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Aligning with External Ontologies: Insights from the Gene Ontology Project

The Gene Ontology (GO) Project emphasizes the importance of utilizing terms from external ontologies to define GO terms. This approach aids in enhancing the logical structure of metabolic processes, such as glycolysis, by integrating terms from ChEBI and other relevant ontologies. Key challenges include effective communication and reconciling differences between ontologies. The project reveals the need for logical definitions, especially for plant developmental stages and anatomical structures, to improve consistency and responsiveness in GO classifications.

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Aligning with External Ontologies: Insights from the Gene Ontology Project

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  1. The Gene Ontology Project Aligning with and leveraging external ontologies Jane Lomax

  2. GO terms can be defined using terms from other ontologies

  3. glycol metabolic process

  4. 'metabolic process' and ('has participant' some glycol)

  5. 'metabolic process' and ('has participant' some glycol) ChEBI

  6. 'metabolic process' and ('has participant' some glycol) GO

  7. chemicalscell typesanatomical structures

  8. Increase in the number of classes with logical definitions:

  9. TermGenie

  10. http://go.termgenie.org/

  11. reasoning

  12. lessons from working with other ontologies

  13. 1. communication

  14. 2. differences can be very difficult to reconcile

  15. 3. both ontologies need to be responsive

  16. plants in GO

  17. anatomy, cell types -> GO logical definitions?

  18. plant developmental stages -> happens_during?

  19. growth and development in GO

  20. currently no logical defs in GO

  21. high-level terms species generic

  22. logical definitions with anatomy ontologies

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