Literature DB >> 25997651

Biocuration at the Saccharomyces genome database.

Marek S Skrzypek1, Robert S Nash1.   

Abstract

Saccharomyces Genome Database is an online resource dedicated to managing information about the biology and genetics of the model organism, yeast (Saccharomyces cerevisiae). This information is derived primarily from scientific publications through a process of human curation that involves manual extraction of data and their organization into a comprehensive system of knowledge. This system provides a foundation for further analysis of experimental data coming from research on yeast as well as other organisms. In this review we will demonstrate how biocuration and biocurators add a key component, the biological context, to our understanding of how genes, proteins, genomes and cells function and interact. We will explain the role biocurators play in sifting through the wealth of biological data to incorporate and connect key information. We will also discuss the many ways we assist researchers with their various research needs. We hope to convince the reader that manual curation is vital in converting the flood of data into organized and interconnected knowledge, and that biocurators play an essential role in the integration of scientific information into a coherent model of the cell.
© 2015 Wiley Periodicals, Inc.

Entities:  

Keywords:  biocuration; database; yeast

Mesh:

Year:  2015        PMID: 25997651      PMCID: PMC4545726          DOI: 10.1002/dvg.22862

Source DB:  PubMed          Journal:  Genesis        ISSN: 1526-954X            Impact factor:   2.487


  20 in total

1.  Evolution and variation of the yeast (Saccharomyces) genome.

Authors:  R K Mortimer
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

2.  Using the Saccharomyces Genome Database (SGD) for analysis of genomic information.

Authors:  Marek S Skrzypek; Jodi Hirschman
Journal:  Curr Protoc Bioinformatics       Date:  2011-09

Review 3.  Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system.

Authors:  Andrea A Duina; Mary E Miller; Jill B Keeney
Journal:  Genetics       Date:  2014-05       Impact factor: 4.562

4.  New mutant phenotype data curation system in the Saccharomyces Genome Database.

Authors:  Maria C Costanzo; Marek S Skrzypek; Robert Nash; Edith Wong; Gail Binkley; Stacia R Engel; Benjamin Hitz; Eurie L Hong; J Michael Cherry
Journal:  Database (Oxford)       Date:  2009-03-16       Impact factor: 3.451

5.  Genealogy of principal strains of the yeast genetic stock center.

Authors:  R K Mortimer; J R Johnston
Journal:  Genetics       Date:  1986-05       Impact factor: 4.562

6.  Saccharomyces Genome Database: the genomics resource of budding yeast.

Authors:  J Michael Cherry; Eurie L Hong; Craig Amundsen; Rama Balakrishnan; Gail Binkley; Esther T Chan; Karen R Christie; Maria C Costanzo; Selina S Dwight; Stacia R Engel; Dianna G Fisk; Jodi E Hirschman; Benjamin C Hitz; Kalpana Karra; Cynthia J Krieger; Stuart R Miyasato; Rob S Nash; Julie Park; Marek S Skrzypek; Matt Simison; Shuai Weng; Edith D Wong
Journal:  Nucleic Acids Res       Date:  2011-11-21       Impact factor: 16.971

7.  YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit.

Authors:  Rama Balakrishnan; Julie Park; Kalpana Karra; Benjamin C Hitz; Gail Binkley; Eurie L Hong; Julie Sullivan; Gos Micklem; J Michael Cherry
Journal:  Database (Oxford)       Date:  2012-03-20       Impact factor: 3.451

8.  The BioGRID interaction database: 2015 update.

Authors:  Andrew Chatr-Aryamontri; Bobby-Joe Breitkreutz; Rose Oughtred; Lorrie Boucher; Sven Heinicke; Daici Chen; Chris Stark; Ashton Breitkreutz; Nadine Kolas; Lara O'Donnell; Teresa Reguly; Julie Nixon; Lindsay Ramage; Andrew Winter; Adnane Sellam; Christie Chang; Jodi Hirschman; Chandra Theesfeld; Jennifer Rust; Michael S Livstone; Kara Dolinski; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2014-11-26       Impact factor: 19.160

9.  Saccharomyces Genome Database provides mutant phenotype data.

Authors:  Stacia R Engel; Rama Balakrishnan; Gail Binkley; Karen R Christie; Maria C Costanzo; Selina S Dwight; Dianna G Fisk; Jodi E Hirschman; Benjamin C Hitz; Eurie L Hong; Cynthia J Krieger; Michael S Livstone; Stuart R Miyasato; Robert Nash; Rose Oughtred; Julie Park; Marek S Skrzypek; Shuai Weng; Edith D Wong; Kara Dolinski; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971

10.  The reference genome sequence of Saccharomyces cerevisiae: then and now.

Authors:  Stacia R Engel; Fred S Dietrich; Dianna G Fisk; Gail Binkley; Rama Balakrishnan; Maria C Costanzo; Selina S Dwight; Benjamin C Hitz; Kalpana Karra; Robert S Nash; Shuai Weng; Edith D Wong; Paul Lloyd; Marek S Skrzypek; Stuart R Miyasato; Matt Simison; J Michael Cherry
Journal:  G3 (Bethesda)       Date:  2014-03-20       Impact factor: 3.154

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  7 in total

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Authors:  Marek S Skrzypek; Jonathan Binkley; Gavin Sherlock
Journal:  Methods Mol Biol       Date:  2022

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Authors:  Leonore Reiser; Tanya Z Berardini; Donghui Li; Robert Muller; Emily M Strait; Qian Li; Yarik Mezheritsky; Andrey Vetushko; Eva Huala
Journal:  Database (Oxford)       Date:  2016-03-17       Impact factor: 3.451

3.  Outreach and online training services at the Saccharomyces Genome Database.

Authors:  Kevin A MacPherson; Barry Starr; Edith D Wong; Kyla S Dalusag; Sage T Hellerstedt; Olivia W Lang; Robert S Nash; Marek S Skrzypek; Stacia R Engel; J Michael Cherry
Journal:  Database (Oxford)       Date:  2017-01-01       Impact factor: 3.451

4.  AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.

Authors:  Lisa Harper; Jacqueline Campbell; Ethalinda K S Cannon; Sook Jung; Monica Poelchau; Ramona Walls; Carson Andorf; Elizabeth Arnaud; Tanya Z Berardini; Clayton Birkett; Steve Cannon; James Carson; Bradford Condon; Laurel Cooper; Nathan Dunn; Christine G Elsik; Andrew Farmer; Stephen P Ficklin; David Grant; Emily Grau; Nic Herndon; Zhi-Liang Hu; Jodi Humann; Pankaj Jaiswal; Clement Jonquet; Marie-Angélique Laporte; Pierre Larmande; Gerard Lazo; Fiona McCarthy; Naama Menda; Christopher J Mungall; Monica C Munoz-Torres; Sushma Naithani; Rex Nelson; Daureen Nesdill; Carissa Park; James Reecy; Leonore Reiser; Lacey-Anne Sanderson; Taner Z Sen; Margaret Staton; Sabarinath Subramaniam; Marcela Karey Tello-Ruiz; Victor Unda; Deepak Unni; Liya Wang; Doreen Ware; Jill Wegrzyn; Jason Williams; Margaret Woodhouse; Jing Yu; Doreen Main
Journal:  Database (Oxford)       Date:  2018-01-01       Impact factor: 3.451

5.  Degree of Freedom of Gene Expression in Saccharomyces cerevisiae.

Authors:  Zhen Yang; Feng Xu; Aijuan Xue; Hong Lv; Yungang He
Journal:  Microbiol Spectr       Date:  2022-03-01

6.  New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources.

Authors:  Stacia R Engel; Edith D Wong; Robert S Nash; Suzi Aleksander; Micheal Alexander; Eric Douglass; Kalpana Karra; Stuart R Miyasato; Matt Simison; Marek S Skrzypek; Shuai Weng; J Michael Cherry
Journal:  Genetics       Date:  2022-04-04       Impact factor: 4.402

7.  Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.

Authors:  Birgit H M Meldal; Hema Bye-A-Jee; Lukáš Gajdoš; Zuzana Hammerová; Aneta Horácková; Filip Melicher; Livia Perfetto; Daniel Pokorný; Milagros Rodriguez Lopez; Alžbeta Türková; Edith D Wong; Zengyan Xie; Elisabeth Barrera Casanova; Noemi Del-Toro; Maximilian Koch; Pablo Porras; Henning Hermjakob; Sandra Orchard
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

  7 in total

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