I’ve just returned from the 17th Annual International Biocuration Conference at the Indian Biological Data Centre (IBDC) in Faridabad, India. I wanted to highlight some of the interesting conversations I had while I was there, and ideas for follow-up. Most were centered around the Bioregistry and the Semantic Mapping Assembler and Reasoner (SeMRA), which I gave an oral presentation on.

I talked to Guy Cochrane and Chuck Cook from the Global Biodata Coalition (GBC). They chaired a session on sustainability of biocurated resources, with specific focus on the Global Biodata Coalition’s Global Biodata Core Resources (GBCR) initiative. I felt like my talk from last year’s biocuration conference on the Open Code, Open Data, Open Infrastructure (O3) roadmap (preprint) would have fit right in here. I am very keen to have their perspectives, as GBC has first worked on evaluation of resources and is second working towards funding resources. Since they have not worked on practical recommendations for supporting sustainability, I eagerly volunteered to join their work in some capacity to help advise on this.

GBC also published a workflow for evaluating the landscape of biological databases (press release / publication / code). When possible, this workflow aligned on FAIRsharing, but given that it is a limited resource and only has partial mappings to relevant related resources like re3code, BARTOC, etc. I suggested using the Bioregistry as a mapping hub to enrich the output of this workflow, which will definitely be run again on a periodic basis.

Lynn Schriml presented recent updates on the Disease Ontology, which prompted a relevant question from Harpreet Singh - Chief Data Officer at the Indian Council of Medical Research (ICMR) who himself works with clinical data and has wondered how to best annotate - using MeSH, SNOMED, ICD, or other disease resources. I had an interesting discussion with him following the talk which gave big motivation to the talk I was about to give on the large scale assembly and reasoning over semantic mappings. I was very excited, since I love to add (last minute) shout-outs into my conference talks that motivate parts of the work based on questions or discussions from earlier parts of the conference.

There were a series of talks that motivated further discussions about mappings. One of the most interesting was the talk from Shivani Sharma, a curator at the Indian Biological Data Centre (IBDC) and one of the local organizers. She works on the Indian Metabolome Data Archive. Many of the lines of work at the IBDC have practical applications towards agriculture and integrate medium- and large-scale experimental work, biocuration, and downstream analysis. Often, these applications are oriented towards improving crop yields and avoiding disease. Shivani showed a slide where they considered a large number of metabolomics nomenclature resources to use for annotating their data. However, they were not familiar with methods for incorporating multiple nomenclature resources, meaning that their curators were running into issues where their chosen metabolomics database did not cover chemicals they needed to annotate. This often lead to them having to create their own ad hoc annotations, which also create issues for data integration. I am looking forwards to catching up with them again, incorporating new metabolomics resource into PyOBO, ingesting mappings into SeMRA, and filling in the gaps using Biomappings to support their curators.

Scott V. Nguyen from the American Type Culture Collection (ATCC) also approached me about this work, since he’s currently trying to curate mappings between cell lines in their resource and other public resources. It was lucky that one of the examples from my talk was specifically about the cell lince scenario, which I hope he can ingest and reduce his curation workload. Rachel Lyne also presented on COSMIC, a cancer cell line resource that also creates its own accession numbers and could benefit from this work, but I didn’t get a chance to talk about it with her yet.

I also met Yasunori Yamamoto, who works on TogoID, a secondary database of semantic mappings that covers select domains within biomedicine. We discussed how they could make use of the Simple Standard for Sharing Ontology Mappings (SSSOM) to ingest more mappings from different resources, especially from Biomappings or potentially from the outputs of SeMRA (which I presented on).

Matt Jeffreys presented on the annotations database in European PubMed Central which allows for tagging articles, sentences, or tokens in articles with annotations. They already showed how this applies to named entity recognition (NER) and MeSH term annotations, but we discussed how SeMRA and comprehensive semantic mapping databases could help unify other annotations of overlapping vocabularies, e.g., if someone put Disease Ontology (DO) NER annotations, which overlap with MeSH terms in the disease (C) and psychiatric disorders (F) branches.

I discussed with Raja Mazumdar and Jeet Vora from George Washington University who both work on GlyGen and are plugged into the NIH’s Common Fund Data Ecosystem (CFDE) about how they can continue to use the Bioregistry to standardize the annotations in their resources. Jeet has got in touch earlier this year and helped update the records in the Bioregistry related to GlyGen. Raja’s talk also motivated two new prefix additions to the Bioregistry for Biocompute Objects and for OncoMX data objects. Further, Raja is very interested in improving his data using the Bioregistry, since it already uses a Python script to validate its JSON and TSV components, it will be easy to incorporate the Bioregistry Python package’s validation functions.

Earlier this winter, I presented to the American National Institutes of Health (NIH) BISTI group about different avenues through which they could use the Bioregistry to create more value for the NIH and its grantees. One of those discussions was about improving GenBank’s internal database catalog. By chance, I talked with Ilene Karsch Mizrachi, a program head at the NIH about this. She was attending the conference and made big contributions to the discussions about the Indian relation to the International Nucleotide Sequence Database Collaboration (INSDC). However, it turns out she was the one who made/contributed to this GenBank table, many years ago. We will try and follow up by enriching this table with information from the Bioregistry.

At last year’s biocuration conference, Chris Hunter presented on GigaDB, and we had some initial discussions about using the Bioregistry (or other related parts of the Biopragmatics Stack) to make standardized annotations on data sets deposited in their database, such as cell line annotations. We picked back up that conversation, and it seems that the GigaDB developers are working with PHP - since we got CZI funding to make the Bioregistry available in other languages, making a wrapper from Rust to PHP (within the curies.rs framework).

There was an entire session on the final day of the conference on structural bioinformatics, which included several presentations from the American and European loci of the Protein Databank (PDB). The first discussion was with Marcus Bage, who is currently trying to annotate protein modifications. We discussed the implications of the vast number of resources that partially cover this domain in different senses, including GO, MOD, SBO, MOP / PSI-MI, and UniProt’s internal vocabulary. A long time ago, I mapped these together in PyBEL, but this was only a partial solution, too!

The second discussion was with Brinda Vallat about the upcoming change for PDB accession numbers. It turns out that the 4 character code is estimated to fill up in 2029, so it’s time for PDB to make a change. Unfortunately, their solution is to switch to local unique identifiers that look like pdb_000002GC4, which is problematic for two main reasons. First, it’s not backwards compatible with existing IDs. Second, it introduces a banana (i.e., a redundant copy of the name/acronym of the database in the local unique identifier). The reasoning behind adding in the banana was to make it easier to find references in papers. I can understand this, since we don’t yet have general solutions for referencing concepts across different publishers (though, we solved this in Manubot by integrating the Bioregistry). However, this increases confusion for consumers. I suggested they simply extend the existing IDs to be able to have more than 4 characters, and suggest people reference their entities with CURIEs like PDB:2GC4 within papers, which solves both issues simultaneously. Similarly, I talked to Ibrahim Roshan Kunnakkattu about creating more careful identifier recommendations for the PDB’s Chemical Component Dictionary as well as using some of the automated mapping tools I presented for filling out references to ChEBI, ChEMBL, PubChem, and more.

I also had the unique pleasure to spend time in person with Tiago Lubiana, who is highly aligned on many of my interests in data standardization, semantic web, and open science. He has been a helpful contributor in the Bioregistry, Wikidata, and the OBO Foundry. Writing up some of the things we discussed would take a whole blog post, so instead, here’s a nice picture we got together.

Charlie Hoyt and Tiago Lubiana

Overall, like every Biocuration conference, I was very happy to find people interested in my work, and more importantly, interested in the idea of improving their own data standardization! I also had lots of other interesting discussions that don’t require any follow-up. I am also planning on writing a post that gives a more high-level summary of the different parts of the conference itself, not just focusing on my work.