A3 - Ontology Alignment Method Selection and Testing

biobricks-ai / biobricks-okg

An open knowledge graph for BioBricks.ai

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A3 - Ontology Alignment Method Selection and Testing #3

Closed tomlue closed 7 months ago

tomlue commented 11 months ago

From the grant

Ontology alignment methods will be reviewed, proposed, and preliminary testing completed to automate the recognition of equivalent classes between knowledge graphs and synchronize them to the core graph.

It is a good idea to start exploring these before implementing too many of the local knowledge graphs in #1 as harmonization methods may inform ontology creation #2 and local knowledge graph constraints #1

[ ] update Jan-2024 slideshow https://docs.google.com/presentation/d/1eqqYe_bLByoUER-4d1xwMprUH6zA88OCdL4g-7cDpNs/edit#slide=id.g2a965312a63_0_10

zmughal commented 11 months ago

Adding a collection of notes about ontologies that already exist:

Environmental conditions, treatments and exposures ontology (ECTO)
- GitHub - EnvironmentOntology/environmental-exposure-ontology: Modular environmental exposures ontology
- Part of OBO.
- Composed of other ontologies including: ExO GitHub - CTDbase/exposure-ontology: First pass at repo for Exo
OpenTox:
- Described in paper OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia (2012)
- Older resources:
  - Toxicological Ontology — OpenTox
  - Ontology — OpenTox
- Is now associated with ToxBank | Data warehouse for toxicity data management:
  - GitHub - ToxBank/toxbank-ontology
ComptoxAI
- Described in paper Automating Predictive Toxicology Using ComptoxAI (2022)
- ComptoxAI OWL2 Ontology