{ "bcoid": "GLY_000231", "title": "Rat Phosphorylation Sites (UniProtKB)", "description": "The Rat Phosphorylation Sites (UniProtKB) dataset contains rat [taxid:10116] UniProtKB canonical accessions ...", "filename": "rat_proteoform_phosphorylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Phosphorylation Sites", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "O35815-1...", "Atxn3..." ], [ "O35815-1...", "Atxn3..." ] ], "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": "phosphorylated_residue" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "phosphorylation_site_uniprotkb" }, { "type": "string", "label": "phosphorylation_annotation" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "eco_id" } ], [ "O35815-1", "Atxn3", "Phosphoserine", "Ser", "273", "Phosphoserine", "", "", "" ], [ "O35815-1", "Atxn3", "Phosphoserine", "Ser", "321", "Phosphoserine", "", "", "" ], [ "O35815-1", "Atxn3", "Phosphoserine", "Ser", "272", "Phosphoserine", "", "", "" ], [ "O35815-1", "Atxn3", "Phosphoserine", "Ser", "268", "Phosphoserine", "", "", "" ], [ "P07174-1", "Ngfr", "Phosphoserine", "Ser", "312", "Phosphoserine", "", "", "" ], [ "P21707-1", "Syt1", "Phosphoserine", "Ser", "264", "Phosphoserine", "", "", "" ], [ "P21707-1", "Syt1", "Phosphotyrosine", "Tyr", "229", "Phosphotyrosine", "", "", "" ], [ "P31652-1", "Slc6a4", "Phosphothreonine", "Thr", "276", "Phosphothreonine", "", "", "" ], [ "P31652-1", "Slc6a4", "Phosphoserine", "Ser", "611", "Phosphoserine", "", "", "" ], [ "P31652-1", "Slc6a4", "Phosphotyrosine", "Tyr", "47", "Phosphotyrosine", "", "", "" ], [ "P31652-1", "Slc6a4", "Phosphothreonine", "Thr", "613", "Phosphothreonine", "", "", "" ], [ "P31652-1", "Slc6a4", "Phosphothreonine", "Thr", "616", "Phosphothreonine", "", "", "" ], [ "P31652-1", "Slc6a4", "Phosphotyrosine", "Tyr", "142", "Phosphotyrosine", "", "", "" ], [ "P32851-1", "Stx1a", "Phosphoserine", "Ser", "188", "Phosphoserine; by DAPK1", "", "", "" ], [ "P59241-1", "Aurka", "Phosphoserine", "Ser", "335", "Phosphoserine; by PKA and PAK", "", "", "" ], [ "P59241-1", "Aurka", "Phosphothreonine", "Thr", "281", "Phosphothreonine", "", "", "" ], [ "P59241-1", "Aurka", "Phosphoserine", "Ser", "40", "Phosphoserine", "", "", "" ], [ "P59241-1", "Aurka", "Phosphoserine", "Ser", "50", "Phosphoserine", "", "", "" ], [ "P59241-1", "Aurka", "Phosphothreonine", "Thr", "280", "Phosphothreonine", "", "", "" ], [ "P60881-1", "Snap25", "Phosphoserine", "Ser", "154", "Phosphoserine", "", "", "" ], [ "P60881-1", "Snap25", "Phosphothreonine", "Thr", "138", "Phosphothreonine; by PKC and PKA", "", "", "" ], [ "P60881-1", "Snap25", "Phosphoserine", "Ser", "187", "Phosphoserine; by PKC", "", "", "" ], [ "Q91V26-1", "Sphk1", "Phosphoserine", "Ser", "225", "Phosphoserine", "", "", "" ], [ "Q91V26-1", "Sphk1", "Phosphothreonine", "Thr", "193", "Phosphothreonine", "", "", "" ], [ "A1A5P5-1", "Armc9", "Phosphoserine", "Ser", "583", "Phosphoserine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "404", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "424", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "227", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "411", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "438", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphoserine", "Ser", "303", "Phosphoserine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "430", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "442", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphothreonine", "Thr", "415", "Phosphothreonine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphoserine", "Ser", "417", "Phosphoserine", "", "", "" ], [ "O08837-1", "Cdc5l", "Phosphoserine", "Ser", "358", "Phosphoserine", "", "", "" ], [ "O35240-1", "Asic3", "Phosphothreonine", "Thr", "40", "Phosphothreonine; by PKC", "", "", "" ], [ "O35240-1", "Asic3", "Phosphoserine", "Ser", "523", "Phosphoserine; by PKC", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "1335", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphothreonine", "Thr", "1337", "Phosphothreonine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "589", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "216", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "256", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "424", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "1245", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "1206", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "1133", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphothreonine", "Thr", "1218", "Phosphothreonine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "562", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "557", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "246", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "1180", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphothreonine", "Thr", "1239", "Phosphothreonine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "1701", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "655", "Phosphoserine", "", "", "" ], [ "O35889-1", "Afdn", "Phosphoserine", "Ser", "1179", "Phosphoserine", "", "", "" ], [ "P0DP29-1", "Calm1", "Phosphothreonine", "Thr", "45", "Phosphothreonine; by CaMK4", "", "", "" ], [ "P0DP30-1", "Calm2", "Phosphothreonine", "Thr", "45", "Phosphothreonine; by CaMK4", "", "", "" ], [ "P12711-1", "Adh5", "Phosphoserine", "Ser", "247", "Phosphoserine", "", "", "" ], [ "P12711-1", "Adh5", "Phosphoserine", "Ser", "324", "Phosphoserine", "", "", "" ], [ "P12711-1", "Adh5", "Phosphoserine", "Ser", "351", "Phosphoserine", "", "", "" ], [ "P15650-1", "Acadl", "Phosphoserine", "Ser", "191", "Phosphoserine", "", "", "" ], [ "P15650-1", "Acadl", "Phosphoserine", "Ser", "362", "Phosphoserine", "", "", "" ], [ "P19357-1", "Slc2a4", "Phosphoserine", "Ser", "274", "Phosphoserine; by SGK1", "", "", "" ], [ "P19490-1", "Gria1", "Phosphoserine", "Ser", "710", "Phosphoserine; by PKC", "", "", "" ], [ "P19490-1", "Gria1", "Phosphoserine", "Ser", "863", "Phosphoserine; by PKC, PKA and PKG/PRKG2", "", "", "" ], [ "P19490-1", "Gria1", "Phosphoserine", "Ser", "645", "Phosphoserine", "", "", "" ], [ "P19490-1", "Gria1", "Phosphoserine", "Ser", "849", "Phosphoserine; by PKC, PKA and CAMK2", "", "", "" ], [ "P19491-1", "Gria2", "Phosphotyrosine", "Tyr", "876", "Phosphotyrosine", "", "", "" ], [ "P21575-1", "Dnm1", "Phosphoserine", "Ser", "512", "Phosphoserine", "", "", "" ], [ "P21575-1", "Dnm1", "Phosphoserine", "Ser", "774", "Phosphoserine", "", "", "" ], [ "P21575-1", "Dnm1", "Phosphoserine", "Ser", "778", "Phosphoserine", "", "", "" ], [ "P21575-1", "Dnm1", "Phosphoserine", "Ser", "857", "Phosphoserine", "", "", "" ], [ "P21575-1", "Dnm1", "Phosphoserine", "Ser", "347", "Phosphoserine", "", "", "" ], [ "P21575-1", "Dnm1", "Phosphoserine", "Ser", "851", "Phosphoserine", "", "", "" ], [ "P21575-1", "Dnm1", "Phosphoserine", "Ser", "822", "Phosphoserine", "", "", "" ], [ "P26769-1", "Adcy2", "Phosphoserine", "Ser", "490", "Phosphoserine; by PKC", "", "", "" ], [ "P26769-1", "Adcy2", "Phosphoserine", "Ser", "543", "Phosphoserine; by PKC", "", "", "" ], [ "P28647-1", "Adora3", "Phosphothreonine", "Thr", "318", "Phosphothreonine", "", "", "" ], [ "P28647-1", "Adora3", "Phosphothreonine", "Thr", "319", "Phosphothreonine", "", "", "" ], [ "P28647-1", "Adora3", "Phosphothreonine", "Thr", "307", "Phosphothreonine", "", "", "" ], [ "P31000-1", "Vim", "Phosphoserine", "Ser", "55", "Phosphoserine", "", "", "" ], [ "P35213-1", "Ywhab", "Phosphoserine", "Ser", "232", "Phosphoserine", "", "", "" ], [ "P35213-1", "Ywhab", "Phosphothreonine", "Thr", "2", "Phosphothreonine", "", "", "" ] ] }, "readme": "Name\n - Rat Phosphorylation Sites (UniProtKB)\n\nVersion\n - 1.5.18\n\nCreated on\n - 2019-09-06T14:06:38.959200\n\nModified on\n - 2020-04-10T11:53:53.248846\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 Rat Phosphorylation Sites (UniProtKB) dataset contains rat [taxid:10116] UniProtKB canonical accessions with information on reported and predicted phosphoryation sites with evidence in UniProtKB database. The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - phosphoryation Sites\n - ptm processing\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script loads the phosphorylation information from the triplestore conatining triples from the nt file and extracts as a csv dataset\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-proteoform-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-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/uniprot-proteome-rattus-norvegicus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/rat_protein_masterlist.csv\n Output Subdomain\n Name: rat_proteoform_phosphorylation_sites_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/rat_proteoform_phosphorylation_sites_uniprotkb.csv\n Name: rat_proteoform_phosphorylation_sites_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/rat_proteoform_phosphorylation_sites_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: \"3912\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"1\"\n Name: \"phosphorylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where phosphorylation is observed\"\n Unique Values: \"1983\"\n Name: \"phosphorylation_annotation\"\n Description: \"The phosphorylation annotation in UniProtKB that provides more context and description of a phosphorylation event on a protein.\"\n Unique Values: \"440\"\n Name: \"phosphorylated_residue\"\n Description: \"The amino acid that is modified by phosphorylation\"\n Unique Values: \"4\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"4\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"1\"\n Name: \"gene_symbol\"\n Description: \"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\n Unique Values: \"3871\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.18/reviewed/rat_proteoform_phosphorylation_sites_uniprotkb.csv" }