Promoting the longevity of curated scientific resources through open code, open data, and public infrastructure
The 16th Annual International Biocuration Conference (Biocuration 2023) is taking place in Padua, Italy from April 24-26th, 2023. While I’m serving as a co-chair of the conference, I also think this is a great venue to communicate some of my thoughts on longevity and sustainability that have been gestating during the development of the Bioregistry and other Biopragmatics projects. This blog post contains the abstract I’ve submitted for oral presentation.
Note: if you want to submit your own abstract, you have until the end of today (January 3rd, 2023, anywhere on earth) to submit via EasyChair.
Many model organism databases, pathway databases, ontologies, and other curated resources that support research in the life and natural sciences combine expert-curated data with surrounding software code and services. However, such resources are often maintained internally by members of a single institution and are therefore susceptible to fluctuations in funding, personnel, and institutional priorities. Too often, resources go out of date, are abandoned, or become inaccessible, for example, when a grant runs out or a key person moves on. Therefore, we need better solutions for creating resources that are less susceptible to such external factors and can continue to be used and maintained by the community that they serve.
We propose a new model for the creation and maintenance of curated resources that promotes longevity through a combination of technical and social workflows, and a progressive governance model that supports and encourages community-driven curation. 1) The technical aspect of our model necessitates open data, open code, and open infrastructure. Both code and data are permissively licensed and kept together under public version control. This enables anyone to directly suggest improvements and updates. Further, automation is used for continuous integration (e.g., semi-automated curation, quality assurance) and continuous delivery (e.g., static website generation, export in multiple formats). 2) The social aspect of our model first prescribes the composition of training material, curation guidelines, contribution guidelines, and a community code of conduct that encourage and support potential community curators. Second, it requires the use of public tools for suggestions, questions, discussion as well as social workflows like pull requests for the submission and review of changes. 3) The governance aspect of our model necessitates the division of responsibilities and authority (e.g., for reviewing/merging changes to the code/data) across multiple institutions such that it is more robust to fluctuation in funding and personnel that can also be updated over time. It prescribes liberal attribution and acknowledgement of the individuals and institutions (both internal and external to the project) who contribute on a variety of levels (e.g., code, data, discussion, funding). More generally, our model requires that a minimal governance model is codified and instituted as early as possible in a project’s lifetime.
This talk will provide a perspective on how existing resources relate to our model, describe each of our model’s aspects in more detail (illustrated through the Bioregistry resource), and provide a practical path towards both creating new sustainable resources as well as revitalizing existing ones.
Later, I will update this post with a link to the slides for the related talk. Please let me know if you’ll be in Padua for the conference! I’d love to catch up.