{ "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": [ [ "41493209...", "Q8BHJ7-1..." ], [ "41493209...", "P31644-1..." ] ], "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": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "41493209", "Q8BHJ7-1", "10090", "protein_xref_mgi_homologset", "41493209" ], [ "41493209", "P31644-1", "9606", "protein_xref_mgi_homologset", "41493209" ], [ "41493209", "P19969-1", "10116", "protein_xref_mgi_homologset", "41493209" ], [ "41493208", "Q9D658-1", "10090", "protein_xref_mgi_homologset", "41493208" ], [ "41493208", "O75365-1", "9606", "protein_xref_mgi_homologset", "41493208" ], [ "41493208", "B0K032-1", "10116", "protein_xref_mgi_homologset", "41493208" ], [ "41502219", "P61514-1", "10090", "protein_xref_mgi_homologset", "41502219" ], [ "41502219", "P61513-1", "9606", "protein_xref_mgi_homologset", "41502219" ], [ "41502218", "Q4G0F8-1", "10090", "protein_xref_mgi_homologset", "41502218" ], [ "41502218", "Q9NPG3-1", "9606", "protein_xref_mgi_homologset", "41502218" ], [ "41502218", "D4A8C6-1", "10116", "protein_xref_mgi_homologset", "41502218" ], [ "41497278", "Q8CH77-1", "10090", "protein_xref_mgi_homologset", "41497278" ], [ "41497278", "Q8NEY1-1", "9606", "protein_xref_mgi_homologset", "41497278" ], [ "41497278", "F1LYK3-1", "10116", "protein_xref_mgi_homologset", "41497278" ], [ "41497279", "Q3TBT3-1", "10090", "protein_xref_mgi_homologset", "41497279" ], [ "41497279", "Q86WV6-1", "9606", "protein_xref_mgi_homologset", "41497279" ], [ "41497279", "F1M391-1", "10116", "protein_xref_mgi_homologset", "41497279" ], [ "41493203", "E9PX57-1", "10090", "protein_xref_mgi_homologset", "41493203" ], [ "41493203", "Q6ZMV9-1", "9606", "protein_xref_mgi_homologset", "41493203" ], [ "41493203", "E9PSL8-1", "10116", "protein_xref_mgi_homologset", "41493203" ], [ "41493202", "P26361-1", "10090", "protein_xref_mgi_homologset", "41493202" ], [ "41493202", "P13569-1", "9606", "protein_xref_mgi_homologset", "41493202" ], [ "41493202", "P34158-1", "10116", "protein_xref_mgi_homologset", "41493202" ], [ "41493201", "Q8K411-1", "10090", "protein_xref_mgi_homologset", "41493201" ], [ "41493201", "Q5JRX3-1", "9606", "protein_xref_mgi_homologset", "41493201" ], [ "41493201", "A0A0G2K6D5-1", "10116", "protein_xref_mgi_homologset", "41493201" ], [ "41493200", "Q811B1-1", "10090", "protein_xref_mgi_homologset", "41493200" ], [ "41493200", "Q86Y38-1", "9606", "protein_xref_mgi_homologset", "41493200" ], [ "41493207", "Q61409-1", "10090", "protein_xref_mgi_homologset", "41493207" ], [ "41493207", "Q13370-1", "9606", "protein_xref_mgi_homologset", "41493207" ], [ "41493207", "Q63085-1", "10116", "protein_xref_mgi_homologset", "41493207" ], [ "41493206", "P46938-1", "10090", "protein_xref_mgi_homologset", "41493206" ], [ "41493206", "P46937-1", "9606", "protein_xref_mgi_homologset", "41493206" ], [ "41493206", "Q2EJA0-1", "10116", "protein_xref_mgi_homologset", "41493206" ], [ "41493205", "Q8VCX5-1", "10090", "protein_xref_mgi_homologset", "41493205" ], [ "41493205", "Q9BPX6-1", "9606", "protein_xref_mgi_homologset", "41493205" ], [ "41493205", "Q6P6Q9-1", "10116", "protein_xref_mgi_homologset", "41493205" ], [ "41493204", "O70324-1", "10090", "protein_xref_mgi_homologset", "41493204" ], [ "41493204", "P36021-1", "9606", "protein_xref_mgi_homologset", "41493204" ], [ "41493204", "Q8K1P8-1", "10116", "protein_xref_mgi_homologset", "41493204" ], [ "41504438", "A2RTS7-1", "10090", "protein_xref_mgi_homologset", "41504438" ], [ "41504438", "Q5T089-1", "9606", "protein_xref_mgi_homologset", "41504438" ], [ "41504438", "Q641X6-1", "10116", "protein_xref_mgi_homologset", "41504438" ], [ "41502748", "E9Q9Y3-1", "10090", "protein_xref_mgi_homologset", "41502748" ], [ "41502748", "Q96M83-1", "9606", "protein_xref_mgi_homologset", "41502748" ], [ "41502748", "Q6AYJ6-1", "10116", "protein_xref_mgi_homologset", "41502748" ], [ "41504721", "A0A1L1SVH0-1", "10090", "protein_xref_mgi_homologset", "41504721" ], [ "41504721", "Q8NGF6-1", "9606", "protein_xref_mgi_homologset", "41504721" ], [ "41504721", "D3ZE76-1", "10116", "protein_xref_mgi_homologset", "41504721" ], [ "41502223", "Q8BGH7-1", "10090", "protein_xref_mgi_homologset", "41502223" ], [ "41502223", "Q9NRR3-1", "9606", "protein_xref_mgi_homologset", "41502223" ], [ "41502223", "A1L1K4-1", "10116", "protein_xref_mgi_homologset", "41502223" ], [ "41500523", "Q6P3B9-1", "10090", "protein_xref_mgi_homologset", "41500523" ], [ "41500523", "Q8N0V3-1", "9606", "protein_xref_mgi_homologset", "41500523" ], [ "41500523", "A0A0G2K1B0-1", "10116", "protein_xref_mgi_homologset", "41500523" ], [ "41505102", "Q7TRE6-1", "10090", "protein_xref_mgi_homologset", "41505102" ], [ "41505102", "Q8NGG6-1", "9606", "protein_xref_mgi_homologset", "41505102" ], [ "41505102", "D4AE39-1", "10116", "protein_xref_mgi_homologset", "41505102" ], [ "41505102", "A0A8I6AQV2-1", "10116", "protein_xref_mgi_homologset", "41505102" ], [ "41502146", "Q9EPJ9-1", "10090", "protein_xref_mgi_homologset", "41502146" ], [ "41502146", "Q8N6T3-1", "9606", "protein_xref_mgi_homologset", "41502146" ], [ "41502146", "Q62848-1", "10116", "protein_xref_mgi_homologset", "41502146" ], [ "41504720", "Q8VF55-1", "10090", "protein_xref_mgi_homologset", "41504720" ], [ "41504720", "Q8NGI7-1", "9606", "protein_xref_mgi_homologset", "41504720" ], [ "41504720", "D3ZT33-1", "10116", "protein_xref_mgi_homologset", "41504720" ], [ "41502441", "Q5XF90-1", "10090", "protein_xref_mgi_homologset", "41502441" ], [ "41502441", "Q4VNC1-1", "9606", "protein_xref_mgi_homologset", "41502441" ], [ "41502441", "F1M9L4-1", "10116", "protein_xref_mgi_homologset", "41502441" ], [ "41504064", "Q8BJ34-1", "10090", "protein_xref_mgi_homologset", "41504064" ], [ "41504064", "Q9Y4F3-1", "9606", "protein_xref_mgi_homologset", "41504064" ], [ "41504064", "Q8VIG2-1", "10116", "protein_xref_mgi_homologset", "41504064" ], [ "41503628", "Q6PDM4-1", "10090", "protein_xref_mgi_homologset", "41503628" ], [ "41503628", "Q8IYA8-1", "9606", "protein_xref_mgi_homologset", "41503628" ], [ "41503628", "M0R8J7-1", "10116", "protein_xref_mgi_homologset", "41503628" ], [ "41496036", "Q99LJ6-1", "10090", "protein_xref_mgi_homologset", "41496036" ], [ "41496036", "Q96SL4-1", "9606", "protein_xref_mgi_homologset", "41496036" ], [ "41496036", "A0A8I6ARN0-1", "10116", "protein_xref_mgi_homologset", "41496036" ], [ "41505334", "D3YUJ6-1", "10090", "protein_xref_mgi_homologset", "41505334" ], [ "41505334", "O95521-1", "9606", "protein_xref_mgi_homologset", "41505334" ], [ "41505334", "O60809-1", "9606", "protein_xref_mgi_homologset", "41505334" ], [ "41505334", "O60813-1", "9606", "protein_xref_mgi_homologset", "41505334" ], [ "41505334", "O95522-1", "9606", "protein_xref_mgi_homologset", "41505334" ], [ "41505334", "Q5VWM6-1", "9606", "protein_xref_mgi_homologset", "41505334" ], [ "41505334", "P0DUQ2-1", "9606", "protein_xref_mgi_homologset", "41505334" ] ] }, "readme": "Name\n - Homolog Clusters\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2019-09-06T14:06:38.985197\n\nModified on\n - 2022-09-26T09:04:47.943513\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - Not Applicable []\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/glygener/glygen-backend-integration/blob/master/dataset-maker/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: protein_homolog_clusters.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/compiled/protein_homolog_clusters.csv\n Name: fruitfly_protein_transcriptlocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/fruitfly_protein_transcriptlocus.csv\n Name: fruitfly_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/fruitfly_protein_xref_geneid.csv\n Name: fruitfly_protein_xref_oma.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/fruitfly_protein_xref_oma.csv\n Name: human_protein_transcriptlocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_transcriptlocus.csv\n Name: human_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_xref_geneid.csv\n Name: human_protein_xref_hgnc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_xref_hgnc.csv\n Name: human_protein_xref_oma.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_xref_oma.csv\n Name: mouse_protein_transcriptlocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/mouse_protein_transcriptlocus.csv\n Name: mouse_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/mouse_protein_xref_geneid.csv\n Name: mouse_protein_xref_mgi.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/mouse_protein_xref_mgi.csv\n Name: mouse_protein_xref_oma.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/mouse_protein_xref_oma.csv\n Name: rat_protein_transcriptlocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_transcriptlocus.csv\n Name: rat_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_xref_geneid.csv\n Name: rat_protein_xref_oma.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_xref_oma.csv\n Name: sarscov1_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov1_protein_xref_geneid.csv\n Name: sarscov2_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/sarscov2_protein_xref_geneid.csv\n Name: mgi_homologs.csv\n URI: /data/shared/glyds/downloads/mgi/2022_07_07/mgi_homologs.csv\n Name: fruitfly_human_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/fruitfly_human_oma_orthologs_july2022.csv\n Name: fruitfly_mouse_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/fruitfly_mouse_oma_orthologs_july2022.csv\n Name: fruitfly_rat_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/fruitfly_rat_oma_orthologs_july2022.csv\n Name: human_fruitfly_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/human_fruitfly_oma_orthologs_july2022.csv\n Name: human_mouse_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/human_mouse_oma_orthologs_july2022.csv\n Name: human_rat_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/human_rat_oma_orthologs_july2022.csv\n Name: mouse_fruitfly_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/mouse_fruitfly_oma_orthologs_july2022.csv\n Name: mouse_human_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/mouse_human_oma_orthologs_july2022.csv\n Name: mouse_rat_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/mouse_rat_oma_orthologs_july2022.csv\n Name: rat_fruitfly_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/rat_fruitfly_oma_orthologs_july2022.csv\n Name: rat_human_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/rat_human_oma_orthologs_july2022.csv\n Name: rat_mouse_oma_orthologs_july2022.csv\n URI: /data/shared/glyds/downloads/oma/2022_07_07/rat_mouse_oma_orthologs_july2022.csv\n Output Subdomain\n Name: protein_homolog_clusters.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/protein_homolog_clusters.csv\n Name: protein_homolog_clusters.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/protein_homolog_clusters.stat.csv\n\nFields\n Name: \"homolog_cluster_id\"\n Description: \"NA\"\n Unique Values: \"32719\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"55207\"\n Name: \"tax_id\"\n Description: \"NCBI Taxonomy database Identifier\"\n Unique Values: \"8\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"4\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"32718\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/protein_homolog_clusters.csv" }