{ "bcoid": "GLY_000758", "title": "Yeast Protein Information (NCBI RefSeq)", "description": "The Yeast Protein Information (NCBI RefSeq) dataset contains yeast [taxid:559292] protein information ...", "filename": "yeast_protein_info_refseq.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Protein Information" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Robel...", " mapped NP_0..." ], [ "Robel...", " feat NP_009..." ] ], "headers": [ "uniprotkb_ca...", "p_refseq_ac_..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "p_refseq_ac_best_match" }, { "type": "string", "label": "refseq_protein_name" }, { "type": "string", "label": "refseq_protein_length" }, { "type": "string", "label": "refseq_protein_summary" } ], [ "Robel", " mapped NP_009305" ], [ "Robel", " feat NP_009305" ], [ "P00401-1", "NP_009305", "cytochrome c oxidase subunit 1", "534", "" ], [ "Robel", " mapped NP_009306" ], [ "Robel", " feat NP_009306" ], [ "Q9ZZX1-1", "NP_009306", "intron-encoded DNA endonuclease aI5 alpha", "630", "" ], [ "Robel", " mapped NP_009307" ], [ "Robel", " feat NP_009307" ], [ "P03878-1", "NP_009307", "intron-encoded DNA endonuclease aI4", "556", "" ], [ "Robel", " mapped NP_009308" ], [ "Robel", " feat NP_009308" ], [ "P03877-1", "NP_009308", "intron-encoded DNA endonuclease aI3", "415", "" ], [ "Robel", " mapped NP_009309" ], [ "Robel", " feat NP_009309" ], [ "P03876-1", "NP_009309", "intron-encoded reverse transcriptase aI2", "854", "" ], [ "Robel", " mapped NP_009310" ], [ "Robel", " feat NP_009310" ], [ "P03875-1", "NP_009310", "intron-encoded reverse transcriptase aI1", "834", "" ], [ "Robel", " mapped NP_009311" ], [ "Robel", " feat NP_009311" ], [ "Q9ZZX0-1", "NP_009311", "intron-encoded DNA endonuclease aI5 beta", "354", "" ], [ "Robel", " mapped NP_009312" ], [ "Robel", " feat NP_009312" ], [ "P00856-1", "NP_009312", "F1F0 ATP synthase subunit 8", "48", "" ], [ "Robel", " mapped NP_009313" ], [ "Robel", " feat NP_009313" ], [ "P00854-1", "NP_009313", "F1F0 ATP synthase subunit a", "259", "" ], [ "Robel", " mapped NP_009315" ], [ "Robel", " feat NP_009315" ], [ "P00163-1", "NP_009315", "cytochrome b", "385", "" ], [ "Robel", " mapped NP_009316" ], [ "Robel", " feat NP_009316" ], [ "P03879-1", "NP_009316", "intron-encoded RNA maturase bI4", "638", "" ], [ "Robel", " mapped NP_009317" ], [ "Robel", " feat NP_009317" ], [ "Q9ZZW7-1", "NP_009317", "cytochrome b mRNA maturase bI3", "517", "" ], [ "Robel", " mapped NP_009318" ], [ "Robel", " feat NP_009318" ], [ "P03873-1", "NP_009318", "cytochrome b mRNA maturase bI2", "423", "" ], [ "Robel", " mapped NP_009319" ], [ "Robel", " feat NP_009319" ], [ "P61829-1", "NP_009319", "F0 ATP synthase subunit c", "76", "" ], [ "Robel", " mapped NP_009320" ], [ "Robel", " feat NP_009320" ], [ "P02381-1", "NP_009320", "mitochondrial 37S ribosomal protein VAR1", "398", "" ], [ "Robel", " mapped NP_009324" ], [ "Robel", " feat NP_009324" ], [ "P03882-1", "NP_009324", "intron-encoded endonuclease I-SceI", "235", "" ], [ "Robel", " mapped NP_009326" ], [ "Robel", " feat NP_009326" ], [ "P00410-1", "NP_009326", "cytochrome c oxidase subunit 2", "251", "" ], [ "Robel", " mapped NP_009327" ], [ "Robel", " feat NP_009327" ], [ "P03881-1", "NP_009327", "maturase-like protein", "472", "" ], [ "Robel", " mapped NP_009328" ], [ "Robel", " feat NP_009328" ], [ "P00420-1", "NP_009328", "cytochrome c oxidase subunit 3", "269", "" ], [ "Robel", " mapped NP_009332" ], [ "Robel", " feat NP_009332" ], [ "P0CE93-1", "NP_009332", "seripauperin PAU8", "120", "" ], [ "Robel", " mapped NP_878038" ], [ "Robel", " feat NP_878038" ], [ "Q8TGK6-1", "NP_878038", "uncharacterized protein", "75", "" ], [ "Robel", " mapped NP_009333" ], [ "Robel", " feat NP_009333" ], [ "P39709-1", "NP_009333", "putative permease SEO1", "593", "" ], [ "Robel", " mapped NP_009335" ], [ "Robel", " feat NP_009335" ], [ "O13511-1", "NP_009335", "uncharacterized protein", "128", "" ], [ "Robel", " mapped NP_009336" ], [ "Robel", " feat NP_009336" ], [ "O13512-1", "NP_009336", "uncharacterized protein", "126", "" ], [ "Robel", " mapped NP_058136" ], [ "Robel", " feat NP_058136" ], [ "Q6B2U8-1", "NP_058136", "Tda8p", "126", "" ], [ "Robel", " mapped NP_009337" ], [ "Robel", " feat NP_009337" ], [ "P39711-1", "NP_009337", "uncharacterized protein", "94", "" ], [ "Robel", " mapped NP_878039" ], [ "Robel", " feat NP_878039" ], [ "Q3E791-1", "NP_878039", "uncharacterized protein", "96", "" ], [ "Robel", " mapped NP_009338" ], [ "Robel", " feat NP_009338" ], [ "P39712-1", "NP_009338", "flocculin FLO9", "1322", "" ] ] }, "readme": "Name\n - Yeast Protein Information (NCBI RefSeq)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2022-08-30T16:17:01.573604\n\nModified on\n - 2023-09-11T19:08:41\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], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Yeast Protein Information (NCBI RefSeq) dataset contains yeast [taxid:559292] protein information such as protein accession, name, length and protein function summary from NCBI RefSeq database. The dataset is derived from NCBI RefSeq Release 96, September 9, 2019. If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen\n\nDescription Domain\n Keywords\n - protein information\n - protein length\n - NCBI RefSeq\n - protein summary\n\n Pipeline Steps\n - Step-1: The script parses the NCBI RefSeq gpff files to extract the accession, length, protein summary and then maps the NCBI RefSeq accesion to the UniProtKB Canonical accessions\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: yeast_protein_xref_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_xref_refseq.csv\n Name: refseq_protein_all_559292.gpff\n URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2024_02_18/refseq_protein_all_559292.gpff\n Output Subdomain\n Name: yeast_protein_info_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_info_refseq.csv\n Name: yeast_protein_info_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_info_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5845\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"17532\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"5079\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"1293\"\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/yeast_protein_info_refseq.csv" }