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Title: AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Abstract

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [3];  [7];  [8];  [9];  [1];  [10];  [11];  [12];  [13];  [14];  [15];  [4];  [1];  [15] more »;  [16];  [17];  [4];  [12];  [18];  [7];  [19];  [20];  [21];  [22];  [23];  [23];  [12];  [1];  [24];  [17];  [17];  [8];  [25];  [20];  [11];  [8];  [26];  [4];  [13];  [26];  [27];  [16];  [28];  [29];  [4];  [4] « less
  1. Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
  2. Computer Science, Iowa State University, Ames, IA, USA
  3. Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA, Computer Science, Iowa State University, Ames, IA, USA
  4. Horticulture, Washington State University, Pullman, WA, USA
  5. National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD, USA
  6. Cyverse, University of Arizona, Tucson, AZ, USA
  7. Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France
  8. The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA
  9. USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA
  10. Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
  11. Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA
  12. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
  13. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  14. Division of Animal Sciences and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
  15. National Center for Genome Resources, Santa Fe, NM, USA
  16. Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
  17. Animal Science, Iowa State University, Ames, USA
  18. Laboratory of Informatics, Robotics, Microelectronics of Montpellier, University of Montpellier & CNRS, Montpellier, France
  19. DIADE, University of Montpellier, IRD, Montpellier, France
  20. Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA
  21. School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
  22. Boyce Thompson Institute, Ithaca, NY, USA
  23. Genomics Division, Lawrence Berkeley National Laboratories, Berkeley, CA, USA
  24. Marriott Library, University of Utah, Salt Lake City, UT, USA
  25. Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
  26. Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
  27. USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA, Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
  28. Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring Harbor, NY, USA
  29. Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
AgBioData consortium
OSTI Identifier:
1471253
Alternate Identifier(s):
OSTI ID: 1490698
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Database
Additional Journal Information:
Journal Name: Database Journal Volume: 2018; Journal ID: ISSN 1758-0463
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Harper, Lisa, Campbell, Jacqueline, Cannon, Ethalinda K. S., Jung, Sook, Poelchau, Monica, Walls, Ramona, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., Birkett, Clayton, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angélique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Yu, Jing, and Main, Doreen. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. United Kingdom: N. p., 2018. Web. doi:10.1093/database/bay088.
Harper, Lisa, Campbell, Jacqueline, Cannon, Ethalinda K. S., Jung, Sook, Poelchau, Monica, Walls, Ramona, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., Birkett, Clayton, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angélique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Yu, Jing, & Main, Doreen. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. United Kingdom. doi:10.1093/database/bay088.
Harper, Lisa, Campbell, Jacqueline, Cannon, Ethalinda K. S., Jung, Sook, Poelchau, Monica, Walls, Ramona, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., Birkett, Clayton, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angélique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Yu, Jing, and Main, Doreen. Tue . "AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture". United Kingdom. doi:10.1093/database/bay088.
@article{osti_1471253,
title = {AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture},
author = {Harper, Lisa and Campbell, Jacqueline and Cannon, Ethalinda K. S. and Jung, Sook and Poelchau, Monica and Walls, Ramona and Andorf, Carson and Arnaud, Elizabeth and Berardini, Tanya Z. and Birkett, Clayton and Cannon, Steve and Carson, James and Condon, Bradford and Cooper, Laurel and Dunn, Nathan and Elsik, Christine G. and Farmer, Andrew and Ficklin, Stephen P. and Grant, David and Grau, Emily and Herndon, Nic and Hu, Zhi-Liang and Humann, Jodi and Jaiswal, Pankaj and Jonquet, Clement and Laporte, Marie-Angélique and Larmande, Pierre and Lazo, Gerard and McCarthy, Fiona and Menda, Naama and Mungall, Christopher J. and Munoz-Torres, Monica C. and Naithani, Sushma and Nelson, Rex and Nesdill, Daureen and Park, Carissa and Reecy, James and Reiser, Leonore and Sanderson, Lacey-Anne and Sen, Taner Z. and Staton, Margaret and Subramaniam, Sabarinath and Tello-Ruiz, Marcela Karey and Unda, Victor and Unni, Deepak and Wang, Liya and Ware, Doreen and Wegrzyn, Jill and Williams, Jason and Woodhouse, Margaret and Yu, Jing and Main, Doreen},
abstractNote = {The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.},
doi = {10.1093/database/bay088},
journal = {Database},
number = ,
volume = 2018,
place = {United Kingdom},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1093/database/bay088

Citation Metrics:
Cited by: 3 works
Citation information provided by
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Figures / Tables:

Table 1 Table 1: Survey results for ontology use in databases for each data type (from 29 respondents)

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Works referenced in this record:

Uberon, an integrative multi-species anatomy ontology
journal, January 2012

  • Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V.
  • Genome Biology, Vol. 13, Issue 1
  • DOI: 10.1186/gb-2012-13-1-r5

Araport: the Arabidopsis Information Portal
journal, November 2014

  • Krishnakumar, Vivek; Hanlon, Matthew R.; Contrino, Sergio
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1200

Attitudes and norms affecting scientists’ data reuse
journal, December 2017


The Arabidopsis Information Resource (TAIR): gene structure and function annotation
journal, December 2007

  • Swarbreck, D.; Wilks, C.; Lamesch, P.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm965

Data Archiving
journal, March 2010


MaizeGDB update: new tools, data and interface for the maize model organism database
journal, October 2015

  • Andorf, Carson M.; Cannon, Ethalinda K.; Portwood, John L.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1007

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
journal, October 2016

  • Ong, Edison; Xiang, Zuoshuang; Zhao, Bin
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw918

Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era
journal, November 2012

  • Hu, Zhi-Liang; Park, Carissa A.; Wu, Xiao-Lin
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1150

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
journal, October 2017

  • Kersey, Paul Julian; Allen, James E.; Allot, Alexis
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1011

Ensembl 2018
journal, November 2017

  • Zerbino, Daniel R.; Achuthan, Premanand; Akanni, Wasiu
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1098

Reactome graph database: Efficient access to complex pathway data
journal, January 2018


MouseMine: a new data warehouse for MGI
journal, June 2015


Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes : Using The Arabidopsis Information Resource (TAIR)
journal, December 2017

  • Reiser, Leonore; Subramaniam, Shabari; Li, Donghui
  • Current Protocols in Bioinformatics, Vol. 60, Issue 1
  • DOI: 10.1002/cpbi.36

Canto: an online tool for community literature curation
journal, February 2014


The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
journal, May 2016

  • Afgan, Enis; Baker, Dannon; van den Beek, Marius
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw343

Complete genomes in WWW Entrez: data representation and analysis
journal, July 1999


Our path to better science in less time using open data science tools
journal, May 2017

  • Lowndes, Julia S. Stewart; Best, Benjamin D.; Scarborough, Courtney
  • Nature Ecology & Evolution, Vol. 1, Issue 6
  • DOI: 10.1038/s41559-017-0160

A review of genomic data warehousing systems
journal, May 2013

  • Triplet, T.; Butler, G.
  • Briefings in Bioinformatics, Vol. 15, Issue 4
  • DOI: 10.1093/bib/bbt031

A Chado case study: an ontology-based modular schema for representing genome-associated biological information
journal, July 2007


Developmental progress and current status of the Animal QTLdb
journal, November 2015

  • Hu, Zhi-Liang; Park, Carissa A.; Reecy, James M.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1233

Bovine Genome Database: new tools for gleaning function from the Bos taurus genome
journal, October 2015

  • Elsik, Christine G.; Unni, Deepak R.; Diesh, Colin M.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1077

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
journal, December 2012

  • Cooper, Laurel; Walls, Ramona L.; Elser, Justin
  • Plant and Cell Physiology, Vol. 54, Issue 2
  • DOI: 10.1093/pcp/pcs163

Ensembl 2017
journal, November 2016

  • Aken, Bronwen L.; Achuthan, Premanand; Akanni, Wasiu
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1104

The Ensembl genome database project
journal, January 2002


Logical Development of the Cell Ontology
journal, January 2011

  • Meehan, Terrence F.; Masci, Anna Maria; Abdulla, Amina
  • BMC Bioinformatics, Vol. 12, Issue 1
  • DOI: 10.1186/1471-2105-12-6

Towards recommendations for metadata and data handling in plant phenotyping
journal, June 2015

  • Krajewski, Paweł; Chen, Dijun; Ćwiek, Hanna
  • Journal of Experimental Botany, Vol. 66, Issue 18
  • DOI: 10.1093/jxb/erv271

InterMOD: integrated data and tools for the unification of model organism research
journal, May 2013

  • Sullivan, Julie; Karra, Kalpana; Moxon, Sierra A. T.
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep01802

FlyMine: an integrated database for Drosophila and Anopheles genomics
journal, January 2007


Expression Atlas: gene and protein expression across multiple studies and organisms
journal, November 2017

  • Papatheodorou, Irene; Fonseca, Nuno A.; Keays, Maria
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1158

The UCSC Genome Browser Database
journal, January 2003


PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
journal, January 2003


Data Archiving
journal, February 2010

  • Whitlock, Michael C.; McPeek, Mark A.; Rausher, Mark D.
  • The American Naturalist, Vol. 175, Issue 2
  • DOI: 10.1086/650340

AgroPortal: A vocabulary and ontology repository for agronomy
journal, January 2018


Plant Reactome: a resource for plant pathways and comparative analysis
journal, October 2016

  • Naithani, Sushma; Preece, Justin; D'Eustachio, Peter
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw932

MTGD: The Medicago truncatula Genome Database
journal, November 2014

  • Krishnakumar, Vivek; Kim, Maria; Rosen, Benjamin D.
  • Plant and Cell Physiology, Vol. 56, Issue 1
  • DOI: 10.1093/pcp/pcu179

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
journal, November 2017

  • Cooper, Laurel; Meier, Austin; Laporte, Marie-Angélique
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1152

Outreach and online training services at the Saccharomyces Genome Database
journal, January 2017


Analysis of disease-associated objects at the Rat Genome Database
journal, January 2013


The FAIR Guiding Principles for scientific data management and stewardship
journal, March 2016

  • Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan
  • Scientific Data, Vol. 3, Issue 1
  • DOI: 10.1038/sdata.2016.18

Ten Simple Rules for a Successful Collaboration
journal, January 2007


Review%3A Interoperability standards
text, January 2016


Evolution of biomedical ontologies and mappings: Overview of recent approaches
journal, January 2016

  • Groß, Anika; Pruski, Cédric; Rahm, Erhard
  • Computational and Structural Biotechnology Journal, Vol. 14
  • DOI: 10.1016/j.csbj.2016.08.002

WormBase 2014: new views of curated biology
journal, November 2013

  • Harris, Todd W.; Baran, Joachim; Bieri, Tamberlyn
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1063

Digital Object Identifiers for scientific data
journal, January 2005


Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes
journal, June 2010


Open data: curation is under-resourced
journal, October 2016


The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences
journal, January 2016


The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding
journal, January 2016


Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine
journal, November 2015

  • Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1208

Measures for interoperability of phenotypic data: minimum information requirements and formatting
journal, November 2016


State of the Dublin Core Metadata Initiative, April 2003
journal, April 2003


Crowdsourcing in biomedicine: challenges and opportunities
journal, April 2015

  • Khare, Ritu; Good, Benjamin M.; Leaman, Robert
  • Briefings in Bioinformatics, Vol. 17, Issue 1
  • DOI: 10.1093/bib/bbv021

Using AberOWL for fast and scalable reasoning over BioPortal ontologies
journal, August 2016

  • Slater, Luke; Gkoutos, Georgios V.; Schofield, Paul N.
  • Journal of Biomedical Semantics, Vol. 7, Issue 1
  • DOI: 10.1186/s13326-016-0090-0

Germinate 3: Development of a Common Platform to Support the Distribution of Experimental Data on Crop Wild Relatives
journal, January 2017


Tripal: a construction toolkit for online genome databases
journal, January 2011


The Sol Genomics Network (SGN)—from genotype to phenotype to breeding
journal, November 2014

  • Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1195

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
journal, December 2011

  • Barrett, T.; Clark, K.; Gevorgyan, R.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1163

Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
journal, October 2017


The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
journal, November 2007

  • Smith, Barry; Ashburner, Michael; Rosse, Cornelius
  • Nature Biotechnology, Vol. 25, Issue 11
  • DOI: 10.1038/nbt1346

XenMine: A genomic interaction tool for the Xenopus community
journal, June 2017


Toward interoperable bioscience data
journal, January 2012

  • Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn
  • Nature Genetics, Vol. 44, Issue 2
  • DOI: 10.1038/ng.1054

The Ontology Lookup Service: bigger and better
journal, May 2010

  • Cote, R.; Reisinger, F.; Martens, L.
  • Nucleic Acids Research, Vol. 38, Issue Web Server
  • DOI: 10.1093/nar/gkq331

The Dublin Core Metadata Initiative: Mission, Current Activities, and Future Directions
journal, December 2000


TreeGenes: A Forest Tree Genome Database
journal, January 2008

  • Wegrzyn, Jill L.; Lee, Jennifer M.; Tearse, Brandon R.
  • International Journal of Plant Genomics, Vol. 2008
  • DOI: 10.1155/2008/412875

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection
journal, December 2017

  • Rigden, Daniel J.; Fernández, Xosé M.
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1235

Gramene 2018: unifying comparative genomics and pathway resources for plant research
journal, November 2017

  • Tello-Ruiz, Marcela K.; Naithani, Sushma; Stein, Joshua C.
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1111

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
journal, September 2012


The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
journal, October 2014

  • Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku950

Biocuration at the Saccharomyces genome database : Biocuration at SGD
journal, July 2015

  • Skrzypek, Marek S.; Nash, Robert S.
  • genesis, Vol. 53, Issue 8
  • DOI: 10.1002/dvg.22862

ZFIN, The zebrafish model organism database: Updates and new directions: zfin updates and new directions
journal, July 2015

  • Ruzicka, Leyla; Bradford, Yvonne M.; Frazer, Ken
  • genesis, Vol. 53, Issue 8
  • DOI: 10.1002/dvg.22868

Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies
journal, June 2004

  • Berardini, Tanya Z.; Mundodi, Suparna; Reiser, Leonore
  • Plant Physiology, Vol. 135, Issue 2
  • DOI: 10.1104/pp.104.040071

BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences
journal, January 2016

  • McQuilton, Peter; Gonzalez-Beltran, Alejandra; Rocca-Serra, Philippe
  • Database, Vol. 2016
  • DOI: 10.1093/database/baw075

How much does curation cost?
journal, January 2016


Re-thinking organisms: The impact of databases on model organism biology
journal, March 2012

  • Leonelli, Sabina; Ankeny, Rachel A.
  • Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Vol. 43, Issue 1
  • DOI: 10.1016/j.shpsc.2011.10.003

Grin-Global: an International Project to Develop a Global Plant Genebank Information Management System
journal, April 2010


The future of biocuration
journal, September 2008

  • Howe, Doug; Costanzo, Maria; Fey, Petra
  • Nature, Vol. 455, Issue 7209
  • DOI: 10.1038/455047a

Assessment of community-submitted ontology annotations from a novel database-journal partnership
journal, January 2012


YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit
journal, January 2012


The BioMart community portal: an innovative alternative to large, centralized data repositories
journal, April 2015

  • Smedley, Damian; Haider, Syed; Durinck, Steffen
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv350

The MetaCyc database of metabolic pathways and enzymes
journal, October 2017

  • Caspi, Ron; Billington, Richard; Fulcher, Carol A.
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx935

Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping
journal, February 2018

  • Krajewski, Paweł; Chen, Dijun; Ćwiek, Hanna
  • Journal of Experimental Botany, Vol. 69, Issue 7
  • DOI: 10.1093/jxb/ery006

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases
journal, January 2013


Biocurators and Biocuration: surveying the 21st century challenges
journal, January 2012


GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
journal, January 2017


BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF
journal, January 2013

  • Salvadores, Manuel; Alexander, Paul R.; Musen, Mark A.
  • Semantic Web, Vol. 4, Issue 3
  • DOI: 10.3233/SW-2012-0086

    Works referencing / citing this record:

    The BioMart community portal: an innovative alternative to large, centralized data repositories
    journal, April 2015

    • Smedley, Damian; Haider, Syed; Durinck, Steffen
    • Nucleic Acids Research, Vol. 43, Issue W1
    • DOI: 10.1093/nar/gkv350

    BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
    journal, December 2011

    • Barrett, T.; Clark, K.; Gevorgyan, R.
    • Nucleic Acids Research, Vol. 40, Issue D1
    • DOI: 10.1093/nar/gkr1163

    Re-thinking organisms: The impact of databases on model organism biology
    journal, March 2012

    • Leonelli, Sabina; Ankeny, Rachel A.
    • Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Vol. 43, Issue 1
    • DOI: 10.1016/j.shpsc.2011.10.003

    Data Archiving
    journal, February 2010

    • Whitlock, Michael C.; McPeek, Mark A.; Rausher, Mark D.
    • The American Naturalist, Vol. 175, Issue 2
    • DOI: 10.1086/650340

    Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases
    journal, January 2013


    GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
    journal, January 2017


    Gramene 2018: unifying comparative genomics and pathway resources for plant research
    journal, November 2017

    • Tello-Ruiz, Marcela K.; Naithani, Sushma; Stein, Joshua C.
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx1111

    The 2018 Nucleic Acids Research database issue and the online molecular biology database collection
    journal, December 2017

    • Rigden, Daniel J.; Fernández, Xosé M.
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx1235

    Grin-Global: an International Project to Develop a Global Plant Genebank Information Management System
    journal, April 2010


    The MetaCyc database of metabolic pathways and enzymes
    journal, October 2017

    • Caspi, Ron; Billington, Richard; Fulcher, Carol A.
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx935

    WormBase 2014: new views of curated biology
    journal, November 2013

    • Harris, Todd W.; Baran, Joachim; Bieri, Tamberlyn
    • Nucleic Acids Research, Vol. 42, Issue D1
    • DOI: 10.1093/nar/gkt1063

    Measures for interoperability of phenotypic data: minimum information requirements and formatting
    journal, November 2016


    The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
    journal, October 2014

    • Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
    • Nucleic Acids Research, Vol. 43, Issue D1
    • DOI: 10.1093/nar/gku950

    Biocurators and Biocuration: surveying the 21st century challenges
    journal, January 2012


    MTGD: The Medicago truncatula Genome Database
    journal, November 2014

    • Krishnakumar, Vivek; Kim, Maria; Rosen, Benjamin D.
    • Plant and Cell Physiology, Vol. 56, Issue 1
    • DOI: 10.1093/pcp/pcu179

    Assessment of community-submitted ontology annotations from a novel database-journal partnership
    journal, January 2012


    YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit
    journal, January 2012


    Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS
    journal, April 2019


    BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences
    journal, January 2016

    • McQuilton, Peter; Gonzalez-Beltran, Alejandra; Rocca-Serra, Philippe
    • Database, Vol. 2016
    • DOI: 10.1093/database/baw075

    How much does curation cost?
    journal, January 2016


    The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    journal, November 2007

    • Smith, Barry; Ashburner, Michael; Rosse, Cornelius
    • Nature Biotechnology, Vol. 25, Issue 11
    • DOI: 10.1038/nbt1346

    Complete genomes in WWW Entrez: data representation and analysis
    journal, July 1999


    MouseMine: a new data warehouse for MGI
    journal, June 2015


    Crowdsourcing in biomedicine: challenges and opportunities
    journal, April 2015

    • Khare, Ritu; Good, Benjamin M.; Leaman, Robert
    • Briefings in Bioinformatics, Vol. 17, Issue 1
    • DOI: 10.1093/bib/bbv021

    The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
    journal, December 2012

    • Cooper, Laurel; Walls, Ramona L.; Elser, Justin
    • Plant and Cell Physiology, Vol. 54, Issue 2
    • DOI: 10.1093/pcp/pcs163

    MaizeGDB update: new tools, data and interface for the maize model organism database
    journal, October 2015

    • Andorf, Carson M.; Cannon, Ethalinda K.; Portwood, John L.
    • Nucleic Acids Research, Vol. 44, Issue D1
    • DOI: 10.1093/nar/gkv1007

    The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences
    journal, January 2016


    Reactome graph database: Efficient access to complex pathway data
    journal, January 2018


    InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
    journal, September 2012


    Araport: the Arabidopsis Information Portal
    journal, November 2014

    • Krishnakumar, Vivek; Hanlon, Matthew R.; Contrino, Sergio
    • Nucleic Acids Research, Vol. 43, Issue D1
    • DOI: 10.1093/nar/gku1200

    The future of biocuration
    journal, September 2008

    • Howe, Doug; Costanzo, Maria; Fey, Petra
    • Nature, Vol. 455, Issue 7209
    • DOI: 10.1038/455047a

    Bovine Genome Database: new tools for gleaning function from the Bos taurus genome
    journal, October 2015

    • Elsik, Christine G.; Unni, Deepak R.; Diesh, Colin M.
    • Nucleic Acids Research, Vol. 44, Issue D1
    • DOI: 10.1093/nar/gkv1077

    XenMine: A genomic interaction tool for the Xenopus community
    journal, June 2017


    Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes : Using The Arabidopsis Information Resource (TAIR)
    journal, December 2017

    • Reiser, Leonore; Subramaniam, Shabari; Li, Donghui
    • Current Protocols in Bioinformatics, Vol. 60, Issue 1
    • DOI: 10.1002/cpbi.36

    Developmental progress and current status of the Animal QTLdb
    journal, November 2015

    • Hu, Zhi-Liang; Park, Carissa A.; Reecy, James M.
    • Nucleic Acids Research, Vol. 44, Issue D1
    • DOI: 10.1093/nar/gkv1233

    Tripal: a construction toolkit for online genome databases
    journal, January 2011


    The Ontology Lookup Service: bigger and better
    journal, May 2010

    • Cote, R.; Reisinger, F.; Martens, L.
    • Nucleic Acids Research, Vol. 38, Issue Web Server
    • DOI: 10.1093/nar/gkq331

    Our path to better science in less time using open data science tools
    journal, May 2017

    • Lowndes, Julia S. Stewart; Best, Benjamin D.; Scarborough, Courtney
    • Nature Ecology & Evolution, Vol. 1, Issue 6
    • DOI: 10.1038/s41559-017-0160

    Canto: an online tool for community literature curation
    journal, February 2014


    Ensembl 2017
    journal, November 2016

    • Aken, Bronwen L.; Achuthan, Premanand; Akanni, Wasiu
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1104

    A Chado case study: an ontology-based modular schema for representing genome-associated biological information
    journal, July 2007


    Towards recommendations for metadata and data handling in plant phenotyping
    journal, June 2015

    • Krajewski, Paweł; Chen, Dijun; Ćwiek, Hanna
    • Journal of Experimental Botany, Vol. 66, Issue 18
    • DOI: 10.1093/jxb/erv271

    Logical Development of the Cell Ontology
    journal, January 2011

    • Meehan, Terrence F.; Masci, Anna Maria; Abdulla, Amina
    • BMC Bioinformatics, Vol. 12, Issue 1
    • DOI: 10.1186/1471-2105-12-6

    The Ensembl genome database project
    journal, January 2002


    The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
    journal, November 2017

    • Cooper, Laurel; Meier, Austin; Laporte, Marie-Angélique
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx1152

    Expression Atlas: gene and protein expression across multiple studies and organisms
    journal, November 2017

    • Papatheodorou, Irene; Fonseca, Nuno A.; Keays, Maria
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx1158

    FlyMine: an integrated database for Drosophila and Anopheles genomics
    journal, January 2007


    TreeGenes: A Forest Tree Genome Database
    journal, January 2008

    • Wegrzyn, Jill L.; Lee, Jennifer M.; Tearse, Brandon R.
    • International Journal of Plant Genomics, Vol. 2008
    • DOI: 10.1155/2008/412875

    PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
    journal, January 2003


    Ten Simple Rules for a Successful Collaboration
    journal, January 2007


    Digital Object Identifiers for scientific data
    journal, January 2005


    Plant Reactome: a knowledgebase and resource for comparative pathway analysis
    journal, November 2019

    • Naithani, Sushma; Gupta, Parul; Preece, Justin
    • Nucleic Acids Research
    • DOI: 10.1093/nar/gkz996

    The UCSC Genome Browser Database
    journal, January 2003


    Attitudes and norms affecting scientists’ data reuse
    journal, December 2017


    Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies
    journal, June 2004

    • Berardini, Tanya Z.; Mundodi, Suparna; Reiser, Leonore
    • Plant Physiology, Vol. 135, Issue 2
    • DOI: 10.1104/pp.104.040071

    Uberon, an integrative multi-species anatomy ontology
    journal, January 2012

    • Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V.
    • Genome Biology, Vol. 13, Issue 1
    • DOI: 10.1186/gb-2012-13-1-r5

    The FAIR Guiding Principles for scientific data management and stewardship
    journal, March 2016

    • Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan
    • Scientific Data, Vol. 3, Issue 1
    • DOI: 10.1038/sdata.2016.18

    Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping
    journal, February 2018

    • Krajewski, Paweł; Chen, Dijun; Ćwiek, Hanna
    • Journal of Experimental Botany, Vol. 69, Issue 7
    • DOI: 10.1093/jxb/ery006

    Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era
    journal, November 2012

    • Hu, Zhi-Liang; Park, Carissa A.; Wu, Xiao-Lin
    • Nucleic Acids Research, Vol. 41, Issue D1
    • DOI: 10.1093/nar/gks1150

    Analysis of disease-associated objects at the Rat Genome Database
    journal, January 2013


    Outreach and online training services at the Saccharomyces Genome Database
    journal, January 2017


    Biocuration at the Saccharomyces genome database : Biocuration at SGD
    journal, July 2015

    • Skrzypek, Marek S.; Nash, Robert S.
    • genesis, Vol. 53, Issue 8
    • DOI: 10.1002/dvg.22862

    Plant Reactome: a resource for plant pathways and comparative analysis
    journal, October 2016

    • Naithani, Sushma; Preece, Justin; D'Eustachio, Peter
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw932

    ZFIN, The zebrafish model organism database: Updates and new directions: zfin updates and new directions
    journal, July 2015

    • Ruzicka, Leyla; Bradford, Yvonne M.; Frazer, Ken
    • genesis, Vol. 53, Issue 8
    • DOI: 10.1002/dvg.22868

    The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
    journal, May 2016

    • Afgan, Enis; Baker, Dannon; van den Beek, Marius
    • Nucleic Acids Research, Vol. 44, Issue W1
    • DOI: 10.1093/nar/gkw343

    State of the Dublin Core Metadata Initiative, April 2003
    journal, April 2003


    Germinate 3: Development of a Common Platform to Support the Distribution of Experimental Data on Crop Wild Relatives
    journal, January 2017


    MaizeGDB 2018: the maize multi-genome genetics and genomics database
    journal, November 2018

    • Portwood, John L.; Woodhouse, Margaret R.; Cannon, Ethalinda K.
    • Nucleic Acids Research, Vol. 47, Issue D1
    • DOI: 10.1093/nar/gky1046

    Evolution of biomedical ontologies and mappings: Overview of recent approaches
    journal, January 2016

    • Groß, Anika; Pruski, Cédric; Rahm, Erhard
    • Computational and Structural Biotechnology Journal, Vol. 14
    • DOI: 10.1016/j.csbj.2016.08.002

    Cyberinfrastructure and resources to enable an integrative approach to studying forest trees
    journal, June 2019

    • Wegrzyn, Jill L.; Falk, Taylor; Grau, Emily
    • Evolutionary Applications, Vol. 13, Issue 1
    • DOI: 10.1111/eva.12860

    Toward interoperable bioscience data
    journal, January 2012

    • Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn
    • Nature Genetics, Vol. 44, Issue 2
    • DOI: 10.1038/ng.1054

    Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
    journal, October 2017

    • Kersey, Paul Julian; Allen, James E.; Allot, Alexis
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx1011

    Ensembl 2018
    journal, November 2017

    • Zerbino, Daniel R.; Achuthan, Premanand; Akanni, Wasiu
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx1098

    The Dublin Core Metadata Initiative: Mission, Current Activities, and Future Directions
    journal, December 2000


    Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
    journal, October 2017


    The Arabidopsis Information Resource (TAIR): gene structure and function annotation
    journal, December 2007

    • Swarbreck, D.; Wilks, C.; Lamesch, P.
    • Nucleic Acids Research, Vol. 36, Issue Database
    • DOI: 10.1093/nar/gkm965

    The Sol Genomics Network (SGN)—from genotype to phenotype to breeding
    journal, November 2014

    • Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D.
    • Nucleic Acids Research, Vol. 43, Issue D1
    • DOI: 10.1093/nar/gku1195

    Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine
    journal, November 2015

    • Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.
    • Nucleic Acids Research, Vol. 44, Issue D1
    • DOI: 10.1093/nar/gkv1208

    The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding
    journal, January 2016


    A review of genomic data warehousing systems
    journal, May 2013

    • Triplet, T.; Butler, G.
    • Briefings in Bioinformatics, Vol. 15, Issue 4
    • DOI: 10.1093/bib/bbt031

    Using AberOWL for fast and scalable reasoning over BioPortal ontologies
    journal, August 2016

    • Slater, Luke; Gkoutos, Georgios V.; Schofield, Paul N.
    • Journal of Biomedical Semantics, Vol. 7, Issue 1
    • DOI: 10.1186/s13326-016-0090-0

    Open data: curation is under-resourced
    journal, October 2016


    Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
    journal, October 2016

    • Ong, Edison; Xiang, Zuoshuang; Zhao, Bin
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw918

    InterMOD: integrated data and tools for the unification of model organism research
    journal, May 2013

    • Sullivan, Julie; Karra, Kalpana; Moxon, Sierra A. T.
    • Scientific Reports, Vol. 3, Issue 1
    • DOI: 10.1038/srep01802

    AgroPortal: A vocabulary and ontology repository for agronomy
    journal, January 2018