{ "bcoid": "GLY_000796", "title": "Yeast UniProtKB Xref RefSeq", "description": "The Yeast UniprotKB Xref RefSeq contains yeast [taxid:559292] UniProtKB canonical accessions cross-referenced ...", "filename": "yeast_protein_xref_refseq.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Refseq cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30619-1...", "protein_xref..." ], [ "P39972-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_label" } ], [ "P30619-1", "protein_xref_refseq", "NP_010448", "" ], [ "P39972-1", "protein_xref_refseq", "NP_010839", "" ], [ "P39970-1", "protein_xref_refseq", "NP_010964", "" ], [ "P39971-1", "protein_xref_refseq", "NP_010837", "" ], [ "P39976-1", "protein_xref_refseq", "NP_010843", "" ], [ "P39977-1", "protein_xref_refseq", "NP_001257672", "" ], [ "P39974-1", "protein_xref_refseq", "NP_010841", "" ], [ "P39975-1", "protein_xref_refseq", "NP_010842", "" ], [ "P39978-1", "protein_xref_refseq", "NP_010847", "" ], [ "P39979-1", "protein_xref_refseq", "NP_010848", "" ], [ "Q07959-1", "protein_xref_refseq", "NP_013123", "" ], [ "P0CX69-1", "protein_xref_refseq", "NP_013766", "" ], [ "P25379-1", "protein_xref_refseq", "NP_001018030", "" ], [ "P25378-1", "protein_xref_refseq", "NP_009956", "" ], [ "P17121-1", "protein_xref_refseq", "NP_010677", "" ], [ "P25374-1", "protein_xref_refseq", "NP_009912", "" ], [ "P17123-1", "protein_xref_refseq", "NP_012022", "" ], [ "P17122-1", "protein_xref_refseq", "NP_012023", "" ], [ "P25371-1", "protein_xref_refseq", "NP_009937", "" ], [ "P25370-1", "protein_xref_refseq", "NP_009894", "" ], [ "P25373-1", "protein_xref_refseq", "NP_009895", "" ], [ "P25372-1", "protein_xref_refseq", "NP_010006", "" ], [ "Q06568-1", "protein_xref_refseq", "NP_013355", "" ], [ "Q03049-1", "protein_xref_refseq", "NP_010830", "" ], [ "Q06567-1", "protein_xref_refseq", "NP_013354", "" ], [ "Q06563-1", "protein_xref_refseq", "NP_013352", "" ], [ "Q00539-1", "protein_xref_refseq", "NP_011954", "" ], [ "Q07748-1", "protein_xref_refseq", "NP_010037", "" ], [ "Q07963-1", "protein_xref_refseq", "NP_013124", "" ], [ "Q07967-1", "protein_xref_refseq", "NP_013130", "" ], [ "Q00246-1", "protein_xref_refseq", "NP_012981", "" ], [ "Q00245-1", "protein_xref_refseq", "NP_012148", "" ], [ "P0CX61-1", "protein_xref_refseq", "NP_058157", "" ], [ "P40422-1", "protein_xref_refseq", "NP_012013", "" ], [ "P0CX62-1", "protein_xref_refseq", "NP_058157", "" ], [ "P0CX64-1", "protein_xref_refseq", "NP_058163", "" ], [ "P0CX67-1", "protein_xref_refseq", "NP_013766", "" ], [ "P18494-1", "protein_xref_refseq", "NP_010958", "" ], [ "P18496-1", "protein_xref_refseq", "NP_013497", "" ], [ "Q03441-1", "protein_xref_refseq", "NP_010283", "" ], [ "Q08748-1", "protein_xref_refseq", "NP_014939", "" ], [ "Q08749-1", "protein_xref_refseq", "NP_014940", "" ], [ "Q08746-1", "protein_xref_refseq", "NP_014937", "" ], [ "Q08747-1", "protein_xref_refseq", "NP_014938", "" ], [ "Q08745-1", "protein_xref_refseq", "NP_014936", "" ], [ "Q08742-1", "protein_xref_refseq", "NP_014929", "" ], [ "Q08743-1", "protein_xref_refseq", "NP_014935", "" ], [ "P32915-1", "protein_xref_refseq", "NP_013482", "" ], [ "P32914-1", "protein_xref_refseq", "NP_011577", "" ], [ "P32917-1", "protein_xref_refseq", "NP_010388", "" ], [ "P32916-1", "protein_xref_refseq", "NP_010578", "" ], [ "P32911-1", "protein_xref_refseq", "NP_014155", "" ], [ "P32910-1", "protein_xref_refseq", "NP_014400", "" ], [ "P32913-1", "protein_xref_refseq", "NP_014775", "" ], [ "P32912-1", "protein_xref_refseq", "NP_011303", "" ], [ "Q04438-1", "protein_xref_refseq", "NP_013825", "" ], [ "Q04439-1", "protein_xref_refseq", "NP_013827", "" ], [ "Q04430-1", "protein_xref_refseq", "NP_010820", "" ], [ "Q04431-1", "protein_xref_refseq", "NP_010821", "" ], [ "Q04432-1", "protein_xref_refseq", "NP_010822", "" ], [ "Q04433-1", "protein_xref_refseq", "NP_010823", "" ], [ "Q04437-1", "protein_xref_refseq", "NP_013824", "" ], [ "P00546-1", "protein_xref_refseq", "NP_009718", "" ], [ "P04385-1", "protein_xref_refseq", "NP_009576", "" ], [ "P04387-1", "protein_xref_refseq", "NP_013661", "" ], [ "P04386-1", "protein_xref_refseq", "NP_015076", "" ], [ "Q08299-1", "protein_xref_refseq", "NP_014484", "" ], [ "Q08562-1", "protein_xref_refseq", "NP_014834", "" ], [ "Q08560-1", "protein_xref_refseq", "NP_014829", "" ], [ "Q08561-1", "protein_xref_refseq", "NP_014832", "" ], [ "P25377-1", "protein_xref_refseq", "NP_010030", "" ], [ "P25376-1", "protein_xref_refseq", "NP_009905", "" ], [ "P32474-1", "protein_xref_refseq", "NP_010806", "" ], [ "P09007-1", "protein_xref_refseq", "NP_009944", "" ], [ "P04037-1", "protein_xref_refseq", "NP_011328", "" ], [ "P04039-1", "protein_xref_refseq", "NP_013499", "" ], [ "Q05955-1", "protein_xref_refseq", "NP_013328", "" ], [ "P00724-1", "protein_xref_refseq", "NP_012104", "" ], [ "P00729-1", "protein_xref_refseq", "NP_014026", "" ], [ "Q03048-1", "protein_xref_refseq", "NP_013050", "" ], [ "P50896-1", "protein_xref_refseq", "NP_010793", "" ], [ "P32786-1", "protein_xref_refseq", "NP_009539", "" ], [ "Q02872-1", "protein_xref_refseq", "NP_015217", "" ], [ "Q02873-1", "protein_xref_refseq", "NP_015218", "" ] ] }, "readme": "Name\n - Yeast UniProtKB Xref RefSeq\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-09-14T12:24:23.479851\n\nModified on\n - 2023-09-11T20:32:03\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@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 Yeast UniprotKB Xref RefSeq contains yeast [taxid:559292] UniProtKB canonical accessions cross-referenced to RefSeq database accessions/identifiers. The script extracts one-to-one UniProtKB isoform ac to RefSeq ac and also UniProtKB ac to RefSeq ac where there is no UniProtKB isoforms other than the canonical ac. The dataset is contributed by EMBL-EBI-UniProtKB and processed by GlyGen. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n - NCBI RefSeq is a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein. \n\nDescription Domain\n Keywords\n - protein accessions\n - RefSeq\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to NCBI RefSeq database accessions/identifiers from the triplestore containing triples from nt file and extracts the data as a csv dataset. \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_xref_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_xref_refseq.csv\n Name: yeast_protein_xref_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_xref_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5912\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"5846\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_protein_xref_refseq.csv" }