{ "bcoid": "GLY_000318", "title": "Rat Protein PTM Annotation (UniProtKB)", "description": "The Rat Protein PTM Annotation (UniProtKB) dataset contains rat [taxid:10116] PTM annotations for UniProtKB ...", "filename": "rat_protein_ptm_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "PTM annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P30349-1...", "..." ], [ "Q6MG56-1...", "Q8R5M8..." ] ], "headers": [ "uniprotkb_ca...", "pmid..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "ptm_annotation" } ], [ "P30349-1", "", "", "Phosphorylation at Ser-415 inhibits enzymatic activity." ], [ "Q6MG56-1", "Q8R5M8", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P19518", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q92484", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P41597", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P04629", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P48023", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P41180", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q6SJQ0", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "10753969", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "P09172", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q96D31", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "O95866", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "7592931", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q8BGT1", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q8BLU0", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "11331877", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "P30989", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P13569", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q92633", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q9EPK8", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "2775174", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "P41181", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "O60704", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q13433", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P07911", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "O60507", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q8R2Z5", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q6UWY2", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q86Y38", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "3121604", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "P14151", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "7669781", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "27294781", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "8939937", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q6UW60", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "14622291", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "9214393", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "P05067", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P07221", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P16070", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "14570927", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q91V24", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "10970803", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q6PGN1", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "20716133", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "E9PX95", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "2255909", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "9221928", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q9Z125", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "D7PDD4", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P30533", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "9950058", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "P42658", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "9774638", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "8943344", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "15817460", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "15618538", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "10760272", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "19217376", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "10896669", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q14003", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q8IWT6", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "17478059", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "11160393", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "1694763", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "2440672", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "8334986", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "1309971", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q8BIK6", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "12016218", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q7Z7D3", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q9D806", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "12595489", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q8C341", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "Q5DTL9", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "10713145", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "Q8BLY3", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "P20239", "ECO_0000250", "N-glycosylated." ], [ "Q6MG56-1", "11328856", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "7476911", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "16980967", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "14970196", "ECO_0000269", "N-glycosylated." ], [ "Q6MG56-1", "12671990", "ECO_0000269", "N-glycosylated." ] ] }, "readme": "Name\n - Rat Protein PTM Annotation (UniProtKB)\n\nVersion\n - 1.5.23\n\nCreated on\n - 2019-11-30T14:07:14.445471\n\nModified on\n - 2020-04-10T12:14:03.498068\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 Protein PTM Annotation (UniProtKB) dataset contains rat [taxid:10116] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. 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 - ptm annotation\n - glycosylation\n - phosphorylation\n\n Pipeline Steps\n - Step-1: The script extracts the ptm annotation strings 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-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/uniprot-proteome-rattus-norvegicus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_masterlist.csv\n Output Subdomain\n Name: rat_protein_ptm_annotation_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_ptm_annotation_uniprotkb.csv\n Name: rat_protein_ptm_annotation_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_ptm_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: \"2502\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"6\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"1787\"\n Name: \"ptm_annotation\"\n Description: \"The Post Translational Modifiaction (PTM) annotation in UniProtKB that provides more context and description about the PTMs occuring on a proein\"\n Unique Values: \"2926\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_ptm_annotation_uniprotkb.csv" }