obographviz 0.2.2 released – now with visualization of equivalence cliques

Update: the stylesheet proposal has its own site: https://berkeleybop.github.io/kgviz-model/
Version 0.2.2 of out obographviz javascript library is up on npm:


obographviz converts ontologies (in  OBO Graph JSON) to dot/graphviz with powerful JSON stylesheet configuration. The JSON style sheets allow for configurable color and sizing of nodes and edges. While graphviz can look a bit static and clunky compared to these newfangled javascript UI libraries, I still find it the most useful way to visualize complex dense ontology graphs.
One of the most challenging things to visualize is the parallel structure of multiple ontologies covering a similar area (e.g. multiple anatomy ontologies, or phenotype ontologies, each covering a different species).
This new release allows for the nesting of equivalence cliques from either xrefs or equivalence axioms. This can be used to visualize the output of algorithms such as our kBOOM (Bayesian OWL Ontology Merging) tool. Starting with a defined set of predicates/properties (for example, the obo “xref” property, or an owl equivalentClasses declaration between two classes), it will transitively expand these until a maximal clique is found for each node. All such mutually connected nodes with then be visualized inside one of these cliques.
An example is shown below (Uberon (yellow) aligned with ZFA (black) and two Allen Brain Atlas ontologies (grey and pink); each ontology has its own color; any set of species-equivalent nodes are clustered together with a box drawn around them. isa=black, part_of=blue). Classes that are unique to a single ontology are shown without a bounding box.

About Chris Mungall
Computer Research Scientist at Berkeley Lab. Interests: AI / Ontologies / Bioinformatics. Projects: GO, Monarch, Alliance, OBOFoundry, NMDC

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