“What drives me is that we share a common goal: to provide the most accurate and up-to-date open knowledge to support research.” Meet Elisabeth Coudert, at SIB since 2000, who is leading the Annotation Enhancements team in the Swiss-Prot Group. From a purpose-driven job supporting the international research community to flexible working conditions, find out what motivates her in her role.
From when you first joined SIB, to Team Lead Biocuration* today: tell us a bit about your career path.
After a PhD in the field of chemistry related to biology, I joined the Swiss-Prot group in 2000, two years after the birth of SIB. At that time, I was a biocurator in the Prokaryotic Protein Annotation Program, which I also led from 2008 to 2018. Since 2018 I have been leading the Annotation Enhancements team. Our main role is to develop standards such as ontologies (e.g. controlled vocabularies), and tools to support functional annotation in leading knowledge resources. These resources include for instance UniProtKB, the universal protein knowledgebase, and Rhea, a database of biochemical reactions curated by our team. Both SIB Resources are recognized as Elixir Core Data Resources and have recently been selected as Global Core Biodata Resources.
Next to this, I keep an active role as a curator and editorial content manager performing quality assurance and focusing on the annotation of enzymes for UniProtKB/Swiss-Prot and reactions for Rhea.
*the art of generating and summarizing machine-readable knowledge of biology from the ever-growing body of scientific publications
What do you enjoy about working as a Team Lead Biocuration in the Swiss-Prot group?
I enjoy the teamwork between curators and developers: nothing would be possible without each other. I also like the fact that the expertise and skills of everyone are exploited to build universal knowledge that is made freely accessible to the scientific community.
What drives me, day in and day out, is that we share a common goal: to provide the most accurate and up-to-date open knowledge to support research. This allows a real team spirit and mutual support.
As a team lead, I aim to ensure that everyone brings his contribution in the best possible way.
Do you have an example of a project you are particularly proud of?
I recently led the standardization of annotations related to biologically relevant ligands* in UniProtKB. This was a massive effort that involved the replacement of free text descriptions of small molecule data accrued over decades of biocuration work, by stable, unique identifiers from the chemical ontology ChEBI. The improved dataset and tools created in this project make UniProtKB even more interoperable with other resources and enable new ways to mine it. This work also provides a rich source of ligands for drug design projects and has the potential to enrich AI-based protein structure predictions such as those of AlphaFold, which currently lack ligands essential for function.
This work led to a publication in January 2023 and has been selected as one of SIB Remarkable Outputs for 2022.
*Small chemical compound that binds a protein, for instance, to regulate its activity
What do you particularly like at SIB (i.e. what makes SIB unique as an employer)?
Working at SIB means an opportunity to work in an internationally recognized organization, offering tools and services that are of great help to the scientific community. That is motivating! It also means working in a flexible and autonomy-driven environment, which is highly appreciated.