monarch-initiative/owlsim-v3

[#58] get data from biolink

[#78] allow labels to be loaded as tsvs

[#72] removing some leftovers

Merge branch 'master' into 72-ontomatch-single-entity

[#72] provide a resolveIri method in the KB

Issue #57 changed uses of 'data' to 'individualAssociations' in conte… …

…xt of the Ontology/OntologySourceData/OwlKnowledgebase in order to be more specific.

[#72] added service for single entity

Issue #57 - Fixed server startup issue. Cleaned-up KnowledgeBaseModule.

Issue #57 - Added new OwlKnowledgeBase class as a main entry point fo… …

…r creating a BMKnowledgeBaseOWLAPIImpl - @deprecated OWLLoader.

Added new supporting classes Ontology and OntologyDataSource, OntologyLoadException to help the OwlKnowledgeBase do its thing.
OWLLoader is only partially removed from the tests at present.
Removed overly verbose logging from FilterEngine.
Added commented-out clean-up of KnowledgeBaseModule - server still fails to start with ot without this.

[#62] we still need the the inject indicator for guice. We can the ma… …

…tcher package through java reflection and let the injector construct the objects.

[#62] moved guice modules away from core

[#44] changed formatting

[#44] almost working generated json. Blocked by a swagger-core bug

[#44] removing unused parameter

[#44] smartapi reported errors

[#46] modified swagger title

[#46] fixed typo in README

[#46] updated swagger-ui and swagger dependency

Merge pull request #41 from monarch-initiative/ontology-matching …

matching between ontology classes (not instances)

Adding enrichment service

matching between ontology classes (not instances) …

Fixes #40

[#24] need some cleaning

[#24] first experiment

fixed unit tests

[#33] configure Jackson to ignore empty beans

switched scicrunch to owlsim

Added parameter to allow comparison of two profiles, fixes #32

Adding enrichment to core and services

Added TypeFilters …

improved tests, and included compressed data for perf tests
switched to java8
switched to owlapi-v4
bumped up version of various frameworks
added additional params to services

fixing tests and adding cosine matcher

Refactors MatcherMapModule for #16

Renames MatcherModule

Adding exceptions

Adds timing and cache to match resource

Uses new exceptions