{ "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": [ [ "Q8TBF5-1...", "PIGX..." ], [ "Q8TBF4-1...", "ZCRB1..." ] ], "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" } ], [ "Q8TBF5-1", "PIGX", "Glycosylation_Annotation", "103", "103", "N-linked (GlcNAc...) asparagine" ], [ "Q8TBF4-1", "ZCRB1", "Modified_Residue_Annotation", "210", "210", "Phosphoserine" ], [ "Q8TBF4-1", "ZCRB1", "Modified_Residue_Annotation", "216", "216", "Phosphoserine" ], [ "Q8TBF4-1", "ZCRB1", "Modified_Residue_Annotation", "155", "155", "Phosphoserine" ], [ "Q9NRJ4-1", "TULP4", "Modified_Residue_Annotation", "1343", "1343", "Phosphoserine" ], [ "Q9NRJ4-1", "TULP4", "Modified_Residue_Annotation", "945", "945", "Asymmetric dimethylarginine" ], [ "Q9NRJ4-1", "TULP4", "Modified_Residue_Annotation", "577", "577", "Phosphoserine" ], [ "Q9NRJ4-1", "TULP4", "Modified_Residue_Annotation", "1374", "1374", "Phosphoserine" ], [ "Q9NRJ4-1", "TULP4", "Modified_Residue_Annotation", "950", "950", "Asymmetric dimethylarginine" ], [ "Q9NQ79-1", "CRTAC1", "Glycosylation_Annotation", "619", "619", "O-linked (GalNAc...) threonine" ], [ "Q9NQ79-1", "CRTAC1", "Glycosylation_Annotation", "608", "608", "O-linked (GalNAc...) threonine" ], [ "Q9NQ79-1", "CRTAC1", "Glycosylation_Annotation", "621", "621", "O-linked (GalNAc...) threonine" ], [ "Q9NQ79-1", "CRTAC1", "Glycosylation_Annotation", "626", "626", "O-linked (GalNAc...) threonine" ], [ "Q9NQ79-1", "CRTAC1", "Glycosylation_Annotation", "618", "618", "O-linked (GalNAc...) threonine" ], [ "Q8IZF5-1", "ADGRF3", "Glycosylation_Annotation", "382", "382", "N-linked (GlcNAc...) asparagine" ], [ "Q8IZF5-1", "ADGRF3", "Glycosylation_Annotation", "441", "441", "N-linked (GlcNAc...) asparagine" ], [ "Q8IZF5-1", "ADGRF3", "Glycosylation_Annotation", "648", "648", "N-linked (GlcNAc...) asparagine" ], [ "Q8IZF5-1", "ADGRF3", "Glycosylation_Annotation", "264", "264", "N-linked (GlcNAc...) asparagine" ], [ "Q8IZF5-1", "ADGRF3", "Glycosylation_Annotation", "188", "188", "N-linked (GlcNAc...) asparagine" ], [ "Q8IZF5-1", "ADGRF3", "Glycosylation_Annotation", "301", "301", "N-linked (GlcNAc...) asparagine" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "525", "525", "Allosteric activator" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "313", "313", "Substrate; via amide nitrogen" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "371", "371", "Substrate" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "338", "338", "Substrate; via amide nitrogen" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "339", "339", "Substrate; via amide nitrogen" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "116", "116", "Substrate" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "532", "532", "Allosteric activator" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "250", "250", "ATP" ], [ "P30613-1", "PKLR", "Binding_Site_Annotation", "163", "163", "ATP" ], [ "P30613-1", "PKLR", "Site_Annotation", "313", "313", "Transition state stabilizer" ], [ "P30613-1", "PKLR", "Metal_Binding_Annotation", "315", "315", "Manganese" ], [ "P30613-1", "PKLR", "Metal_Binding_Annotation", "118", "118", "Potassium" ], [ "P30613-1", "PKLR", "Metal_Binding_Annotation", "157", "157", "Potassium; via carbonyl oxygen" ], [ "P30613-1", "PKLR", "Metal_Binding_Annotation", "156", "156", "Potassium" ], [ "P30613-1", "PKLR", "Metal_Binding_Annotation", "120", "120", "Potassium" ], [ "P30613-1", "PKLR", "Metal_Binding_Annotation", "339", "339", "Manganese" ], [ "P30613-1", "PKLR", "Modified_Residue_Annotation", "292", "292", "Phosphoserine" ], [ "P30613-1", "PKLR", "Modified_Residue_Annotation", "26", "26", "Phosphoserine" ], [ "P30613-1", "PKLR", "Modified_Residue_Annotation", "19", "19", "Phosphoserine" ], [ "P30613-1", "PKLR", "Modified_Residue_Annotation", "43", "43", "Phosphoserine" ], [ "P30613-1", "PKLR", "Modified_Residue_Annotation", "2", "2", "Phosphoserine" ], [ "P30613-1", "PKLR", "NP_Binding_Annotation", "118", "121", "ATP" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "509", "509", "Phosphoserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "427", "427", "Phosphoserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "452", "452", "Phosphoserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "647", "647", "Phosphoserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "399", "399", "Phosphoserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "407", "407", "Phosphoserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "604", "604", "Phosphoserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "2", "2", "N-acetylserine" ], [ "Q9BZL4-1", "PPP1R12C", "Modified_Residue_Annotation", "560", "560", "Phosphothreonine; by CDC42BP and ROCK2" ], [ "Q9NQ75-1", "CASS4", "Modified_Residue_Annotation", "305", "305", "Phosphoserine" ], [ "Q9NQ75-1", "CASS4", "Modified_Residue_Annotation", "249", "249", "Phosphoserine" ], [ "Q9NQ75-1", "CASS4", "Modified_Residue_Annotation", "200", "200", "Phosphoserine" ], [ "Q9NQ75-1", "CASS4", "Modified_Residue_Annotation", "376", "376", "Phosphoserine" ], [ "Q9NQ75-1", "CASS4", "Modified_Residue_Annotation", "390", "390", "Phosphoserine" ], [ "P20933-1", "AGA", "Active_Site_Annotation", "206", "206", "Nucleophile" ], [ "P20933-1", "AGA", "Glycosylation_Annotation", "308", "308", "N-linked (GlcNAc...) asparagine" ], [ "P20933-1", "AGA", "Glycosylation_Annotation", "38", "38", "N-linked (GlcNAc...) asparagine" ], [ "P20933-1", "AGA", "Modified_Residue_Annotation", "24", "24", "Blocked amino end (Ser)" ], [ "P20936-1", "RASA1", "Modified_Residue_Annotation", "615", "615", "Phosphotyrosine" ], [ "P20936-1", "RASA1", "Modified_Residue_Annotation", "831", "831", "Phosphoserine" ], [ "P20936-1", "RASA1", "Modified_Residue_Annotation", "1", "1", "N-acetylmethionine" ], [ "Q8NFX7-1", "STXBP6", "Modified_Residue_Annotation", "2", "2", "N-acetylserine" ], [ "Q9UM21-1", "MGAT4A", "Glycosylation_Annotation", "458", "458", "N-linked (GlcNAc...) asparagine" ], [ "Q9UM21-1", "MGAT4A", "Glycosylation_Annotation", "77", "77", "N-linked (GlcNAc...) asparagine" ], [ "Q9UM21-1", "MGAT4A", "Modified_Residue_Annotation", "474", "474", "Phosphoserine; by FAM20C" ], [ "Q496A3-1", "SPATS1", "Modified_Residue_Annotation", "113", "113", "Phosphoserine" ], [ "P83859-1", "QRFP", "Modified_Residue_Annotation", "91", "91", "Pyrrolidone carboxylic acid" ], [ "P83859-1", "QRFP", "Modified_Residue_Annotation", "133", "133", "Phenylalanine amide" ], [ "P40617-1", "ARL4A", "NP_Binding_Annotation", "75", "79", "GTP" ], [ "P40617-1", "ARL4A", "NP_Binding_Annotation", "134", "137", "GTP" ], [ "P40617-1", "ARL4A", "NP_Binding_Annotation", "27", "34", "GTP" ], [ "Q70EL4-1", "USP43", "Active_Site_Annotation", "110", "110", "Nucleophile" ], [ "Q70EL4-1", "USP43", "Active_Site_Annotation", "668", "668", "Proton acceptor" ], [ "Q70EL4-1", "USP43", "Modified_Residue_Annotation", "1041", "1041", "Phosphoserine" ], [ "Q70EL4-1", "USP43", "Modified_Residue_Annotation", "746", "746", "Asymmetric dimethylarginine" ], [ "Q70EL4-1", "USP43", "Modified_Residue_Annotation", "969", "969", "Phosphoserine" ], [ "Q8TBF2-1", "PRXL2B", "Modified_Residue_Annotation", "108", "108", "Phosphotyrosine" ], [ "Q15572-1", "TAF1C", "Modified_Residue_Annotation", "834", "834", "Phosphothreonine" ], [ "Q15572-1", "TAF1C", "Modified_Residue_Annotation", "848", "848", "Phosphoserine" ], [ "Q9BQP9-1", "BPIFA3", "Glycosylation_Annotation", "36", "36", "N-linked (GlcNAc...) asparagine" ], [ "Q9H999-1", "PANK3", "Binding_Site_Annotation", "207", "207", "Acetyl-CoA" ], [ "Q9H999-1", "PANK3", "Binding_Site_Annotation", "195", "195", "Acetyl-CoA" ] ] }, "readme": "Name\n - Human Protein Site Annotation\n\nVersion\n - 1.5.11\n\nCreated on\n - 2019-12-01T15:29:48.229274\n\nModified on\n - 2019-12-01T15:49:31.921346\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]\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/ln2wwwdata/reviewed/uniprot-proteome-homo-sapiens.nt\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_masterlist.csv\n Output Subdomain\n Name: human_protein_site_annotation_uniprotkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_protein_site_annotation_uniprotkb.csv\n Name: human_protein_site_annotation_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_protein_site_annotation_uniprotkb.stat.csv\n\nFields\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: \"14313\"\n Name: \"ann_type\"\n Description: \"\"\n Unique Values: \"11\"\n Name: \"gene_symbol\"\n Description: \"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\n Unique Values: \"14291\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"3597\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"3602\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"2975\"", "downloadurl": "/ln2data/releases/data/v-1.5.11/reviewed/human_protein_site_annotation_uniprotkb.csv" }