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Publication . Report . 2015

Report on the development of the BioMedBridges registry of biomedical science data services and tools

Ison, Jon; McMurry, Julie; Parkinson, Helen; Conte, Nathalie; van Denderen, Janneke; Belien, Jeroen; Brunak, Søren; +8 Authors
Open Access  
Published: 20 Jan 2015
Publisher: Zenodo
Abstract
The development of a prototype service registry is the objective of BioMedBridges Deliverable 3.3, with contributions from BioMedBridges partners and in collaboration with ELIXIR. The Tools and Data Services Registry is designed to make it easier for researchers to find, compare, and use biomedical software to address a scientific question or research support task. For instance: “What are all of the Gene Ontology tools? Which of these is most highly cited?”. By returning relevant, structured results, the registry aims to complement search engines like Google: The registry user can specify exactly what they need, using various search and filter options, and get a tailored list of suitable resources. From sequencing to structures, imaging to indexing, the registry’s domain scope is very broad; it also encompasses webservices, web GUIs, desktop GUIs, and commandline tools. This broad scope ensures coverage of a substantial portion of the tools and data services of use to Research Infrastructures represented in BioMedBridges. Information about tools includes crucial provenance details, links to relevant publications and grants and key contact information. Consistent with the overall mission of WP3, the service registry implemented and extended existing standards, formats, and ontologies wherever possible. To achieve the objectives, it was necessary to engage with the software community to develop a sustainable, scaleable minimum metadata model and formal schema to describe software; the model was purpose-built to be lightweight and flat in order to facilitate adoption by other software registries that may be looking to provide or aggregate software metadata in the future. The registry data model, software, and content (metadata describing the tools) are fully open access and open source in order to further encourage re-use and community participation. In the following report we summarise technical progress and outcomes of our work to date. Future plans comprise a program of activities lead and coordinated by ELIXIR-DK (tools node) and it is expected that this will ensure long-term sustainability of the registry. The code, schema and data in the prototype tools registry has all been made available to the ELIXIR-DK node and to the wider community via Github. Further contacts have been made with external projects e.g. the NIH funded Gene Ontology and the EC funded RD-Connect project to identify tools that they recommend and to include these in the service registry. This deliverable report provides detailed information on the work performed with BioMedBridges resources.
Subjects

discoverablity, registry, life-science data, tools, services, software description model

Funded by
EC| BIOMEDBRIDGES
Project
BIOMEDBRIDGES
Building data bridges between biological and medical infrastructures in Europe
  • Funder: European Commission (EC)
  • Project Code: 284209
  • Funding stream: FP7 | SP4 | INFRA
Related to Research communities
EGI Federation
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