v0.5.13

Highlights

Fill table now allows for obsoletion rewiring

PR: #625

This fixes #625

given a table of single-cell data sc.tsv:

dataset	term
sc-Martinotti	CL:4023067
sc-Martinotti	CL:4023027

Running

runoak -i sqlite:obo:cl fill-table --relation "{primary_key: term, dependent_column: replacement_term, relation: IAO:0100001}" --allow-missing tests/input/cl-obs.tsv sc.tsv

Will produce:

dataset	term	replacement_term
sc-Martinotti	CL:4023067	PCL:1000004
sc-Martinotti	CL:4023027

Inclusion of ABox some-values-from assertions

PR: #624

Previously axioms like the anonymous Type assertion here we not included in the graph projection:

Now they are:

Logical Definition Analysis

• #610

What's Changed

• Make ensure_strict_prefixes default to False in lexmatch by @hrshdhgd in #601
• Improve descriptor processing for Gilda implementation by @cthoyt in #603
• Enable NER with Gilda by @cthoyt in #607
• Tools to analyze logical definitions by @cmungall in #610
• Fix broken link on README.md by @lubianat in #599
• Projecting anonymous type expressions to graph. Fixes #623 by @cmungall in #624
• Adding arbitrary properties to fill-table. Fixes #625 by @cmungall in #626

New Contributors

• @lubianat made their first contribution in #599

Full Changelog: v0.5.12...v0.5.13