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Towards BioDBcore: a community-defined information specification for biological databases

P. Gaudet, A. Bairoch, D. Field, S.-A. Sansone, C. Taylor, T. K. Attwood, A. Bateman, J. A. Blake, C. J. Bult, J. M. Cherry, R. L. Chisholm, G. Cochrane (+26 others)
2011 Database: The Journal of Biological Databases and Curation  
To address some of these issues we propose the adoption of a community-defined, uniform, generic description of the 'core attributes of biological databases', which we will name BioDBCore.  ...  Table 1 . 1 Proposed core descriptors for inclusion in the BioDBCore specification Proposed core descriptors for a biological database 1. Database name 2. Main resource URL 3.  ... 
doi:10.1093/database/baq027 pmid:21205783 pmcid:PMC3017395 fatcat:zfghil52nramtih22wxuqe2xqq

Towards BioDBcore: a community-defined information specification for biological databases

Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane (+26 others)
2010 Nucleic Acids Research  
To address some of these issues we propose the adoption of a community-defined, uniform, generic description of the 'core attributes of biological databases', which we will name BioDBCore.  ...  Table 1 . 1 Proposed core descriptors for inclusion in the BioDBCore specification Proposed core descriptors for a biological database 1. Database name 2. Main resource URL 3.  ... 
doi:10.1093/nar/gkq1173 pmid:21097465 pmcid:PMC3013734 fatcat:db4bjiqvsbcuvemzbtuqv4k4by

Towards the Collaborative Curation of the Registry underlying

Nick Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe
2013 Database: The Journal of Biological Databases and Curation  
The growing demand for these identifiers results in a significant increase in curational efforts to maintain the underlying registry.  ...  We briefly describe the Registry, the current curation duties entailed, and our plans to extend and distribute this workload through collaborative and community efforts.  ...  Acknowledgements The authors would like to express our gratitude to the users for submitting new collections and contributing updates, which greatly help us to provide a reliable service to the community  ... 
doi:10.1093/database/bat017 pmid:23584831 pmcid:PMC3625955 fatcat:2b2qhz3y6zbs5mfirlglf46peu

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
Many approaches are possible and necessary towards these goals, and many layers need to be tackled, in collaborative community efforts with well-defined scope.  ...  The eSysbio project explored ways of developing a workbench for collaborative data analysis, accessible in various ways for users with various tasks and expertise.  ...  As a related example, the BioDBCore project (Gaudet et al. 2011) has one of its aims to define an information standard for information about lifescientific databases.  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

Biocompute Objects—A Step towards Evaluation and Validation of Biomedical Scientific Computations

Vahan Simonyan, Jeremy Goecks, Raja Mazumder
2016 PDA journal of pharmaceutical science and technology  
We also discuss the reasoning and potential usability for such concept within the larger scientific community through the creation of a biocompute object database initially consisting of records relevant  ...  , dependencies, usage, and other information related to specific computational instance.  ...  Acknowledgments We would like to mention with gratitude the following people for providing valuable comments regarding research and regulatory aspects to HTS:  ... 
doi:10.5731/pdajpst.2016.006734 pmid:27974626 pmcid:PMC5510742 fatcat:bmuqdqok4fevxecpwoekw47euq

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

Toshiaki Katayama, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano (+73 others)
2014 Journal of Biomedical Semantics  
specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability  ...  The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual  ...  There was also inter-group discussion of how to integrate BioDBCore with other projects such as DRCAT [79] , which defines a similar, overlapping set of biological resources and their features.  ... 
doi:10.1186/2041-1480-5-5 pmid:24495517 pmcid:PMC3978116 fatcat:hyb4sddegjbjncdhugr5lm4wu4

Fifth International Biocuration Conference : Meeting for Biocurators
Fifth International Biocuration Conference バイオキュレーターのためのミーティングに参加して

2012 Journal of Information Processing and Management  
2012 J o u r n a l o f I n f o r m a t i o n P r o c e s s i n g a n d M a n a g e m e n t JOHO KANRI June  ...  Database. vol. 2012: bar059. 3) Gaudet, Pascale; Bairoch, Amos; Field, Dawn et al. Towards BioDBcore: A community-defined information specification for biological databases.  ...  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Research. 2012, vol. 40, D1-8. 5 ) 5 白木澤佳子, 高木利久.  ... 
doi:10.1241/johokanri.55.214 fatcat:4pja24uhsbcjld4lwf3ye3iwmi

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

Carsten Kettner, Dawn Field, Susanna-Assunta Sansone, Chris Taylor, Jan Aerts, Nigel Binns, Andrew Blake, Cedrik M. Britten, Ario de Marco, Jennifer Fostel, Pascale Gaudet, Alejandra González-Beltrán (+17 others)
2010 Standards in Genomic Sciences  
The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI  ...  This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through  ...  Acknowledgements The authors would like to thank the Beilstein-Institut for both the financial support and hosting this Workshop.  ... 
doi:10.4056/sigs.147362 pmid:21304730 pmcid:PMC3035314 fatcat:4cttjp3qn5bx3lgmkiv6pbstmq

The health care and life sciences community profile for dataset descriptions

Michel Dumontier, Alasdair J.G. Gray, M. Scott Marshall, Vladimir Alexiev, Peter Ansell, Gary Bader, Joachim Baran, Jerven T. Bolleman, Alison Callahan, José Cruz-Toledo, Pascale Gaudet, Erich A. Gombocz (+18 others)
2016 PeerJ  
Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource  ...  However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata.  ...  ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.2331 pmid:27602295 pmcid:PMC4991880 fatcat:gzzbdencszgaxc4j3yk527ikba

The Comparative Toxicogenomics Database: update 2017

Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Benjamin L. King, Roy McMorran, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly
2016 Nucleic Acids Research  
a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies).  ...  The Comparative Toxicogenomics Database (CTD; provides information about interactions between chemicals and gene products, and their relationships to diseases.  ...  A single, robust, community-accepted disease vocabulary would be valuable for synchronizing the vast arrays of different biological databases.  ... 
doi:10.1093/nar/gkw838 pmid:27651457 pmcid:PMC5210612 fatcat:povogyqyofcebnljc3jnl4fnoq

Comparative Toxicogenomics Database (CTD): update 2021

Allan Peter Davis, Cynthia J Grondin, Robin J Johnson, Daniela Sciaky, Jolene Wiegers, Thomas C Wiegers, Carolyn J Mattingly
2020 Nucleic Acids Research  
The public Comparative Toxicogenomics Database (CTD; is an innovative digital ecosystem that relates toxicological information for chemicals, genes, phenotypes, diseases, and exposures  ...  Literature-based, manually curated interactions are integrated to create a knowledgebase that harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions.  ...  resource (19) , and registration with both BioDBcore ( and the NAR Molecular Biology Database Collection ( journals/nar/database  ... 
doi:10.1093/nar/gkaa891 pmid:33068428 fatcat:bbldcnar55b2vphap7eztmhnp4

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

P. Gaudet, C. Arighi, F. Bastian, A. Bateman, J. A. Blake, M. J. Cherry, P. D'Eustachio, R. Finn, M. Giglio, L. Hirschman, R. Kania, W. Klimke (+16 others)
2012 Database: The Journal of Biological Databases and Curation  
The publication fees of this article has been paid by the 2012 International Biocuration Conference committee and the International Society for Biocuration.  ...  It was decided to create a working group to establish specifications for such a system, for instance, how to describe parameters used to assess the confidence of an annotation and defining a simple confidence  ...  Introduction Biological databases have been a key item in the toolbox of life scientists for 30 years.  ... 
doi:10.1093/database/bas036 pmid:23110974 pmcid:PMC3483532 fatcat:v56fpejv3jftbo62gjdhjyswja

The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons

Shannan J. Ho Sui, Kimberly Begley, Dorothy Reilly, Brad Chapman, Ray McGovern, Philippe Rocca-Sera, Eamonn Maguire, Gabriel M. Altschuler, Terah A. A. Hansen, Ramakrishna Sompallae, Andrei Krivtsov, Ramesh A. Shivdasani (+6 others)
2011 Nucleic Acids Research  
We thank Dr Miguel Andrade-Navarro for access to the StemBase data. Thank you also to Emily Merrill and Dr Sudeshna Das for their input on ontology usage.  ...  ACKNOWLEDGEMENTS We acknowledge assistance from the Harvard Stem Cell Institute for contributing CSC data and are grateful for discussions and assistance from Dr Amit Sinha.  ...  A description of the database in accordance with BioDBCore standards (17) is available in Supplementary Table S1 .  ... 
doi:10.1093/nar/gkr1051 pmid:22121217 pmcid:PMC3245064 fatcat:jf6rmgi74jfjxburc22niclt4y

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

A. E. Bandrowski, J. Cachat, Y. Li, H. M. Muller, P. W. Sternberg, P. Ciccarese, T. Clark, L. Marenco, R. Wang, V. Astakhov, J. S. Grethe, M. E. Martone
2012 Database: The Journal of Biological Databases and Curation  
This challenge is specifically pertinent for online databases, whose dynamic content is 'hidden' from search engines.  ...  We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates.  ...  Acknowledgements We thank Mrs Andrea Stagg and many assistant curators for their hard work on the NIF Registry.  ... 
doi:10.1093/database/bas005 pmid:22434839 pmcid:PMC3308161 fatcat:tc4tvc4tmndsdo7vz52w4kwenq

Propelling the paradigm shift from reductionism to systems nutrition

Jim Kaput, Giuditta Perozzi, Marijana Radonjic, Fabio Virgili
2017 Genes & Nutrition  
As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data.  ...  The complex physiology of living organisms represents a challenge for mechanistic understanding of the action of dietary bioactives in the human body and of their possible role in health and disease.  ...  Table 1 1 Selected standards for biomedical research Acronym Name Portal Reference BioDBcore Core Attributes of Biological Databases -biodbcore/ [35]  ... 
doi:10.1186/s12263-016-0549-8 pmid:28138347 pmcid:PMC5264346 fatcat:n53rwvwuxbh4jbh45qpmazr7le
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