Organized by members of the BioSharing initiative (www.biosharing.org) and the International Society for Biocuration (ISB, www.biocurator.org), this workshop brought together developers, curators, journal editors and researchers to discuss the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications.The focus on the workshop was a strawman uniform system for describing these bio-resources (www.biodbcore.org), in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement (www.biosharing.org/standards).Location: ISMB/ECCB, Vienna.Date: July 18th, 2011.
"Unifying Bio-Resources Descriptors" Workshop at ISMB/ECCB, Vienna, 17-19 July, 2011Organizers Susanna-Assunta Sansone, Philippe Rocca-Serra (University of Bioinformatics Institute); Dawn Field (NERC Bioinformatics Centre). Background High-throughput approaches in genomics and functional genomics bioscience domain have become ubiquitous in the past decade. Several policies have emerged in response to the increased quantity of data available and the correspondingly large variability in their storage and analysis 1. The need to store and share this data helps explaining the explosion in the number and variety of tools and databases that cater to the needs of biological research. Many of those resources have contributed to the development of community-level standards that support the harmonization of the annotation and storing process, so that different data can be comprehensible (in principle), reproducible, but also easily shared, analyzed, compared and integrated. The next challenge is to better integrate those policies and standards and link them to the relevant tools and databases implementing them. The goal is to present researchers with a portfolio of standards and resources to enable use and promote adoption. The grand vision is to ease data management and enable data exchange, shielding researchers from unnecessary complexity, and ultimately facilitate data analysis. The International Society for Biocuration (ISB) and the BioSharing initiative have already taken steps in this direction by i) producing BioDBcore, a community-defined, uniform, generic description of the core attributes of biological databases and ii) releasing a first prototype of "one-stop shop" BioSharing catalogue for those seeking data sharing policy documents and information about the standards. BioDBcore has been developed and published with a wider list of contributors, including NAR and DATABASE editors and published in both journals 2 (Gaudet et al. 2011). The catalogue of policies and standards, an outcome of a Special Interest Group (SIG) 3 at ISMB 2010, works to link to exiting complementary portals, such as MIBBI4, but also open access resources, such as BMC Research Notes and Nature Precedings, with documents or publications on standards, but also standards-compliant systems and research data. Combined, BioDBcore and BioSharing efforts will enable existing and emerging resources - cataloguing tools and database - to have a uniform system for describing the biological databases and indicating what standards they implement. Workshop Objectives and Outline This workshop has brought together developers, curators, journal editors and researchers to discuss on the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications. The focus on the workshop was a strawman uniform system for describing these bio-resources, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement. At the workshop we have provided updates as to the status of the progresses of how BioDBcore core attributes and the BioSharing catalogues can be used in combination, to unify the description of bioresources and seek input as to the future of these resources. In addition, the mechanism to exchange the descriptors has been discussed, providing an opportunity for the many interested participants to engage in community assessment and planning for these new efforts. Ultimately, such uniform system will i) assist the research and bioinformatics communities to locate and access the information distributed in these bio-resources and ii) inform journal editors and funders, implementing data preservation, management and sharing policies, when recommending or requiring that certain standards are met and that data is deposited to a public database. Oxford); Pascale Gaudet (Swiss*References1. Field, Sansone et al. ,,Omics Data Sharing, Science 9, 234 (2009). 2. Gaudet, Bairoch, Field, Sansone et al. Towards BioDBcore: a community-defined information specification for biological databases. Database 4 2011:baq027; and Nucleic Acids Res, 39(Database issue):D7-10 (2011). 3. Field, Sansone et al. Meeting Report: BioSharing at ISMB 2010, Standards in Genomic Sciences, 3 (2010). 4. Taylor, Field, Sansone et al. MIBBI: A Minimum Information Checklist Resource, Nat. Biotechnol. 26, 889 (2008).Workshop Agenda Presentations are available on the Nature Precedings' BioSharing Collection: http://precedings.nature.com/collections/biosharing-meetings*