The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences
Joined April 2016
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The OBO Foundry paper is out! 🎉academic.oup.com/database/ar…
OBO Foundry retweeted
The Disease Ontology and DO-KB are thrilled to join the GCBR @globalbiodata ontology @OBOFoundry resources: Plant Ontology - Planteome Project @Planteome, Gene Ontology @news4go, ChEBI @chebit as together we're dedicated to continue propelling global biomedical research forward!
OBO Foundry retweeted
Congratualtions. UniProt has been a contributing member of the @imexconsortium for 15 years and happy to be part of this valuable effort.
We are proud to announce we have been awarded Global Core data resource status by the @GlobalBiodata Coalition. Congratulations to all our member databases: @intact_project, DIP, @MINT_database, MatrixDB, IID, @innatedb, @uniprot, and also @ISBSIB.
globalbiodata.org/global-bio…
OBO Foundry retweeted
Many thanks to our 2023 expert review panel and chair, @bffo, the team at @globalbiodata, especially @RachelDrysdale4 and @daverocarr, and our supportive Member funding organisations.
The GCBRs provide an essential data foundation for the life sciences, both directly to users and as data providers to more specialised topic-focused resources. GCBR leaders work with @globalbiodata to explore, and drive towards, greater sustainability for biodata resources.
OBO Foundry retweeted
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_DSMZ_en @LPSN10 @RiboconInfo @MarineMicrobio
We’re pleased to announce an additional 15 Global Core Biodata Resources that today join the existing 37, forming an important focus of the GBC’s work with global life science funders towards long-term sustainability.
bit.ly/3RehN6h
#globalbiodata #openscience
OBO Foundry retweeted
github.com/monarch-initiativ… will be of interest to folks using RDF who aren’t allergic to LLMs
The OntoGPT framework and SPIRES tool by @chrismungall 's team provide a principled approach to extract knowledge graph from unstructured text using GPT. Here is my impression. apex974.com/articles/ontogpt…
OBO Foundry retweeted
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? 🧵
OBO Foundry retweeted
We want the results to use @OBOFoundry class IDs from ontologies like @hp_ontology @news4go. 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)...
OBO Foundry retweeted
Here's our pre-print describing our GPT-3 based knowledge extraction tool SPIRES: arxiv.org/abs/2304.02711. Great work from @harry_caufield et al! SPIRES allows you to specify a knowledge schema (in @linkml_data) and then populate instances of that schema from unstructured text
ALT depiction of SPIRES approach: input is a schema and text, the OntoGPT engine will run SPIRES by recursively querying GPT-3 for prompt completions, the end result is grounded using public databases and ontologies
OBO Foundry retweeted
We have released version 0.3.0 of the #OntologyAccessKit #oaklib github.com/INCATools/ontolog…. Includes preliminary compatibility with cytoscape CX format and @NDExProject, upgrade to the latest @bioregistry, and more support for working with the @OBOFoundry #RelationOntology!
OBO Foundry retweeted
@MonarchInit @hp_ontology and #deepPhenotyping in our #exomiser tool improves #rareDisease #diagnostics! @NIH_ORIP @genome_gov @rarediseaseuk @RareDiseases
OBO Foundry retweeted
Great to be back at @us2ts, keynote just starting, @N_Vasilevsky from @MonarchInit talking about how #MondoOntology used for #RareDisease diagnosis
OBO Foundry retweeted
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/h…
OBO Foundry retweeted
The Human Disease Ontology (DO) Knowledgebase has been #NIHfunded under a new @genome_gov U24 $3.7M award to provide a comprehensive #disease feature similarity network for clinical differential diagnosis and biomedical data exploration.
reporter.nih.gov/search/NKzI…
#DiseaseResearch
OBO Foundry retweeted
Our preprint on ODK, the #OntologyDevelopmentKit is up on @arxiv arxiv.org/abs/2207.02056. Thanks to @shawnzktan @NicoMatentzoglu 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/
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OBO Foundry retweeted
The @Bioregistry has an API that links entities to external resolvers and providers like in @OBOFoundry @IdentifiersOrg @EBIOLS:
🧬 TP53 bioregistry.io/api/reference…
🧪 Aspirin bioregistry.io/api/reference…
🐕 Dog bioregistry.io/api/reference…
🦠 COVID-19 bioregistry.io/api/reference…
SSSOM provides a standard way for exchanging mappings between classes in ontologies
Our preprint on Simple Standard for Sharing Ontology Mappings has been submitted and is up on @arxiv arxiv.org/abs/2112.07051. SSSOM is a datamodel and exchange format for mappings between database entities, #ontology terms, etc. Thanks to @NicoMatentzoglu for spearheading this!
OBO Foundry retweeted
We have developed the ontology for Avida digital evolution platform (gitlab.com/fortunalab/ontoav…), and it has been accepted to be part of the @OBOFoundry (obofoundry.org/ontology/onto…). It's our fortunalab.org first contribution in the field of semantic databases.
OBO Foundry retweeted
We just added 63 new prefixes that cover a significant part of the missing prefixes used in @OBOFoundry ontologies.
Check out the huge PR here: github.com/biopragmatics/bio…
OBO Foundry retweeted
Thanks for your help shaping this #biodata primer, providing use cases & sharing w/ #datamanagement folks!
@isostandards
@tdwg
@OBOFoundry
@GBIF
@OBISNetwork
@usioosgov
@EDIgotdata
@DataONEorg
@planetmicrobe
@WRMarineSpecies
@ITISGov
@usdatagov
@NOAANCEI
How great would it be to use data to understand ecological patterns across larger spatial scales?
Let's talk about a new #EarthScienceData resource to help 🧵
#BioData #Ecology #Biogeochem
OBO Foundry retweeted
Meet Dr. @Ramona_Walls the Associate Director of Data Science at @CPathInstitute. Her research focuses on semantic #dataintegration and ontology design. Walls is a contributor to @genomestandards and @OBOFoundry.
Register to learn more about #metadata ➡️bit.ly/NMDCOntologiesNov21
