FAIRification as a Team Sport

The FAIR Principles have succeeded to unit stakeholders world-wide behind a common concept: good data management under common standards. However, putting FAIR into practice is still work in progress and it "takes a village".   I will provide an overview of two community-driven resources, the FAIRsharing (https://fairsharing.org) and the FAIR Cookbook (https://faircookbook.elixir-europe.org), as examples of what we need to turn FAIR into reality. Both resources will also contribute to the UKRN ecosystem

FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies

In this modern, data-driven age, governments, funders and publishers expect greater transparency and reuse of research data, as well as greater access to and preservation of the data that supports research findings. Community-developed standards, such as those for the identification and reporting of data, underpin reproducible and reusable research, aid scholarly publishing, and drive both the discovery and evolution of scientific practice. The number of these standardization efforts, driven by large organizations or at the grass root level, has been on the rise since the early 2000s. Thousands of community-developed standards are available (across all disciplines), many of which have been created and/or implemented by several thousand data repositories. Nevertheless, their uptake by the research community, however, has been slow and uneven. This is mainly because investigators lack incentives to follow and adopt standards. The situation is exacerbated if standards are not promptly implemented by databases, repositories and other research tools, or endorsed by infrastructures. Furthermore, the fragmentation of community efforts results in the development of arbitrarily different, incompatible standards. In turn, this leads to standards becoming rapidly obsolete in fast-evolving research areas. As with any other digital object, standards, databases and repositories are dynamic in nature, with a life cycle that encompasses formulation, development and maintenance; their status in this cycle may vary depending on the level of activity of the developing group or community. There is an urgent need for a service that enhances the information available on the evolving constellation of heterogeneous standards, databases and repositories, guides users in the selection of these resources, and that works with developers and maintainers of these resources to foster collaboration and promote harmonization. Such an informative and educational service is vital to reduce the knowledge gap among those involved in producing, managing, serving, curating, preserving, publishing or regulating data. A diverse set of stakeholders-representing academia, industry, funding agencies, standards organizations, infrastructure providers and scholarly publishers, both national and domain-specific as well global and general organizations, have come together as a community, representing the core adopters, advisory board members, and/or key collaborators of the FAIRsharing resource. Here, we introduce its mission and community network. We present an evaluation of the standards landscape, focusing on those for reporting data and metadata - the most diverse and numerous of the standards - and their implementation by databases and repositories. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We present guidelines that highlight the role each stakeholder group must play to maximize the visibility and adoption of standards, databases and repositories

Standards and infrastructure for managing experimental metadata

*See also "related poster":http://precedings.nature.com/documents/3144/version/1*

Today’s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as ‘omics’). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.

Standards initiatives normally cater to particular domains. However, several synergistic standards activities foster cross-domain harmonization of the three kinds of reporting standard (minimum information checklists, ontologies and file formats). Some 29 groups participate in the "MIBBI":http://www.mibbi.org project, which offers a one-stop shop for those exploring the range of extant ‘minimum information’ checklists, and which fosters integrative development^1^. More than 60 groups participate in the "OBO Foundry":http://www.obofoundry.org ^2^, which coordinates the orthogonal development of ontologies such as "OBI":http://obi-ontology.org for describing experimental (meta)data. And several groups participate in the development of "ISA-Tab":http://isatab.sf.net, a tabular framework for presenting experimental metadata^3^ (analogous to "FuGE":http://fuge.sf.net, a generic data model to underpin various XML file formats^4^).

We have developed an infrastructure that leverages the aforementioned synergistic reporting standards to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies. 

View the "public instance":http://www.ebi.ac.uk/bioinvindex of our ISA-based infrastructure, running at EBI, and/or "download the components":http://isatab.sf.net for your local use.

*References*
1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. _Nature Biotechnology_ Aug;26(8):889-896. "http://www.mibbi.org":http://www.mibbi.org

2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. _Nature Biotechnology_ Nov;25(11):1251-5. "http://www.obofoundry.org":http://www.obofoundry.org

3. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. _OMICS_. Jun;12(2):143-9. "http://isatab.sf.net":http://isatab.sf.net

4. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). _Nature Biotechnology_ Oct;25(10):1127-1133. "http://fuge.sf.net":http://fuge.sf.ne

FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies

In this modern, data-driven age, governments, funders and publishers expect greater transparency and reuse of research data, as well as greater access to and preservation of the data that supports research findings. Community-developed standards, such as those for the identification and reporting of data, underpin reproducible and reusable research, aid scholarly publishing, and drive both the discovery and evolution of scientific practice. The number of these standardization efforts, driven by large organizations or at the grass root level, has been on the rise since the early 2000s. Thousands of community-developed standards are available (across all disciplines), many of which have been created and/or implemented by several thousand data repositories. Nevertheless, their uptake by the research community, however, has been slow and uneven. This is mainly because investigators lack incentives to follow and adopt standards. The situation is exacerbated if standards are not promptly implemented by databases, repositories and other research tools, or endorsed by infrastructures. Furthermore, the fragmentation of community efforts results in the development of arbitrarily different, incompatible standards. In turn, this leads to standards becoming rapidly obsolete in fast-evolving research areas. As with any other digital object, standards, databases and repositories are dynamic in nature, with a life cycle that encompasses formulation, development and maintenance; their status in this cycle may vary depending on the level of activity of the developing group or community. There is an urgent need for a service that enhances the information available on the evolving constellation of heterogeneous standards, databases and repositories, guides users in the selection of these resources, and that works with developers and maintainers of these resources to foster collaboration and promote harmonization. Such an informative and educational service is vital to reduce the knowledge gap among those involved in producing, managing, serving, curating, preserving, publishing or regulating data. A diverse set of stakeholders-representing academia, industry, funding agencies, standards organizations, infrastructure providers and scholarly publishers, both national and domain-specific as well global and general organizations, have come together as a community, representing the core adopters, advisory board members, and/or key collaborators of the FAIRsharing resource. Here, we introduce its mission and community network. We present an evaluation of the standards landscape, focusing on those for reporting data and metadata - the most diverse and numerous of the standards - and their implementation by databases and repositories. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We present guidelines that highlight the role each stakeholder group must play to maximize the visibility and adoption of standards, databases and repositories

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data

Standards and infrastructure for managing experimental metadata

*See also the "related presentation":http://precedings.nature.com/documents/3145/version/1*

We present an infrastructure that leverages synergistic reporting standards and ontologies^1,2,3,4,5^ to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies. 

The infrastructure’s components include: a data capture and editing tool (_ISAcreator_); validator (_ISAvalidator_); database (_BioInvestigation Index_); and converter (_ISAconverter_); and a BioConductor analysis package (_R-ISApackage_). The components are designed for local installation, and can work independently, or as unified system.

View the "public instance":http://www.ebi.ac.uk/bioinvindex running at EBI and/or "download the components":http://isatab.sf.net for your local use.

*References*
1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. _Nature Biotechnology_ Aug;26(8):889-896. "http://www.mibbi.org":http://www.mibbi.org

2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. _Nature Biotechnology_ Nov;25(11):1251-5. "http://www.obofoundry.org":http://www.obofoundry.org

3. Ontology for Biomedical Investigations (OBI) "http://obi-ontology.org":http://obi-ontology.org 

4. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. _OMICS_. Jun;12(2):143-9. "http://isatab.sf.net":http://isatab.sf.net

5. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). _Nature Biotechnology_ Oct;25(10):1127-1133. "http://fuge.sf.net":http://fuge.sf.ne

Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting

Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks