein_xref_oma.csv\n Output Subdomain\n Name: protein_homolog_clusters.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/protein_homolog_clusters.csv\n Name: protein_homolog_clusters.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/protein_homolog_clusters.stat.csv\n\nFields\n Name: \"database\"\n Description: \"\"\n Unique Values: \"2\"\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: \"53811\"\n Name: \"tax_name\"\n Description: \"NCBI Taxonomy name\"\n Unique Values: \"3\"\n Name: \"homolog_cluster_id\"\n Description: \"NA\"\n Unique Values: \"32156\"\n Name: \"tax_id\"\n Description: \"NCBI Taxonomic identifier annotated to the glycan\"\n Unique Values: \"3\"", "downloadurl": "/ln2data/releases/data/v-1.5.18/reviewed/protein_homolog_clusters.csv" }