Editors Guide

Thematic editors are registry-core members responsible for overseeing coverage and quality in specific thematic areas. The editorships will enable expanding accurate high-standard software annotations in bio.tools to most scientific topics in life science.


The sheer number of software and continuous advancements in tool development demand extensive and sustained efforts to provide comprehensive annotations. Such challenges can be overcome by distributing the curation effort across a network of engaged and experienced partners, which contribute to improve bio.tools content and to adjust the EDAM vocabulary (used in bio.tools) to the needs of the respective communities. Careful coordination of the distributed tasks is required to keep similar quality standards and increase tool interoperability.

Thematic editors are well connected with their respective scientific community, experts in their field, have a broad knowledge about commonly used software and are motivated to promote bio.tools. The following tasks will enforce an improvement to the bio.tools content:

  • Review of bio.tools and EDAM to survey conceptual and semantic coverage.
  • Development of a strategy to achieve and sustain a minimum information level, as per the emerging information standard (Section 3.4, Appendix C). Updates and documentation have been provided through assigned Sifterapp issues (e.g. RNA analysis tools, proteomics tools, livestock and plant tools and Metabolomics tools).
  • Engage with their community, supervise hackathons and promote bio.tools in general.
  • Mentor a student for practical work such as manual curation.
  • Implement sustainable procedures for systematic tool reviews (e.g. bio.tools alert service) and curation standards.

Benefits: A thematic editorships provides the opportunity to become a documented expert. Editors will acquire extensive knowledge and experience about available software in their fields e.g. to publish high-quality reviews. The editors will train additional experts during training and curation events (e.g. hackathons) as well as via student supervision. Moreover, the ELIXIR framework will support them to apply for further funding to amplify their activities within their field (at least, this will be pursued).

Current thematic editors

Editor Topics
Anne Wenzel RNA structure
Jon Ison General purpose sequence analysis
Jose M. Carazo Electron microscopy, structural biology
Josep Gelpi Structural bioinformatics
Jurgen Haas Protein structural biology, structural bioinformatics
Marta Villegas Natural language processing
Martin Krallinger Text Mining, natural language processing, named entity recognition
Reza Salek Metabolomics
Veit Schwämmle Proteomics, statistics
Vivi R. Gregersen Agricultural science (association analysis, genomics)

Tentative thematic editors


People listed here in the past served as EDAM Editors; we are aiming for a single, consolidated group of Thematic Edditors serving both EDAM and bio.tools.

Editor Topics
David Sehnal General bioinformatics
Dmitry Repchevsky ES tools & services
Ivan Mičetić Protein structure
Laura Emery EBI tools and training
Lukáš Pravda Structural bioinformatics
Stanislav Geidl Chemoinformatics

bio.tools studentships can support thematic editors. A typical studentship comprises (at least) one full month of full working hours which are mostly distributed over a longer time period. Applications are written on basis of the template (see e.g. proteomics studentship). The students are recruited after proposal dissemination via GitHub, project mailing lists etc.