{ "bcoid": "GLY_000322", "title": "Human Protein Site Annotation", "description": "The Human Protein Site Annotation (UniProtKB) dataset contains human [taxid:9606] site annotations for ...", "filename": "human_protein_site_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "site annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P30613-1...", "PKLR..." ], [ "P30613-1...", "PKLR..." ] ], "headers": [ "uniprotkb_ca...", "gene_symbol..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "ann_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "annotation" }, { "type": "string", "label": "ecoid" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "163", "163", "ATP", "ECO_0000250", "R", "", "protein_xref_uniprotkb", "P30613" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "163", "163", "ATP", "ECO_0000250", "R", "", "protein_xref_pubmed", "P14618" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "250", "250", "ATP", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "P30613" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "250", "250", "ATP", "ECO_0000250", "K", "", "protein_xref_pubmed", "P14618" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "532", "532", "Fructose-1,6-bisphosphate; 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Sassari.", "ECO_0000269", "E", "Q", "protein_xref_uniprotkb", "P30613" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "172", "172", "In PKRD; Sassari.", "ECO_0000269", "E", "Q", "protein_xref_pubmed", "9827908" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "163", "163", "In PKRD; Linz.", "ECO_0000269", "R", "C", "protein_xref_uniprotkb", "P30613" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "163", "163", "In PKRD; Linz.", "ECO_0000269", "R", "C", "protein_xref_pubmed", "2018831" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "331", "331", "In PKRD; Parma.", "ECO_0000269", "D", "E", "protein_xref_uniprotkb", "P30613" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "331", "331", "In PKRD; Parma.", "ECO_0000269", "D", "E", "protein_xref_pubmed", "7706479" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "332", "332", "In PKRD; loss of catalytical activity.", "ECO_0000269", "G", "S", "protein_xref_uniprotkb", "P30613" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "332", "332", "In PKRD; loss of catalytical activity.", "ECO_0000269", "G", "S", "protein_xref_pubmed", "11960989" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "332", "332", "In PKRD; loss of catalytical activity.", "ECO_0000269", "G", "S", "protein_xref_pubmed", "9482576" ], [ "P30613-1", "PKLR", "Natural_Variant_Annotation", "332", "332", "In PKRD; loss of catalytical activity.", "ECO_0000269", "G", "S", "protein_xref_pubmed", "8180378" ] ] }, "readme": "Name\n - Human Protein Site Annotation\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-12-01T15:29:48.229274\n\nModified on\n - 2020-04-11T11:30:23.073973\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], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.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 Human Protein Site Annotation (UniProtKB) dataset contains human [taxid:9606] site annotations for UniProtKB canonical accessions. The dataset contains information about UniProtKB annotations with their amino acid range. The dataset is derived form 2019-09 UniprotKB release. If you use this dataset please give proper attribution to UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - site annotation\n - amino acid range\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script extracts the site annotation triples from the triplestore for the UniProtKB canonical sequnces asnd extracts as a dataset in a csv format\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-homo-sapiens.nt\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/human_protein_ntdata.nt\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/human_protein_masterlist.csv\n Output Subdomain\n Name: human_protein_site_annotation_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/human_protein_site_annotation_uniprotkb.csv\n Name: human_protein_site_annotation_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/human_protein_site_annotation_uniprotkb.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/human_protein_site_annotation_uniprotkb.csv" }