{ "bcoid": "GLY_000454", "title": "SARS-CoV2 UniProtKB Xref Pfam", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCov) UniProtKB Xref Pfam contains sarscov2 [taxid:2697049] ...", "filename": "sarscov2_protein_xref_pfam.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "Pfam cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTD2-1...", "protein_xref..." ], [ "P0DTD1-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_label" } ], [ "P0DTD2-1", "protein_xref_pfam", "PF09399", "bCoV_lipid_BD" ], [ "P0DTD1-1", "protein_xref_pfam", "PF01661", "Macro" ], [ "P0DTD1-1", "protein_xref_pfam", "PF05409", "Peptidase_C30" ], [ "P0DTD1-1", "protein_xref_pfam", "PF06460", "CoV_Methyltr_2" ], [ "P0DTD1-1", "protein_xref_pfam", "PF06471", "CoV_Methyltr_1" ], [ "P0DTD1-1", "protein_xref_pfam", "PF06478", "CoV_RPol_N" ], [ "P0DTD1-1", "protein_xref_pfam", "PF08710", "CoV_NSP9" ], [ "P0DTD1-1", "protein_xref_pfam", "PF08715", "CoV_peptidase" ], [ "P0DTD1-1", "protein_xref_pfam", "PF08716", "CoV_NSP7" ], [ "P0DTD1-1", "protein_xref_pfam", "PF08717", "CoV_NSP8" ], [ "P0DTD1-1", "protein_xref_pfam", "PF09401", "CoV_NSP10" ], [ "P0DTD1-1", "protein_xref_pfam", "PF11501", "bCoV_NSP1" ], [ "P0DTD1-1", "protein_xref_pfam", "PF11633", "bCoV_SUD_M" ], [ "P0DTD1-1", "protein_xref_pfam", "PF12124", "bCoV_SUD_C" ], [ "P0DTD1-1", "protein_xref_pfam", "PF12379", "bCoV_NSP3_N" ], [ "P0DTD1-1", "protein_xref_pfam", "PF16251", "bCoV_NAR" ], [ "P0DTD1-1", "protein_xref_pfam", "PF16348", "CoV_NSP4_C" ], [ "P0DTD1-1", "protein_xref_pfam", "PF00680", "RdRP_1" ], [ "P0DTD1-1", "protein_xref_pfam", "PF01443", "Viral_helicase1" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19211", "CoV_NSP2_N" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19212", "CoV_NSP2_C" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19213", "CoV_NSP6" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19215", "CoV_NSP15_C" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19216", "CoV_NSP15_M" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19217", "CoV_NSP4_N" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19218", "CoV_NSP3_C" ], [ "P0DTD1-1", "protein_xref_pfam", "PF19219", "CoV_NSP15_N" ], [ "P0DTD3-1", "protein_xref_pfam", "PF17635", "bCoV_Orf14" ], [ "P0DTC7-1", "protein_xref_pfam", "PF08779", "bCoV_NS7A" ], [ "P0DTC6-1", "protein_xref_pfam", "PF12133", "bCoV_NS6" ], [ "P0DTC5-1", "protein_xref_pfam", "PF01635", "CoV_M" ], [ "P0DTC4-1", "protein_xref_pfam", "PF02723", "CoV_E" ], [ "P0DTC3-1", "protein_xref_pfam", "PF11289", "bCoV_viroporin" ], [ "P0DTC2-1", "protein_xref_pfam", "PF01601", "CoV_S2" ], [ "P0DTC2-1", "protein_xref_pfam", "PF09408", "bCoV_S1_RBD" ], [ "P0DTC2-1", "protein_xref_pfam", "PF16451", "bCoV_S1_N" ], [ "P0DTC2-1", "protein_xref_pfam", "PF19209", "CoV_S1_C" ], [ "P0DTC1-1", "protein_xref_pfam", "PF01661", "Macro" ], [ "P0DTC1-1", "protein_xref_pfam", "PF05409", "Peptidase_C30" ], [ "P0DTC1-1", "protein_xref_pfam", "PF08710", "CoV_NSP9" ], [ "P0DTC1-1", "protein_xref_pfam", "PF08715", "CoV_peptidase" ], [ "P0DTC1-1", "protein_xref_pfam", "PF08716", "CoV_NSP7" ], [ "P0DTC1-1", "protein_xref_pfam", "PF08717", "CoV_NSP8" ], [ "P0DTC1-1", "protein_xref_pfam", "PF09401", "CoV_NSP10" ], [ "P0DTC1-1", "protein_xref_pfam", "PF11501", "bCoV_NSP1" ], [ "P0DTC1-1", "protein_xref_pfam", "PF11633", "bCoV_SUD_M" ], [ "P0DTC1-1", "protein_xref_pfam", "PF12124", "bCoV_SUD_C" ], [ "P0DTC1-1", "protein_xref_pfam", "PF12379", "bCoV_NSP3_N" ], [ "P0DTC1-1", "protein_xref_pfam", "PF16251", "bCoV_NAR" ], [ "P0DTC1-1", "protein_xref_pfam", "PF16348", "CoV_NSP4_C" ], [ "P0DTC1-1", "protein_xref_pfam", "PF19211", "CoV_NSP2_N" ], [ "P0DTC1-1", "protein_xref_pfam", "PF19212", "CoV_NSP2_C" ], [ "P0DTC1-1", "protein_xref_pfam", "PF19213", "CoV_NSP6" ], [ "P0DTC1-1", "protein_xref_pfam", "PF19217", "CoV_NSP4_N" ], [ "P0DTC1-1", "protein_xref_pfam", "PF19218", "CoV_NSP3_C" ], [ "P0DTD8-1", "protein_xref_pfam", "PF11395", "bCoV_NS7B" ], [ "P0DTC9-1", "protein_xref_pfam", "PF00937", "CoV_nucleocap" ], [ "P0DTC8-1", "protein_xref_pfam", "PF12093", "bCoV_NS8" ] ] }, "readme": "Name\n - SARS-CoV2 UniProtKB Xref Pfam\n\nVersion\n - 1.8.24\n\nCreated on\n - 2020-04-03T12:33:52.055648\n\nModified on\n - 2020-04-10T12:30:41.344898\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCov) UniProtKB Xref Pfam contains sarscov2 [taxid:2697049] UniProtKB canonical accessions cross-referenced to Pfam database accessions/identifiers. The dataset is derived from 2020-01 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n - Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.\n\nDescription Domain\n Keywords\n - protein family\n - Pfam\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to Pfam database accessions/identifiers from the triplestore containing triples from nt file and extracts the data as a csv dataset\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-sars-cov-2.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/uniprot-proteome-sars-cov-2.nt\n Output Subdomain\n Name: sarscov2_protein_xref_pfam.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov2_protein_xref_pfam.csv\n Name: sarscov2_protein_xref_pfam.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/sarscov2_protein_xref_pfam.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.24/reviewed/sarscov2_protein_xref_pfam.csv" }