Our work on designing OBO Foundry ontology extensions for natural products won the Best Poster Award from the Bioontologies COSI at ISMB/ECCB 2021 and is now available - doi.org/10.5281/zenodo… NaPDI

We have developed the ontology for Avida digital evolution platform (gitlab.com/fortunalab/ont…), and it has been accepted to be part of the OBO Foundry (obofoundry.org/ontology/ontoa…). It's our fortunalab.org first contribution in the field of semantic databases.

We just added 63 new prefixes that cover a significant part of the missing prefixes used in OBO Foundry ontologies. Check out the huge PR here: github.com/biopragmatics/…

Thanks for your help shaping this #biodata primer, providing use cases & sharing w/ #datamanagement folks! ISO TDWG OBO Foundry GBIF @biodiversity.social/@gbif OBIS U.S. IOOS Office EDI DataONE Planet Microbe WoRMS ITIS.gov Data.gov NOAA NCEI

SSSOM provides a standard way for exchanging mappings between classes in ontologies

The @Bioregistry has an API that links entities to external resolvers and providers like in OBO Foundry identifiers.org EBISPOT OLS: 🧬 TP53 bioregistry.io/api/reference/… 🧪 Aspirin bioregistry.io/api/reference/… 🐕 Dog bioregistry.io/api/reference/… 🦠 COVID-19 bioregistry.io/api/reference/…

Our preprint on ODK, the #OntologyDevelopmentKit is up on arXiv.org arxiv.org/abs/2207.02056. Thanks to @shawnzktan Nicolas Matentzoglu and the whole team for your work on this. This is a lot of work on infrastructure that makes things work behind the scenes. So what is ODK exactly? 1/

The Human Disease Ontology (DO) Knowledgebase has been #NIHfunded under a new National Human Genome Research Institute U24 $3.7M award to provide a comprehensive #disease feature similarity network for clinical differential diagnosis and biomedical data exploration. reporter.nih.gov/search/NKzIluA… #DiseaseResearch

Great to be back at us2ts, keynote just starting, @N_Vasilevsky from Monarch Initiative talking about how #MondoOntology used for #RareDisease diagnosis

Now talking about the fantastic obook resource, and the guide for "How to be an Open Science Engineer - maximising impact for a better world" oboacademy.github.io/obook/howto/op…

Monarch Initiative HPO and #deepPhenotyping in our #exomiser tool improves #rareDisease #diagnostics! NIH ORIP National Human Genome Research Institute Rare Disease UK National Organization for Rare Disorders (NORD)

We have released version 0.3.0 of the #OntologyAccessKit #oaklib github.com/INCATools/onto…. Includes preliminary compatibility with cytoscape CX format and The NDEx Project, upgrade to the latest Bioregistry, and more support for working with the OBO Foundry #RelationOntology!

Here's our pre-print describing our GPT-3 based knowledge extraction tool SPIRES: arxiv.org/abs/2304.02711. Great work from J. Harry Caufield et al! SPIRES allows you to specify a knowledge schema (in LinkML - Linked (Open) Data Modeling Language) and then populate instances of that schema from unstructured text

We want the results to use OBO Foundry class IDs from ontologies like HPO Gene Ontology @[email protected]. However, so far GPT-3 sucks as ontology term IDs (or rather it will hallucinate plausible sequences of digits that bear no relation to the actual term)...

Are #LLMs capable of interpreting the results of high-throughput genomics experiments? Given a list of genes (e.g. all genes over expressed under a certain condition), can an LLM tell us what those genes have in common, suggesting underlying biological mechanisms? 🧵

github.com/monarch-initia… will be of interest to folks using RDF who aren’t allergic to LLMs

Many thanks to our 2023 expert review panel and chair, BF Francis Ouellette, the team at GlobalBiodata, especially @RachelDrysdale4 and David Carr, and our supportive Member funding organisations.

SILVA was selected as Global Core Biodata Resource! See our acknowledgements here: arb-silva.de/news/view/2023… 🥳🎉 Congratulations to the other resources selected! Leibniz-Institut DSMZ LPSN - lpsn.dsmz.de Ribocon Max Planck Institute for Marine Microbiology

Congratualtions. UniProt has been a contributing member of the imexconsortium for 15 years and happy to be part of this valuable effort.

The Disease Ontology and DO-KB are thrilled to join the GCBR GlobalBiodata ontology OBO Foundry resources: Plant Ontology - Planteome Project Planteome project, Gene Ontology Gene Ontology @[email protected], ChEBI ChEBI as together we're dedicated to continue propelling global biomedical research forward!