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Workshop: A common vocabulary to classify resources in the life sciences | BioMedBridges

Workshop: A common vocabulary to classify resources in the life sciences


A one day workshop, organised by ELIXIR, BioMedBridges and RDA, was held on 16 October 2014 in Brussels to kick-start agreement on a common topics vocabulary to classify resources in the life sciences domain, including databases, tools, courses, training materials, meetings, jobs and publications. Service providers and registries currently use different vocabularies to classify resources. From the user point of view, a common topics vocabulary would enhance the ability to find related resources of interest. From the provider point of view, a common vocabulary would be an important step to facilitate the interoperability of existing resources and significantly increase the impact and reach to different user communities. Workshop participants included representatives of societies, networks, institutes, organisations, research infrastructures and projects.

In preparation of the workshop 20 volunteers mapped the terms or vocabularies used by 24 resources to the EDAM controlled vocabulary. Mapping revealed that EDAM provided a good basis for the topics vocabulary and that there was already significant agreement between the terms used by the individual resources: about 82% of possible terms were successfully mapped. At the same time, it was possible to identify new terms not covered that might be included in a new iteration of the topics vocabulary, indicating that the approach of driving adaptations via the needs (topics used) of resources would be both straightforward and present an objective approach to optimising it.

The workshop, both in terms of participation and the reaction in the wider community, revealed that there is widespread interest in and support for the development of a common topics vocabulary, and it provided the basis and strategies for moving forward. While there was general agreement on the aims and content of the proposed vocabulary, there were indications that the structure may need further discussion and possible adjustment. Ultimately, wide adoption is necessary to realise its potential impact. To achieve this, a critical mass of initial resources needs to adopt the vocabulary to be able to demonstrate its utility with the first use cases. Funding will eventually be necessary to further develop and adapt the vocabulary itself  as well as to develop further applications.

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Agenda and presentations


Chair: Francis Rowland

11:00 - 11:05 | Welcome (Niklas Blomberg)

11:05 - 11:20 | Introductions

11:20 - 11:30 | Aims of the workshop (Rafael Jimenez)

11:30 - 11:50 | Presentation: Contextualising resources in the life sciences domain using minimal metadata (Susanna-Assunta Sansone)

11:50 - 12:00 | Presentation: Agreement on a common topics vocabulary (Jon Ison)

12:00 - 13:00 | 5’ Lightning talks

ELIXIR Tools & Data Services Registry (Kristoffer Rapacki)
toolinfowarehouse (Matus Kalas)
SeqWIKI and MetaBase (Dan Bolser)
BioSharing (Susanna Sansone)
BioCatalogue (Niall Beard)
BioRegistry (Marie-Dominique Devignes) (Camille Laibe)
EMBL-EBI resources (Bren Vaughan)
The EDAM vocabulary (Jon Ison)


Topics discussion

Chair: Rafael Jimenez

13:30 - 14:00 | Presentation: Mapping of topics from providers and registries (Cath Brooksbank)

14:00 - 14:10 | Presentation: Mapping topics across life-science resources (Stephanie Suhr)

14:15 - 14:25 | Presentation: Explanation of group sessions (Francis Rowland)

14:30 - 16:30 | Group hands-on (over coffee)
(1) Root vocabulary: high-level topics, Inspect and report
(2) Topic branches: fine-grained topics, Inspect and report


Agreement on a common topics vocabulary

Chair: Stephanie Suhr

16:45 - 17:30 | Discussion: Agreement on a common topics vocabulary (Jon Ison)
(1) Commitments to promote, adopt, develop the vocabulary
(2) Practical issues in building our community: open discussion


Future development

Chair: Carole Goble

17:30 - 17:40 | Introduction to the Panel Discussion: "Strategies to adopt and develop the common topics vocabulary in support of integration and discovery of resources" (Niklas Blomberg)

18:00 - 19:00 | Discussion: "Vocabulary and metadata use-cases and impact" and "Assembling a coalition of resources"



  • Janet Thornton (EMBL-EBI, BioMedBridges)
  • Niklas Blomberg (ELIXIR)
  • Søren Brunak (ELIXIR-DK, BioMedBridges, ELIXIR/BioMedBridges Services Registry, CBS-DTU tools)
  • Carole Goble (ELIXIR-UK, ISBE, TeSS, Fairport, myExperiment, SSI, BioCatalogue, SEEK4Science, FAIRDOM)
  • Rob Hooft (ELIXIR-NL, NLeSC, DTL, Fairport)
  • Inge Jonassen (ELIXIR-NO, University of Bergen)
  • Heinz Stockinger (ELIXIR-CH, SIB, ExPASy)
  • Terri Attwood (ELIXIR-UK, BioDBCore, EMBnet, GOBLET, iAnn, ISCB, ISB, AllBio, SeqAhead, TeSS)
  • Cath Brooksbank(ELIXIR-UK, EMBL-EBI, EMTRAIN, GOBLET, on-course, TeSS)
  • Manuel Corpas (ELIXIR-UK, BioJS, GOBLET, iAnn, ISCB, TeSS)
  • Vassilios Ioannidis (ELIXIR-CH, SIB, ExPASy)
  • Hervé Ménager (Institut Pasteur, BioWeb2, Mobyle)
  • Helen Parkinson (EMBL-EBI, BioMedBridges, ELIXIR/BioMedBridges Services Registry)
  • Francis Rowland (EMBL-EBI, BioJS)
  • Susanna-Assunta Sansone(ELIXIR-UK, BioDBCore, BioSharing, ISA Commons, TeSS; RDA TAB)
  • Vicky Schneider(ELIXIR-UK, EMBnet, GOBLET, iAnn, TeSS)

Technical organisers

  • Jon Ison (ELIXIR-DK, ELIXIR/BioMedBridges Services Registry, EDAM, Tools@EBI)
  • Rafael Jimenez (ELIXIR Hub)
  • Stephanie Suhr (EMBL-EBI, BioMedBridges)