{ "bcoid": "GLY_000809", "title": "Yeast Phosphorylation Sites (iPTMNet)", "description": "This dataset contains yeast [taxid:559292] phosphorylation sites from iPTMNet database. The protein and ...", "filename": "yeast_proteoform_phosphorylation_sites_iptmnet.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Proteoform" ], "tag": [ "Phosphorylation Sites (iPTMnet)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P04050-1...", "1557..." ], [ "P04050-1...", "1557..." ] ], "headers": [ "uniprotkb_ca...", "phosphorylat..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "phosphorylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "kinase_uniprotkb_canonical_ac" }, { "type": "string", "label": "kinase_gene_name" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P04050-1", "1557", "Ser", "", "", "protein_xref_intact", "P04050", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1557", "Ser", "", "", "protein_xref_iptmnet", "P04050", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1557", "Ser", "", "", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1560", "Ser", "", "", "protein_xref_intact", "P04050", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1560", "Ser", "", "", "protein_xref_iptmnet", "P04050", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1560", "Ser", "", "", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1562", "Ser", "", "", "protein_xref_intact", "P04050", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1562", "Ser", "", "", "protein_xref_iptmnet", "P04050", "protein_xref_iptmnet", "P04050" ], [ "P04050-1", "1562", "Ser", "", "", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P04050" ], [ "P14737-1", "462", "Ser", "", "", "protein_xref_intact", "P14737", "protein_xref_iptmnet", "P14737" ], [ "P14737-1", "462", "Ser", "", "", "protein_xref_iptmnet", "P14737", "protein_xref_iptmnet", "P14737" ], [ "P14737-1", "462", "Ser", "", "", "protein_xref_pubmed", "21946560", "protein_xref_iptmnet", "P14737" ], [ "P14737-1", "474", "Thr", "", "", "protein_xref_intact", "P14737", "protein_xref_iptmnet", "P14737" ], [ "P14737-1", "474", "Thr", "", "", "protein_xref_iptmnet", "P14737", "protein_xref_iptmnet", "P14737" ], [ "P14737-1", "474", "Thr", "", "", "protein_xref_pubmed", "21946560", "protein_xref_iptmnet", "P14737" ], [ "P27692-1", "19", "Ala", "", "", "protein_xref_intact", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "19", "Ala", "", "", "protein_xref_iptmnet", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "19", "Ala", "", "", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "13", "Asp", "", "", "protein_xref_intact", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "13", "Asp", "", "", "protein_xref_iptmnet", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "13", "Asp", "", "", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "1", "Met", "", "", "protein_xref_intact", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "1", "Met", "", "", "protein_xref_iptmnet", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "1", "Met", "", "", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "7", "Thr", "", "", "protein_xref_intact", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "7", "Thr", "", "", "protein_xref_iptmnet", "P27692", "protein_xref_iptmnet", "P27692" ], [ "P27692-1", "7", "Thr", "", "", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P27692" ], [ "P32356-1", "21", "Ser", "", "", "protein_xref_intact", "P32356", "protein_xref_iptmnet", "P32356" ], [ "P32356-1", "21", "Ser", "", "", "protein_xref_iptmnet", "P32356", "protein_xref_iptmnet", "P32356" ], [ "P32356-1", "21", "Ser", "", "", "protein_xref_pubmed", "17916074", "protein_xref_iptmnet", "P32356" ], [ "P32356-1", "23", "Ser", "", "", "protein_xref_intact", "P32356", "protein_xref_iptmnet", "P32356" ], [ "P32356-1", "23", "Ser", "", "", "protein_xref_iptmnet", "P32356", "protein_xref_iptmnet", "P32356" ], [ "P32356-1", "23", "Ser", "", "", "protein_xref_pubmed", "17916074", "protein_xref_iptmnet", "P32356" ], [ "P34244-1", "1220", "Ser", "", "", "protein_xref_intact", "P34244", "protein_xref_iptmnet", "P34244" ], [ "P34244-1", "1220", "Ser", "", "", "protein_xref_iptmnet", "P34244", "protein_xref_iptmnet", "P34244" ], [ "P34244-1", "1220", "Ser", "", "", "protein_xref_pubmed", "16688223", "protein_xref_iptmnet", "P34244" ], [ "P35187-1", "451", "Thr", "", "", "protein_xref_intact", "P35187", "protein_xref_iptmnet", "P35187" ], [ "P35187-1", "451", "Thr", "", "", "protein_xref_iptmnet", "P35187", "protein_xref_iptmnet", "P35187" ], [ "P35187-1", "451", "Thr", "", "", "protein_xref_pubmed", "22820947", "protein_xref_iptmnet", "P35187" ], [ "P38634-1", "80", "Ser", "", "", "protein_xref_intact", "P38634", "protein_xref_iptmnet", "P38634" ], [ "P38634-1", "80", "Ser", "", "", "protein_xref_iptmnet", "P38634", "protein_xref_iptmnet", "P38634" ], [ "P38634-1", "80", "Ser", "", "", "protein_xref_pubmed", "19008353", "protein_xref_iptmnet", "P38634" ], [ "P43601-1", "42", "Glu", "", "", "protein_xref_intact", "P43601", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "42", "Glu", "", "", "protein_xref_iptmnet", "P43601", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "42", "Glu", "", "", "protein_xref_pubmed", "22333915", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "240", "Val", "", "", "protein_xref_intact", "P43601", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "240", "Val", "", "", "protein_xref_iptmnet", "P43601", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "240", "Val", "", "", "protein_xref_pubmed", "22333915", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "47", "Tyr", "", "", "protein_xref_intact", "P43601", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "47", "Tyr", "", "", "protein_xref_iptmnet", "P43601", "protein_xref_iptmnet", "P43601" ], [ "P43601-1", "47", "Tyr", "", "", "protein_xref_pubmed", "22333915", "protein_xref_iptmnet", "P43601" ], [ "P53135-1", "622", "Ser", "", "", "protein_xref_intact", "P53135", "protein_xref_iptmnet", "P53135" ], [ "P53135-1", "622", "Ser", "", "", "protein_xref_iptmnet", "P53135", "protein_xref_iptmnet", "P53135" ], [ "P53135-1", "622", "Ser", "", "", "protein_xref_pubmed", "21946560", "protein_xref_iptmnet", "P53135" ], [ "P53135-1", "600", "Thr", "", "", "protein_xref_intact", "P53135", "protein_xref_iptmnet", "P53135" ], [ "P53135-1", "600", "Thr", "", "", "protein_xref_iptmnet", "P53135", "protein_xref_iptmnet", "P53135" ], [ "P53135-1", "600", "Thr", "", "", "protein_xref_pubmed", "21946560", "protein_xref_iptmnet", "P53135" ], [ "P06738-1", "31", "Thr", "", "", "protein_xref_pelm", "P06738", "protein_xref_iptmnet", "P06738" ], [ "P06738-1", "31", "Thr", "", "", "protein_xref_iptmnet", "P06738", "protein_xref_iptmnet", "P06738" ], [ "P06738-1", "31", "Thr", "", "", "protein_xref_pubmed", "1613787", "protein_xref_iptmnet", "P06738" ], [ "P06782-1", "210", "Thr", "", "", "protein_xref_pelm", "P06782", "protein_xref_iptmnet", "P06782" ], [ "P06782-1", "210", "Thr", "", "", "protein_xref_iptmnet", "P06782", "protein_xref_iptmnet", "P06782" ], [ "P06782-1", "210", "Thr", "", "", "protein_xref_pubmed", "7905477", "protein_xref_iptmnet", "P06782" ], [ "P06784-1", "359", "Ser", "", "", "protein_xref_pelm", "P06784", "protein_xref_iptmnet", "P06784" ], [ "P06784-1", "359", "Ser", "", "", "protein_xref_iptmnet", "P06784", "protein_xref_iptmnet", "P06784" ], [ "P06784-1", "359", "Ser", "", "", "protein_xref_pubmed", "8131746", "protein_xref_iptmnet", "P06784" ], [ "P06784-1", "363", "Thr", "", "", "protein_xref_pelm", "P06784", "protein_xref_iptmnet", "P06784" ], [ "P06784-1", "363", "Thr", "", "", "protein_xref_iptmnet", "P06784", "protein_xref_iptmnet", "P06784" ], [ "P06784-1", "363", "Thr", "", "", "protein_xref_pubmed", "8131746", "protein_xref_iptmnet", "P06784" ], [ "P06786-1", "1087", "Ser", "", "", "protein_xref_pelm", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1087", "Ser", "", "", "protein_xref_iptmnet", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1087", "Ser", "", "", "protein_xref_pubmed", "1332607", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1266", "Ser", "", "", "protein_xref_pelm", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1266", "Ser", "", "", "protein_xref_iptmnet", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1266", "Ser", "", "", "protein_xref_pubmed", "1332607", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1269", "Ser", "", "", "protein_xref_pelm", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1269", "Ser", "", "", "protein_xref_iptmnet", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1269", "Ser", "", "", "protein_xref_pubmed", "1332607", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1272", "Ser", "", "", "protein_xref_pelm", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1272", "Ser", "", "", "protein_xref_iptmnet", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1272", "Ser", "", "", "protein_xref_pubmed", "1332607", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1353", "Ser", "", "", "protein_xref_pelm", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1353", "Ser", "", "", "protein_xref_iptmnet", "P06786", "protein_xref_iptmnet", "P06786" ], [ "P06786-1", "1353", "Ser", "", "", "protein_xref_pubmed", "1332607", "protein_xref_iptmnet", "P06786" ] ] }, "readme": "Name\n - Yeast Phosphorylation Sites (iPTMNet)\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-09-06T09:56:04.354720\n\nModified on\n - 2023-09-11T20:47:35\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - This dataset contains yeast [taxid:559292] phosphorylation sites from iPTMNet database. The protein and sites are mapped to UniProtKB canonical accessions and fasta sequence. If you use this dataset please provide proper attribution to iPTMnet-GlyGen.\n\nDescription Domain\n Keywords\n - iPTMnet\n - Phosphorylation sites\n\n Pipeline Steps\n - Step-0: The script extracts the phosphorylation information from the source dataset as per taxid and extracts as a csv dataset. The protein accession and sites are mapped to the UniProtKB canonical accession and fasta sequence.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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: yeast_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_masterlist.csv\n Name: ptm.txt\n URI: https:/data.glygen.org/ln2downloads/iptmnet/2023_07_18/ptm.txt\n Output Subdomain\n Name: yeast_proteoform_phosphorylation_sites_iptmnet.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_proteoform_phosphorylation_sites_iptmnet.csv\n Name: yeast_proteoform_phosphorylation_sites_iptmnet.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_proteoform_phosphorylation_sites_iptmnet.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"3462\"\n Name: \"phosphorylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where phosphorylation is observed\"\n Unique Values: \"1761\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"10\"\n Name: \"kinase_uniprotkb_canonical_ac\"\n Description: \"The UniProtKB canonical accession for the kinase enzyme that is phosphorylating the protein\"\n Unique Values: \"60\"\n Name: \"kinase_gene_name\"\n Description: \"\"\n Unique Values: \"60\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"10\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"4452\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"3462\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_proteoform_phosphorylation_sites_iptmnet.csv" }