{ "bcoid": "GLY_000749", "title": "Yeast Protein Citations (UniProtKB)", "description": "The Yeast Protein Citations dataset contains publication information for yeast [taxid:559292] UniProtKB ...", "filename": "yeast_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Protein Citations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30619-1...", "Global analy..." ], [ "P30619-1...", "The referenc..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P30619-1", "Global analysis of protein expression in yeast.", "Nature", "2003", "Dephoure N., Weissman J.S., Howson R.W., Huh W.-K., O'Shea E.K., Belle A., Bower K., Ghaemmaghami S.", "protein_xref_pubmed", "14562106", "protein_xref_uniprotkb", "P30619" ], [ "P30619-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P30619" ], [ "P30619-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.", "Nature", "1997", "Andrews S., Bahr A., Bloecker H., Brandt P., Connor R., Du Z., Fulton L., Gentles S., Hawkins J., Hillier L.W., Johnson D., Latreille P., Mardis E., Mewes H.-W., Miller N., Niblett D., Oliver K., Schaefer M., Scharfe M., Vaudin M., Wambutt R., Waterston R., Wedler H., Wilson R., Chen E., Le T., Verhasselt P., Bowman S., Hunt S., Wagner G., Chung E., Nakahara K., Botstein D., Brueckner M., Davis R.W., Lin D., Hankeln T., Schneider C., Schmidt E.R., Duncan M., Favello A., Kucaba T., Rifkin L., Trevaskis E., Wohldman P., Barrell B.G., Rieger M., Berno A., Schroeder M., Ding H., Oh C., Oefner P., Schwarz S., Woelfl S., Kleine K., Becker A., Prydz H., Cooper J., Arnold W., Eide L.G., Kraemer C., Lashkari D., Allen E., Jimenez A., Kuester H., Hoheisel J.D., Pauley A., Paulin L., Brown D., Jaeger W., Volckaert G., Hyman R.W., Andre B., Perez-Alonso M., Araujo R., Komp C., Lew H., Namath A., Roberts D., Paricio N., Boskovic J., Louis E.J., Mulligan J.T., Delaveau T., Greco T., Johnston L., Nhan M., Jones L., Odell C., Menezes S., Johnston M., Pohl T.M., Harris D.E., Schramm S., McDonald S., Salom D., Bargues M., Cherry J.M., Ballesta J.P.G., Churcher C.M., Dedman K., Dietrich F.S., Dujon B., Goffeau A., Hamlin N., Hani J., Jacq C., Mueller-Auer S., Perea J., Perez-Ortin J.E., Rajandream M.A., Remacha M.A., Revuelta J.L., Vissers S., Walsh S.V., Zollner A., del Rey F., Jonniaux J.-L., Purnelle B., Saiz J.E., Urrestarazu L.A., Voet M., Wilcox L., Albermann K., Alt-Moerbe J., Aviles E., Baron L., Biteau N., Blugeon C., Brinkman R., Buitrago M.J., Carpenter J., Coster F., Garcia-Cantalejo J.M., Gattung S., Gomez-Peris A., Granotier C., Hallsworth K., Hanemann V., Heumann K., Hunicke-Smith S., Jier M., Kirsten J., Laamanen P., Langston Y., Legros Y., Moeller-Rieker S., Monnet A., Moro M., Mosedale D., Murphy L.D., Nussbaumer B., Peluso D., Petel F.X., Rasmussen S.W., Richards C., Riles L., Saluz H.P., Saren A.-M., Scholler P., Shogren T., Shore L., Shroff N., Soler-Mira A., Taich A., Vignati D., Wedler E., Winant A., Yelton M.A., Zaccaria P.", "protein_xref_pubmed", "9169867", "protein_xref_uniprotkb", "P30619" ], [ "P30619-1", "Cloning and sequencing of the yeast Saccharomyces cerevisiae SEC1 gene localized on chromosome IV.", "Yeast", "1991", "Keraenen S., Hosono K., Ruohonen L., Aalto M.K.", "protein_xref_pubmed", "1767592", "protein_xref_uniprotkb", "P30619" ], [ "P39972-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39972" ], [ "P39972-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "Nature", "1997", "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "protein_xref_pubmed", "9169868", "protein_xref_uniprotkb", "P39972" ], [ "P39970-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39970" ], [ "P39970-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "Nature", "1997", "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "protein_xref_pubmed", "9169868", "protein_xref_uniprotkb", "P39970" ], [ "P39970-1", "Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress.", "Mol. Cell. Biol.", "2000", "Struhl K., Garcia-Gimeno M.A.", "protein_xref_pubmed", "10825197", "protein_xref_uniprotkb", "P39970" ], [ "P39970-1", "ATF/CREB sites present in sub-telomeric regions of Saccharomyces cerevisiae chromosomes are part of promoters and act as UAS/URS of highly conserved COS genes.", "J. Mol. Biol.", "2002", "Hollenberg C.P., Maiwald D., Spode I., Suckow M.", "protein_xref_pubmed", "12051917", "protein_xref_uniprotkb", "P39970" ], [ "P39970-1", "Barrier proteins remodel and modify chromatin to restrict silenced domains.", "Mol. Cell. Biol.", "2004", "Chiba T., Ito T., Oki M., Kamakaka R.T., Valenzuela L.", "protein_xref_pubmed", "14966276", "protein_xref_uniprotkb", "P39970" ], [ "P39970-1", "Transcriptional activators in yeast.", "Nucleic Acids Res.", "2006", "Chiba T., Ito T., Thomas S., Uetz P., Titz B., Rajagopala S.V.", "protein_xref_pubmed", "16464826", "protein_xref_uniprotkb", "P39970" ], [ "P39970-1", "The nature of the nitrogen source added to nitrogen depleted vinifications conducted by a Saccharomyces cerevisiae strain in synthetic must affects gene expression and the levels of several volatile compounds.", "Antonie Van Leeuwenhoek", "2007", "Aranda A., Jimenez-Marti E., Mendes-Faia A., Mendes-Ferreira A., del Olmo M.L.", "protein_xref_pubmed", "17252314", "protein_xref_uniprotkb", "P39970" ], [ "P39971-1", "Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.", "Genome Res.", "2007", "Hu Y., LaBaer J., Moreira D., Raphael J., Rolfs A., Zuo D., Richardson A., Simpson A.J.G., Zhu C., Harlow E., Camargo A.A., Jepson D., Kelley F., McCarron S., Taycher E., Kolodner R.D., Kane M.F., Williamson J., Berger M.F., Bulyk M.L., Bhullar B., Mohr S., Marsischky G., Murthy T.V.S.", "protein_xref_pubmed", "17322287", "protein_xref_uniprotkb", "P39971" ], [ "P39971-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39971" ], [ "P39971-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "Nature", "1997", "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "protein_xref_pubmed", "9169868", "protein_xref_uniprotkb", "P39971" ], [ "P39976-1", "N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.", "Proc. Natl. Acad. Sci. U.S.A.", "2012", "Van Damme P, Lasa M, Polevoda B, Gazquez C, Elosegui-Artola A, Kim DS, De Juan-Pardo E, Demeyer K, Hole K, Larrea E, Timmerman E, Prieto J, Arnesen T, Sherman F, Gevaert K, Aldabe R", "protein_xref_pubmed", "22814378", "protein_xref_uniprotkb", "P39976" ], [ "P39976-1", "A proteomics approach to understanding protein ubiquitination.", "Nat. Biotechnol.", "2003", "Peng Junmin, Schwartz Daniel, Elias Joshua E, Thoreen Carson C, Cheng Dongmei, Marsischky Gerald, Roelofs Jeroen, Finley Daniel, Gygi Steven P", "protein_xref_pubmed", "12872131", "protein_xref_uniprotkb", "P39976" ], [ "P39976-1", "Global analysis of protein expression in yeast.", "Nature", "2003", "Dephoure N., Weissman J.S., Howson R.W., Huh W.-K., O'Shea E.K., Belle A., Bower K., Ghaemmaghami S.", "protein_xref_pubmed", "14562106", "protein_xref_uniprotkb", "P39976" ], [ "P39976-1", "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "Mol. Cell. Proteomics", "2008", "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "protein_xref_pubmed", "18407956", "protein_xref_uniprotkb", "P39976" ], [ "P39976-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39976" ], [ "P39976-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "Nature", "1997", "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "protein_xref_pubmed", "9169868", "protein_xref_uniprotkb", "P39976" ], [ "P39976-1", "Signalling between mitochondria and the nucleus regulates the expression of a new D-lactate dehydrogenase activity in yeast.", "Yeast", "1999", "Liu Z., Jia Y., Butow R.A., Amberg D., Chelstowska A.", "protein_xref_pubmed", "10509019", "protein_xref_uniprotkb", "P39976" ], [ "P39976-1", "Saccharomyces cerevisiae forms D-2-hydroxyglutarate and couples its degradation to D-lactate formation via a cytosolic transhydrogenase.", "J. 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Chem.", "2016", "Linster C.L., Paczia N., Becker-Kettern J., Conrotte J.F., Kay D.P., Guignard C., Jung P.P.", "protein_xref_pubmed", "26774271", "protein_xref_uniprotkb", "P39976" ], [ "P39977-1", "Global analysis of protein expression in yeast.", "Nature", "2003", "Dephoure N., Weissman J.S., Howson R.W., Huh W.-K., O'Shea E.K., Belle A., Bower K., Ghaemmaghami S.", "protein_xref_pubmed", "14562106", "protein_xref_uniprotkb", "P39977" ], [ "P39977-1", "Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.", "Genome Res.", "2007", "Hu Y., LaBaer J., Moreira D., Raphael J., Rolfs A., Zuo D., Richardson A., Simpson A.J.G., Zhu C., Harlow E., Camargo A.A., Jepson D., Kelley F., McCarron S., Taycher E., Kolodner R.D., Kane M.F., Williamson J., Berger M.F., Bulyk M.L., Bhullar B., Mohr S., Marsischky G., Murthy T.V.S.", "protein_xref_pubmed", "17322287", "protein_xref_uniprotkb", "P39977" ], [ "P39977-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39977" ], [ "P39977-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "Nature", "1997", "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "protein_xref_pubmed", "9169868", "protein_xref_uniprotkb", "P39977" ], [ "P39974-1", "Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.", "Genome Res.", "2007", "Hu Y., LaBaer J., Moreira D., Raphael J., Rolfs A., Zuo D., Richardson A., Simpson A.J.G., Zhu C., Harlow E., Camargo A.A., Jepson D., Kelley F., McCarron S., Taycher E., Kolodner R.D., Kane M.F., Williamson J., Berger M.F., Bulyk M.L., Bhullar B., Mohr S., Marsischky G., Murthy T.V.S.", "protein_xref_pubmed", "17322287", "protein_xref_uniprotkb", "P39974" ], [ "P39974-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39974" ], [ "P39974-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "Nature", "1997", "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "protein_xref_pubmed", "9169868", "protein_xref_uniprotkb", "P39974" ], [ "P39975-1", "Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae.", "Genetics", "2003", "Saunders W.S., Enyenihi A.H.", "protein_xref_pubmed", "12586695", "protein_xref_uniprotkb", "P39975" ], [ "P39975-1", "Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.", "Genome Res.", "2007", "Hu Y., LaBaer J., Moreira D., Raphael J., Rolfs A., Zuo D., Richardson A., Simpson A.J.G., Zhu C., Harlow E., Camargo A.A., Jepson D., Kelley F., McCarron S., Taycher E., Kolodner R.D., Kane M.F., Williamson J., Berger M.F., Bulyk M.L., Bhullar B., Mohr S., Marsischky G., Murthy T.V.S.", "protein_xref_pubmed", "17322287", "protein_xref_uniprotkb", "P39975" ], [ "P39975-1", "The reference genome sequence of Saccharomyces cerevisiae: Then and now.", "G3 (Bethesda)", "2014", "Engel Stacia R, Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39975" ], [ "P39975-1", "Pls1 Is a Peroxisomal Matrix Protein with a Role in Regulating Lysine Biosynthesis.", "Cells", "2022", 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Dietrich Fred S, Fisk Dianna G, Binkley Gail, Balakrishnan Rama, Costanzo Maria C, Dwight Selina S, Hitz Benjamin C, Karra Kalpana, Nash Robert S, Weng Shuai, Wong Edith D, Lloyd Paul, Skrzypek Marek S, Miyasato Stuart R, Simison Matt, Cherry J Michael", "protein_xref_pubmed", "24374639", "protein_xref_uniprotkb", "P39978" ], [ "P39978-1", "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.", "Nature", "1997", "Smith V., Chen E., Guzman E., Chung E., Nakahara K., Botstein D., Davis R.W., Lin D., Wei Y., Duncan M., Berno A., Oh C., Oefner P., Taylor P., Lashkari D., Allen E., Hyman R.W., Araujo R., Komp C., Lew H., Namath A., Roberts D., Mulligan J.T., Sehl P., Schramm S., Hartzell G., Cherry J.M., Dietrich F.S., Aviles E., Brennan T., Carpenter J., Hennessy K.M., Hunicke-Smith S., Kayser A., Mosedale D., Norgren R., Petel F.X., Shogren T., Yelton M.A.", "protein_xref_pubmed", "9169868", "protein_xref_uniprotkb", "P39978" ], [ "P39979-1", "N-terminal acetylome analyses 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U.S.A.", "2012", "Van Damme P, Lasa M, Polevoda B, Gazquez C, Elosegui-Artola A, Kim DS, De Juan-Pardo E, Demeyer K, Hole K, Larrea E, Timmerman E, Prieto J, Arnesen T, Sherman F, Gevaert K, Aldabe R", "protein_xref_pubmed", "22814378", "protein_xref_uniprotkb", "P17123" ], [ "P17123-1", "Separase, polo kinase, the kinetochore protein Slk19, and Spo12 function in a network that controls Cdc14 localization during early anaphase.", "Cell", "2002", "Stegmeier F., Amon A., Visintin R.", "protein_xref_pubmed", "11832211", "protein_xref_uniprotkb", "P17123" ], [ "P17123-1", "Global analysis of protein expression in yeast.", "Nature", "2003", "Dephoure N., Weissman J.S., Howson R.W., Huh W.-K., O'Shea E.K., Belle A., Bower K., Ghaemmaghami S.", "protein_xref_pubmed", "14562106", "protein_xref_uniprotkb", "P17123" ] ] }, "readme": "Name\n - Yeast Protein Citations (UniProtKB)\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2022-08-30T14:17:09.307325\n\nModified on\n - 2023-09-11T18:58:26\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 Protein Citations dataset contains publication information for yeast [taxid:559292] UniProtKB accessions that includes PMID, journal name, date and author and title. Publications of large scale studies, and high frequency publications pertaining to genome sequencing, cDNA, chromosomes have been filtered out as per https://data.glygen.org/ln2data/releases/data/v-1.12.3/compiled/yeast_protein_blacklisted_pmids_uniprotkb.csv. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - publications\n - PMID\n - journal\n - citations\n - authors\n - UniProtKB\n - PubMed\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB publication data from the triplestore containing triples from nt file to retrieve the publication information associated with the UniProtKB accession and maps it to the UniProtKB canonical accessions. The script also filters out publications of large scale studies, and high frequency publications pertaining to DNA sequencing, cDNA, chromosomes using blacklisted PMIDs file.\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_citations_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_protein_citations_uniprotkb.csv\n Name: yeast_protein_citations_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"6060\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"12770\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"349\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"63\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"12372\"\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: \"12772\"\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: \"6060\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/yeast_protein_citations_uniprotkb.csv" }