v0.6.4

Highlights

Most-specific relationships

This release adds the ability to get the most-specific entailed relationships for any class (either via Python or command line)

See

• #739

For background.

The motivation here is that many OBO ontologies contain highly useful relationships beyond is-a. For example, anatomy ontologies like Uberon have relationships for every structure:

• what is it part of?
• what are its parts?
• where does it come from (developmental precursor)
• what's it's function?
• at what stage does it come into existence (and when does it end)?

In addition, some hierarchies have more specific relationships:

• blood and lymph vessels have relationships describing sources and targets of fluid
• neurons and brain regions have connectomics

However, in order to get at this information it's necessary to use reasoning/entailment or Graph Traversal, because relationships may be Asserted at a broader level.

E.g.the trigeminal ganglion is part of the nervous system, the head, but this is not asserted directly, it's on a superclass:

OAK has the ability to query entailed edges (using Relation Graph), but this usually returns too much information.

With this release of OAK, it's possible to ask for the most specific entailed edges. This can be thought of roughly as "walking up" the is-a graph to get the most specific asserted relationships.

E.g

uberon relationships uberon relationships --non-redundant-entailed "trigeminal ganglion" -p i,p

gives:

subject	subject_label	predicate	predicate_label	object	object_label
UBERON:0001675	trigeminal ganglion	BFO:0000050	part of	RO:0002577	system
UBERON:0001675	trigeminal ganglion	BFO:0000050	part of	UBERON:0000033	head
UBERON:0001675	trigeminal ganglion	BFO:0000050	part of	UBERON:0001016	nervous system
UBERON:0001675	trigeminal ganglion	rdfs:subClassOf	None	UBERON:0001714	cranial ganglion
UBERON:0001675	trigeminal ganglion	rdfs:subClassOf	None	UBERON:0001800	sensory ganglion
UBERON:0001675	trigeminal ganglion	rdfs:subClassOf	None	UBERON:0010313	neural crest-derived structure

For more examples, see the Relationships Command example notebook

What's Changed

• Adding option for non-redundant entialed relationships. by @cmungall in #740

Full Changelog: v0.6.3...v0.6.4