chrismungall

5 ms·

1. 1.▲
   by chrismungall 7y ago

   I am part of OBO (and GO, which has also been mentioned here a few times). It's nice to see the discussion here, lots of good comments, including the critical ones! I'm going to address a few themes that have emerged, hopefully th
2. 2.▲
   by chrismungall 7y ago

   For a general purpose OWL python library there is OWLReady2 and funowl: https://github.com/hsolbrig/funowl For a Python library that intends to provide a level of abstraction more appropriate to bioinformatics use case
3. 3.▲
   by chrismungall 7y ago

   Many large OBO ontologies use EL++ reasoning (e.g. Elk), performing DL reasoning on smaller chunks (e.g. relations). Having said that newer reasoners like Konklude apparently do well with DL reasoning over combinations of large ontologies.
4. 4.▲
   by chrismungall 7y ago

   Can you expand on that? One of the main use cases for GO is statistical enrichment analyses. Of course, there are definitely problems here, from choice of appropriate way to correct for multiple hypotheses to appropriateness of frequentist
5. 5.▲
   by chrismungall 7y ago

   > I am really split by wanting to use full graph databases vs. RDF/RDFS/OWL I think having an alternative OWL->graph mapping that utilized the features of property graphs would help a lot with using non-RDF graph databases.
6. 6.▲
   by chrismungall 7y ago

   I don't have any recommendations for Julia, but for Rust have you tried fastobo? - https://github.com/fastobo/fastobo - https://github.com/fastobo/fastobo-owl It has been tested heavily on a