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Searches on cl.obo
, uberon.obo
fail
#49
Comments
Yes, see althonos/pronto#159 and althonos/pronto#156 V soon it will be possible to work with local rdf/owl files in OAK... |
There are now a few more options that don't depend on pronto: https://incatools.github.io/ontology-access-kit/selectors.html ubergraph: runoak -i ubergraph:cl search 'epithelial cell of lung' warning: this is a relevancy ranked list that uses blazegraph so you will get a lot of partial matches after the first exact match if you give it an OWL file it will use rdflib: wget http://purl.obolibrary.org/obo/cl.owl -O /tmp/cl.owl
runoak -i /tmp/cl.owl search 'epithelial cell of lung' however, rdflib is quite slow to do the initial parse you can use a ready-made sqlite db:
very soon it will be possible to do this: wget http://purl.obolibrary.org/obo/cl.owl -O /tmp/cl.owl
runoak -i sqlite:/tmp/cl.owl search 'epithelial cell of lung' and rdftab/relation graph will be used behind the scenes to build the db Each implementation will implement search a little differently but the goal is to come up with a unified search datamodel so that this can be better specified by the user and explained by the provider, comments welcome: https://incatools.github.io/ontology-access-kit/datamodels/search/index.html |
Great - local search on an OWL works, though it is slow as promised.
And the same with the identical term in Uberon:
|
I'm following the tutorial, and diverged a bit to try searches in other OBO ontologies.
The following search fails:
Looks like a
pronto
parsing issue?Searching
cl.owl
instead produces numerous errors but eventually yields the desired result (CL:0000082 ! epithelial cell of lung
)I get a similar result when running
for Uberon, though in that case searching
uberon.owl
instead raises anAttributeError
:The text was updated successfully, but these errors were encountered: