Long-term Funding for Small Biomedical Databases
Way back in 2021, during the annual general assembly of the International Society for Biocuration (ISB) at the the 14th Annual International Biocuration Conference (Biocuration 2021) , there was a discussion about the notably underutilized budget of the society that resulted in an informal open call for ideas for new small funding schemes. Concurrently, discussions with external stakeholders for the relatively new (at the time) Bioregistry project often included questions about the sustainability and longevity of the resource. We had conservatively estimated it would cost about 100 USD/year to run the Bioregistry site, so this seemed like the perfect opportunity to ask for a small amount funding distributed over a relatively long period of time. This post is about the more general reality of funding for small resources in the life sciences, how we petitioned the ISB for funding, and what happened next.
Bioregistry Cost Estimate
The Bioregistry is an integrative registry of biomedical ontologies, databases, and other identifier resources that is useful for standardizing the identification of biomedical concepts, making data more FAIR, and enabling data- and knowledge integration.
It runs a fully automated nightly workflow that updates its data, packages its code and data, and pushes it to the Python Package Index (PyPI). We carefully constructed this workflow to fully run on free, open infrastructure (e.g., GitHub Actions) and require little maintenance. After running this workflow for nearly three years, we’ve empirically found that the maintenance effort averages between 10-15 minutes per month for bug fixes and/or additional data curation. We won’t factor this into our initial cost estimate as this effort could be discretionary (i.e., not tied to a grant, donated by maintainers, users, etc.).
After, the workflow builds a Docker image and pushes it to the biopragmatics/bioregistry repository on DockerHub. This image is built with the the latest Python alpine base image, which significantly reduces non-essential components. It also has the benefit of being compatible with Docker environments running on both Intel and ARM architectures. The final compressed image weights less than 40 MB of disk space and runs inside Docker with about 65 MB of memory at baseline. This easily fits on a dedicated t4g.nano instance on Amazon Web Services (AWS) which costs about 37 USD/year on-demand or around 20 USD/year reserved (i.e., if you pay up front). Two or more of these instances could be set up behind a load balancer to ensure uptime in case one goes down, but we won’t factor this into our initial cost estimate.
bioregistry.io domain is registered with Namecheap and costs about
33 USD/year. The SSL/TLS certificate for
bioregistry.io (so it can be served with HTTPS) is managed through the
AWS Certificate Manager and does not cost anything additional.
Finally, we’re going to exclude the costs of proactive curation of the resource. The combination of import from 23+ external registries, the ability for community members to suggest new prefixes in a streamlined way, and the decentralization of moderation effort across many institutions results in a negligible cost.
In a best case scenario, using a reserved instance and paying for a domain name brings this bill to 53 USD/year. Duplicating the deployment behind a load balancer would bring it up to 73 USD/year. For good measures in case costs go up, let’s call it 100 USD/year. That’s pretty darn cheap for a resource that’s already proven useful in several applications and is being pretty widely adopted. Most resources don’t last more than two or three years (disclaimer: I’m spit-balling here). If we got 1,000 USD, we could already promise people that this service will be running consistently for ten years. If we got 1,500 USD, we could extend that promise to fifteen years.
In order to gauge how small this amount is, consider that the International Society of Biocuration is currently offering six travel grants worth about the same amount each to attend the 16th Annual International Biocuration Conference (Biocuration 2023). Sure, I’m biased since the Bioregistry is my baby, but it would be difficult to argue that this is not pennies on the dollar compared to what some other resources cost to deploy and maintain.
What’s the Problem with Funding the Bioregistry
The Bioregistry was a spin-off project of a spin-off project. A long time ago, I was working on parsing and validating biomedical knowledge encoded in the Biological Expression Language. In order to support the validation of names and identifiers from various ontologies and databases, I started developing PyOBO as a tool for unified access to ontologies and databases. I curated extra rules for standardizing prefixes, CURIEs, and URIs that eventually got spun out into the Bioregistry and took on a life of its own. Each of these steps was part of a bigger project with bigger goals that weren’t necessarily focused on the development of high-quality, reusable underlying technology. But, developing high-quality, reusable underlying technology is just the way that I think, so that’s how I did it. And I took those nice tools with me from project to project, improving them as I went. This means that the Bioregistry has now played a role in several of my recent projects, but never sat up front and center when it came to writing grants.
So here’s the more general issue: grants are usually about building new, big things with big budgets that are done within the short timeframe of a project, then they’re usually lost or forgotten. The Bioregistry is a small, important resource that does not need massive development but it does need a long commitment to maintenance in order to provide the stability to the community that other resources have yet been able to provide. Further, the fact that it already exists makes it much less novel and therefore effectively disqualified from being the focus of most potential grants.
With potential costs so low, it would actually feasible for my current department, the Laboratory of Systems Pharmacology to commit discretionary funding external to a grant. However, this doesn’t engender trust the same as having external funding or being part of an institution that is well-known for the longevity of its infrastructure platforms (e.g., the NIH). Further, discretionary funding also raises questions about what happens when the main people on my team working on the Bioregistry leave, both from a responsibility and technical perspective. This seemed to be the sentiment from potential stakeholders of the Bioregistry that were shared at the Fall 2021 Workshop on Prefixes, CURIEs, and IRIs.
Communication with the ISB
After thinking about all of this, I finally write up a proposal (somewhere between one and two pages) and shared it with the executive board of the ISB. Unfortunately, I shared this on Slack and have been unable to find the original message since you can’t search Slack messages older than 90 days now. As a paraphrase, I focused on some of the following ideas:
As opposed to monolithic infrastructures and projects maintained by large organizations like the United States National Library of Medicines (NLM), the European Bioinformatics Institute (EMBL-EBI), and the Swiss Institute of Bioinformatics, most biocuration projects are small and limited in scope. There are several public systems that could support many of them:
- archival systems (e.g., Zenodo, FigShare)
- hosting of static sites (e.g., institutional websites, GitHub Pages)
- hosting of dynamic sites (e.g., Amazon Web Services, Microsoft Azure, Heroku, Shiny, Google Could Platform)
- domain name registration (e.g., institutional domain, NameCheap)
- continuous integration and deployment (e.g., GitHub Actions, GitLab Pipelines)
These are relatively inexpensive and can be used to build resources that have high longevity and sustainability. Most biocuration projects end up being one-off publications anyway and are never updated, so I suggested that the ISB give small grants to groups that are using best practices and the above tools to create things that could have longevity, if given appropriate small funding across a long period of time. The biggest problem facing small curation projects and websites is that they can not acquire small amounts of long-term funding to support their technical infrastructure (e.g., domain name hosting, cloud compute resources). It’s becoming easier to build websites for new small biocuration projects, but again, there are small, recurring costs associated with them like paying for a domain name and cloud compute resources. I would suggest introducing a small grant whose award would be spread across a potentially long time (e.g., 10-15 years) to support those costs (but not explicitly not for major development nor maintenance).
Is this really a big deal?
My group has recently been thinking about how bad the longevity situation really is. We build the Bioregistry Health Report that checks on a weekly basis how many prefixes’ homepages still resolve and how many URI format strings still resolve. The results were bleak - only about 27% (as of today) do. This isn’t an indictment of the badness of the Bioregistry or the registries that it imports and aligns either - it’s true that sometimes the URLs for sites change, but this number reflects the more general problem that most just go away.
Unfortunately, the ISB EC didn’t accept the proposal. I didn’t get very direct feedback as to why, but I think the general concept of funding research was problematic for one reason or another for their organizational structure. I’m not discouraged, I still think this is important and will continue to write and re-write this proposal until it finally convinces the right funding body. I’ll also be touching on this point at my (hopefully accepted abstract) for Biocuration 2023 that I posted about yesterday. Please let me know if you’ve got any other arguments supporting doing this that I can include!