Attitudes and norms affecting scientists' data reuse, PLoS One, vol.12, 2017. ,
Re-thinking organisms: the impact of databases on model organism biology, Stud. Hist. Philos. Biol. Biomed. Sci, vol.43, pp.29-36, 2012. ,
, , 2018.
Outreach and online training services at the Saccharomyces Genome Database, 2017. ,
The FAIR Guiding Principles for scientific data management and stewardship, Sci. Data, vol.3, p.160018, 2016. ,
Big data: the future of biocuration, Nature, vol.455, pp.47-50, 2008. ,
Biocurators and biocuration: surveying the 21st century challenges, Database, 2012. ,
Biocuration at the Saccharomyces genome database, Genesis, vol.53, pp.450-457, 2015. ,
The Arabidopsis information resource: making and mining the "gold standard" annotated reference plant genome, Genesis, vol.53, pp.474-485, 2015. ,
The Arabidopsis Information Resource (TAIR): gene structure and function annotation, Nucleic Acids Res, vol.36, pp.1009-1014, 2008. ,
Functional annotation of the Arabidopsis genome using controlled vocabularies, Plant Physiol, vol.135, pp.745-755, 2004. ,
The MetaCyc database of metabolic pathways and enzymes, Nucleic Acids Res, vol.46, pp.633-639, 2018. ,
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants, Plant Physiol, vol.153, pp.1479-1491, 2010. ,
Plant Reactome: a resource for plant pathways and comparative analysis, Nucleic Acids Res, vol.45, pp.1029-1039, 2017. ,
How much does curation cost? Database, 2016. ,
Open data: curation is under-resourced, Nature, vol.538, p.41, 2016. ,
Unmet needs for analyzing biological big data: a survey of 704 NSF principal investigators, PLoS Comput. Biol, vol.13, p.1005755, 2017. ,
SoyBase: a comprehensive database for soybean genetic and genomic data, pp.193-211, 2017. ,
Using The Arabidopsis Information Resource (TAIR) to find information about Arabidopsis genes, Curr. Protoc. Bioinformatics, vol.60, 2017. ,
Expression atlas: gene and protein expression across multiple studies and organisms, Nucleic Acids Res, vol.46, pp.246-251, 2018. ,
Assessment of community-submitted ontology annotations from a novel database-journal partnership, Database, 2012. ,
Crowdsourcing in biomedicine: challenges and opportunities, Brief Bioinform, vol.17, pp.23-32, 2016. ,
MaizeGDB update: new tools, data and interface for the maize model organism database, Nucleic Acids Res, vol.44, pp.1195-1201, 2016. ,
Evolution of biomedical ontologies and mappings: overview of recent approaches, Comput. Struct. Biotechnol. J, vol.14, pp.333-340, 2016. ,
, Expansion of the Gene Ontology knowledgebase and resources, The Gene Ontology Consortium, vol.45, pp.331-338, 2016.
The Plant Ontology: a tool for plant genomics, Methods Mol. Biol, vol.1374, pp.89-114, 2016. ,
The plant ontology as a tool for comparative plant anatomy and genomic analyses, Plant Cell Physiol, vol.54, p.1, 2013. ,
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics, Nucleic Acids Res, vol.46, pp.1168-1180, 2018. ,
Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice, Front Physiol, vol.3, p.326, 2012. ,
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nat. Biotechnol, vol.25, pp.1251-1255, 2007. ,
BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF, Semant Web, vol.4, pp.277-284, 2013. ,
Ontobee: a linked ontology data server to support ontology term dereferencing, linkage, query and integration, Nucleic Acids Res, vol.45, pp.347-352, 2017. ,
The Ontology Lookup Service: bigger and better, Nucleic Acids Res, vol.38, pp.155-160, 2010. ,
Using AberOWL for fast and scalable reasoning over BioPortal ontologies, J. Biomed. Semantics, vol.7, p.49, 2016. ,
AgroPortal: a vocabulary and ontology repository for agronomy, Comput. Electron Agric, vol.144, pp.126-143, 2018. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01679502
PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature, Curr. Protoc. Bioinformatics, vol.9, 2006. ,
Canto: an online tool for community literature curation, Bioinformatics, vol.30, pp.1791-1792, 2014. ,
Uberon, an integrative multi-species anatomy ontology, Genome Biol, vol.13, p.5, 2012. ,
Logical development of the cell ontology, BMC Bioinformatics, vol.12, p.6, 2011. ,
, Nucleic Acids Res, vol.46, pp.754-761, 2018.
Developmental progress and current status of the Animal QTLdb, Nucleic Acids Res, vol.44, pp.827-833, 2016. ,
TreeGenes: a forest tree genome database, Int. J. Plant Genomics, p.412875, 2008. ,
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases, Database, 2013. ,
Measures for interoperability of phenotypic data: minimum information requirements and formatting, Plant Methods, vol.12, p.44, 2016. ,
The Dublin Core Metadata Initiative. D-Lib Magazine, vol.6, 2000. ,
State of the Dublin Core Metadata Initiative, vol.9, 2003. ,
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences, Database, 2016. ,
, Review: interoperability standards, 2016.
FAIRsharing: working with and for the community to describe and link data standards, repositories and policies, 2018. ,
Toward interoperable bioscience data, Nat. Genet, vol.44, pp.121-126, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00695792
Towards recommendations for metadata and data handling in plant phenotyping, J. Exp. Bot, vol.66, pp.5417-5427, 2015. ,
Corrigendum: towards recommendations for metadata and data handling in plant phenotyping, J. Exp. Bot, vol.69, p.1819, 2018. ,
Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era, Nucleic Acids Res, vol.41, pp.871-879, 2013. ,
Meta-analysis of quantitative trait association and mapping studies using parametric and non-parametric models, J. Biom. Biostat, 2011. ,
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification, Nucleic Acids Res, vol.43, pp.1099-1106, 2015. ,
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata, Nucleic Acids Res, vol.40, pp.57-63, 2012. ,
Digital Object Identifiers for scientific data, Data Sci. J, vol.4, pp.12-20, 2005. ,
Identifiers for the 21st century: how to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data, PLoS Biol, vol.15, p.2001414, 2017. ,
Chapter 25 ACeDB and Macace, Methods Cell Biol, pp.583-605, 1995. ,
Complete genomes in WWW Entrez: data representation and analysis, Bioinformatics, vol.15, pp.536-543, 1999. ,
The Ensembl genome database project, Nucleic Acids Res, vol.30, pp.38-41, 2002. ,
The UCSC genome browser database, Nucleic Acids Res, vol.31, pp.51-54, 2003. ,
An integrated computational pipeline and database to support whole-genome sequence annotation, Genome Biol, vol.3, 2002. ,
The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant, Nucleic Acids Res, vol.29, pp.102-105, 2001. ,
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data, Nucleic Acids Res, vol.31, pp.212-215, 2003. ,
Gringlobal: an international project to develop a global plant genebank information management system, Acta Hortic, pp.49-55, 2010. ,
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection, Nucleic Acids Res, vol.46, pp.1-7, 2018. ,
Tripal: a construction toolkit for online genome databases, Database, p.44, 2011. ,
A Chado case study: an ontology-based modular schema for representing genome-associated biological information, Bioinformatics, vol.23, pp.337-346, 2007. ,
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data, Bioinformatics, vol.28, pp.3163-3165, 2012. ,
FlyMine: an integrated database for Drosophila and Anopheles genomics, 2007. ,
, Genome Biol, vol.8, p.129
WormBase 2014: new views of curated biology, Nucleic Acids Res, vol.42, pp.789-793, 2014. ,
YeastMine-an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit, Database, 2012. ,
, Article ID bay088, vol.2018
Araport: the Arabidopsis Information Portal, Nucleic Acids Res, vol.43, pp.1003-1009, 2015. ,
MouseMine: a new data warehouse for MGI, Mamm. Genome, vol.26, pp.325-330, 2015. ,
, ZFIN, the zebrafish model organism database: updates and new directions, 2015.
, Genesis, vol.53, pp.498-509
Analysis of disease-associated objects at the Rat Genome Database, Database, 2013. ,
XenMine: a genomic interaction tool for the Xenopus community, Dev. Biol, vol.426, pp.155-164, 2017. ,
InterMOD: integrated data and tools for the unification of model organism research, Sci. Rep, vol.3, p.1802, 2013. ,
MTGD: The Medicago truncatula genome database, Plant Cell Physiol, vol.56, p.1, 2015. ,
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine, Nucleic Acids Res, vol.44, pp.793-800, 2016. ,
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome, Nucleic Acids Res, vol.44, pp.834-839, 2016. ,
A review of genomic data warehousing systems, Brief Bioinform, vol.15, pp.471-483, 2014. ,
Germinate 3: development of a common platform to support the distribution of experimental data on crop wild relatives, Crop Sci, vol.57, p.1259, 2017. ,
, Nucleic Acids Res, vol.45, pp.635-642, 2017.
Gramene 2018: unifying comparative genomics and pathway resources for plant research, Nucleic Acids Res, vol.46, pp.1181-1189, 2018. ,
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species, Nucleic Acids Res, vol.46, pp.802-808, 2018. ,
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species, 2017. ,
The Sol Genomics Network (SGN)-from genotype to phenotype to breeding, Nucleic Acids Res, vol.43, pp.1036-1041, 2014. ,
The Triticeae Toolbox: combining phenotype and genotype data to advance small-grains breeding, Plant Genome, vol.9, 2016. ,
Reactome graph database: efficient access to complex pathway data, PLoS Comput. Biol, vol.14, p.1005968, 2018. ,
Our path to better science in less time using open data science tools, Nat. Ecol. Evol, vol.1, p.160, 2017. ,
The BioMart community portal: an innovative alternative to large, centralized data repositories, Nucleic Acids Res, vol.43, pp.589-598, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01146849
Linked Data: Evolving the Web into a Global Data Space, Synthesis Lectures on the Semantic Web: Theory and Technology, vol.1, pp.1-136, 2011. ,
Software-asa-service: the iPlant foundation API, 5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS, 2012. ,
The iPlant Collaborative: cyberinfrastructure for enabling data to discovery for the life sciences, PLoS Biol, vol.14, p.1002342, 2016. ,
The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update, Nucleic Acids Res, vol.44, pp.3-10, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01360125
Data archiving, Am. Nat, vol.175, pp.145-146, 2010. ,
Ten simple rules for a successful collaboration, PLoS Comput. Biol, vol.3, p.44, 2007. ,
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model, Database, 2016. ,