Releases: INCATools/ontology-access-kit
v0.6.16
v0.6.15
v0.6.14
v0.6.13
What's Changed
- Supporting skos mappings for simpleobo and pronto. by @cmungall in #766
- structured_format.pattern-style permissible value creation eg for MIxS by @turbomam in #785
- Update sql_implementation.py to include sqlachemy output in debug logging. by @DnlRKorn in #782
New Contributors
Full Changelog: v0.6.12...v0.6.13
v0.6.12
v0.6.11
v0.6.10
v0.6.9
v0.6.8
Highlights
This PR adds a new interface, UsageInterface, and accompanying command usages
.
Fixes #777
One of the primary use cases here is for an ontology developer to know whether it is safe and who to alert when considering obsoleting a term.
Due to OAK's architecture it is easy to use this command to multiplex a query across multiple endpoints: QuickGO, AmiGO, Ubergraph, multiple sqlite databases, Ontobee....
Usage: runoak usages [OPTIONS] [TERMS]...
List usages of a term or set of terms.
Usages of neuron in GO:
runoak -i sqlite:obo:go usages CL:0000540
Association/annotations sources can also be used:
runoak -i quickgo: usages GO:0031969
Note this query may be slow - you can restrict to a species:
runoak -i quickgo:NCBITaxon:9606 usages GO:0031969
(this should return no results, as there should be no human proteins
annotated to chloroplast membrane)
Using amigo:
runoak -i amigo: usages GO:0031969
Using ubergraph:
runoak -i ubergraph: usages CL:0000540
This will include usages over multiple ontologies
You can multiple queries over multiple sources (an
AggregatorImplementation):
runoak -i sqlite:obo:go -a ubergraph: -a amigo: -a quickgo: usages
GO:0031969
Options:
-o, --output FILENAME Output file, e.g. obo file
--autolabel / --no-autolabel If set, results will automatically have labels
assigned [default: autolabel]
-O, --output-type TEXT Desired output type
-o, --output FILENAME Output file, e.g. obo file
-P, --used-by-prefix TEXT
--help Show this message and exit.
To support this, this PR also includes a QuickGO adapter
Current behavior may be incomplete. For example, if a term is used in axiom annotation this may not be detected. This functionality is currently for exploration and to drive requirements for a complete tool
What's Changed
Full Changelog: v0.6.7...v0.6.8
v0.6.7
What's Changed
- removing unneccessary quotes in expression language guide by @cmungall in #762
- Adding has-part glyph to config. by @cmungall in #765
- More efficient association-based IC calculation. by @cmungall in #764
- Pass custom IC map to Semsimian through CLI by @caufieldjh in #759
- Adding MRCA example to expression docs by @cmungall in #768
- Adding link to ontogenesis chapter on annotations. by @cmungall in #771
- Python level access to query expression language by @cmungall in #769
Full Changelog: v0.6.6...v0.6.7