The EBP project generates tons of data. Apart from storing the generated data itself (sequencing data, genome assemblies, genome annotations, …), it is strongly recommended to also store the so-called “metadata”. Metadata is information that tells us more about our data. Some examples of metadata are location and time of sampling, who has sampled and/or identified a species, or how a sample was obtained. Metadata for computational data can include the software used to generate the data, but also its version and specific parameters.
A big problem regarding metadata for computationally created data (for example genome assemblies and annotations), is that the metadata is often not or barely documented, and there is often no good way of searching metadata. Even though we would like to submit the metadata of our analyses, there is currently no real way of submitting this metadata to databases such as NCBI GenBank or ENA. The metadata could be described in the publication(s), but that makes it hard for other people to recover. (It is not straight forward parsing tables in PDFs). Imagine having to go through every paper associated with a genome if you are analysing tens or hundreds of genomes/annotations at the same time!
Luckily, there are initiatives that aim to set up metadata standards to make it easier for people to both store and submit metadata, but also easier to search metadata. One of these projects is organised by the RDA (Research Data Alliance) working group “FAIRification of Genomic Annotations - metadata harmonisation at scale”. This working group, led by Sveinung Gundersun from UiO, aims to create standards to store and share genome annotation data in a FAIR way: Findable, Accessible, Interoperable, and Reusable. Together with Gavin Chait, they submitted a project to the 2024 Elixir Biohackaton in Barcelona, and got accepted. In a (bio)hackathon, people from different fields and backgrounds come together to work on specific problems without any other distractions
From the EBP-Nor project, Ole K. Tørresen and Bram Danneels joined the Biohackaton in Barcelona. The biohackathon took place from the 4th to the 8th of November, and started off with a 3h flight delay due to the very bad weather in Barcelona. A red rain/storm weather alert led to the Barcelona airport not allowing any planes to land, creating long delays for most participants of the hackathon. While they sadly had to miss the introduction session of the hackathon, they were just in time for the excellent dinner at the venue (the first of many to follow during the week).
The next three days were all about the hacking. We got to meet our team, composed of the two co-leads (Sveinung and Gavin), four in-person attendees (including Ole and Bram), an online participant from the UK, and a team of 7 people from Australia. Coordinating with the Australian team was a challenge in itself due to the time difference. We had to start a bit earlier than other teams to manage to coordinate with them, while they committed to shifting their working hours to the afternoon/evening to create a useful overlap where we could work together. This did however allow us to have people working almost around the clock on the project. We were working on a specific use case (provided by Katharina Hoff, one of the developers of the BRAKER genome annotation software). She provided us with the metadata from one of their projects, which we would try to extract the parts we found the most important to make it FAIR. As our team was composed of people from a range of different backgrounds, we spent a lot of time discussing and explaining. It took some time to figure out how to approach the problem, but after two days of intense discussion we came to a preliminary conclusion. We decided to create an intermediate schema/spreadsheet based on the FAIRtracks schemas which hopefully cover the most important metadata about genomic annotations. We managed to create a first draft of that schema, which can then be used in the larger RDA working group as a basis for further developments.
This accomplishment was celebrated with drinks and karaoke and after a short night for some, it was time to wrap up the biohackathon and fly home. For both of us it was the first time we participated in this kind of event, and although we were both exhausted at the end, it was a really valuable experience. Hopefully, the results of our work can soon be used to easily store and share the metadata of our genome annotations with the rest of the scientific community.
You can read more about our work at the biohackathon on the Github page!