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This has been around for a while. It’s excellent, and I’ve tried to get it adopted at several life science organizations. The problem is culture. Principal in

This has been around for a while. It’s excellent, and I’ve tried to get it adopted at several life science organizations. The problem is culture. Principal investigators are notoriously stubborn about how they do things, and that includes what they call things. Manufacturers and supply companies also don’t see much benefit to standardizing around this, and of course realize the large downside (alienating the aforementioned PIs). What would help this would be the introduction of OWL into major software suites, primarily LIMS and ELN packages, and include tools for aligning terminology and concepts with OWL.

dan_fornika 7y ago
I think the various OBOFoundry ontologies are at different stages of maturity. One of their design principles is interoperability, but I'm not sure how often one is able to reason effectively across ontologies unless great care is taken to ensure that logical axioms are sound. I'm involved in a project[0] that has an aim to provide better data integration by using OBOFoundry ontologies, but it's been a challenge in practice to merge the software with the ontologies in a coherent way. [0] https://www.irida.ca/data-integration/ https://www.irida.ca/data-integration/
- jerven 7y ago
  There are a few which are really great. Basically my shortcut is Chris Mungall involved then it is logically and biologically ;) sound. While we at SIB are more towards the RDF/SPARQL part of the spectrum (https://edu.sib.swiss/course/view.php?id=440 https://edu.sib.swiss/course/view.php?id=440). We do use OWL and obofoundry projects like Uberon and GO. For UniProt I took a lot of pain to make sure it is really compatible. We did the same for Rhea and ChEBI. This has paid of handsomely in new query capabilities.
sndean 7y ago
> Principal investigators are notoriously stubborn about how they do things I've come across things a simple as "I wrote a Perl script that does that, but it uses KEGG not GO terms" for their reasoning. That, or – if they're okay with using gene ontology – we have to also use the other system in parallel. And then the results becomes a discussion of how the two different annotation systems display the results. Life science could use a benevolent dictator.
- bordercases 7y ago
  > Life science could use a benevolent dictator. If there's going to be one it has to be the NIH. Since they've been investing a lot in this field.

dan_fornika 7y ago

I think the various OBOFoundry ontologies are at different stages of maturity. One of their design principles is interoperability, but I'm not sure how often one is able to reason effectively across ontologies unless great care is taken to ensure that logical axioms are sound. I'm involved in a project[0] that has an aim to provide better data integration by using OBOFoundry ontologies, but it's been a challenge in practice to merge the software with the ontologies in a coherent way. [0] https://www.irida.ca/data-integration/ https://www.irida.ca/data-integration/

jerven 7y ago
There are a few which are really great. Basically my shortcut is Chris Mungall involved then it is logically and biologically ;) sound. While we at SIB are more towards the RDF/SPARQL part of the spectrum (https://edu.sib.swiss/course/view.php?id=440 https://edu.sib.swiss/course/view.php?id=440). We do use OWL and obofoundry projects like Uberon and GO. For UniProt I took a lot of pain to make sure it is really compatible. We did the same for Rhea and ChEBI. This has paid of handsomely in new query capabilities.

sndean 7y ago

> Principal investigators are notoriously stubborn about how they do things I've come across things a simple as "I wrote a Perl script that does that, but it uses KEGG not GO terms" for their reasoning. That, or – if they're okay with using gene ontology – we have to also use the other system in parallel. And then the results becomes a discussion of how the two different annotation systems display the results. Life science could use a benevolent dictator.

bordercases 7y ago
> Life science could use a benevolent dictator. If there's going to be one it has to be the NIH. Since they've been investing a lot in this field.