Editors Guide

Thematic editors are registry-dev 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 the life sciences.

..note:: The concept of “thematic editors” is a work in progress which we will develop as funding and capacity permits.


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 maintain quality standards and increase tool interoperability across the board.

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. Editors normally oversee the work of one or more student curators, on a range of tasks to improve EDAM and bio.tools content:

  • Review of bio.tools and EDAM to survey coverage of concepts, terms and tools.
  • Help develop strategy to achieve and sustain a minimum information level in bio.tools, as per the emerging information standard.
  • Engage with their community, supervise hackathons and promote bio.tools in general.
  • Mentor a student for practical curation work
  • Implement sustainable procedures for systematic tool reviews and curation standards.

Benefits: A thematic editorships provides the opportunity to become a curation expert and contribute to a project for the benefit of the whole bioinformatics community. Editors will acquire extensive knowledge and experience about available software in their fields e.g. with opportunity 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 infrastructure will support them to amplify their activities within a broader context.

Candidate thematic editors

We have expressions of interest from the following people:

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)

People listed below, 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.