v0.6.16

What's Changed

• Fix test suite by @gouttegd in #796
• Bug in calculating all_by_all_pairwise_similarity by @hrshdhgd in #800

New Contributors

• @gouttegd made their first contribution in #796

Full Changelog: v0.6.15...v0.6.16

v0.6.15

What's Changed

• Implementing NodeDeletion which was earlier a comment. by @hrshdhgd in #791

Full Changelog: v0.6.14...v0.6.15

v0.6.14

What's Changed

• set_label will INSERT if label not already presented. Fixes #788 by @cmungall in #789

Full Changelog: v0.6.13...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

• @turbomam made their first contribution in #785
• @DnlRKorn made their first contribution in #782

Full Changelog: v0.6.12...v0.6.13

v0.6.12

What's Changed

• information content enhancements by @cmungall in #781
• Added change handler for kgcl.RemoveNodeFromSubset by @hrshdhgd in #783

Full Changelog: v0.6.11...v0.6.12

v0.6.11

What's Changed

• Solves ClassCreation duplication & formats Mappings md table properly by @hrshdhgd in #780

Full Changelog: v0.6.10...v0.6.11

v0.6.10

What's Changed

• rename edge to mapping by @twhetzel in #775

New Contributors

• @twhetzel made their first contribution in #775

Full Changelog: v0.6.9...v0.6.10

v0.6.9

What's Changed

• Making prefix mapping less strict, fixes #702 by @cmungall @matentzn @gouttegd in #761

Full Changelog: v0.6.8...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

• New functionality: term usages by @cmungall in #776

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