v2.1.1

What's Changed

• Extend Aspect enum with "Past medical history" by @iimpulse in #464

Full Changelog: v2.1.0...v2.1.1

v2.1.0

What's Changed

• Implement HpoCategoryLookup by @iimpulse in #462

Full Changelog: v2.0.5...v2.1.0

v2.0.5

What's Changed

• Augment OntologyGraph API by @ielis in #458
• Audit pre-computation of IC MICA values by @ielis in #457
• Add support for serialization of GeneIdentifiers by @ielis in #456

Full Changelog: v2.0.4...v2.0.5

v2.0.4

v2.0.4

Minor release, no breaking changes.

What's Changed

• Update docs on TermAnnotation by @ielis in #451
• Implement mono graph and add I/O microbenchmark by @ielis in #448
• Fix broken implementation of MinimalOntology.subOntology by @ielis in #453
• Update dependencies by @ielis in #454

Full Changelog: v2.0.3...v2.0.4

v2.0.3

Minor release, no breaking changes.

• MinimalOntology is enough for the phenol-annotations functionality to work by @ielis in #440
• Add ontology checks by @ielis in #441
  • we have Terms for all subjects and objects of the ontology graph edges
  • the ontology graph is simple - no self-loops and duplicated edges are present.
    Note: >1 edges between a pair of nodes is allowed as long as the edges are of a different relation type.
  • the ontology graph is connected - the graph consists of one connected component.
• Allow to opt out of compatibility checks by setting OntologyLoaderOptions.forceBuild to true by @ielis in #442
• Improve Javadocs

Full Changelog: v2.0.2...v2.0.3

v2.0.2

No breaking changes, deprecation of MinimalOntology and Ontology methods and introduction of the OntologyGraph.

What's Changed

• Implement ontology graph backed by a CSR connectivity matrix. by @ielis in #436
• Setup deployment of documentation and javadocs to github.io by @ielis in #437

Full Changelog: v2.0.1...v2.0.2

v2.0.1

A few minor enhancements and no breaking changes:

• Use Jackson annotations to configure serialization of TermId and Identified
• update dependencies

v2.0.0

• Upgrade to Java 11+, add module-info files
• Support for GO GAF 2.2 files
• Speed up build by adding a new build profile
• phenol-core
  • MinimalOntology has a version
  • do not use non-propagating relationships during ontology traversals
• phenol-io
  • Dropping support for reading OBO/OWL ontologies
  • drop non-modular curie-util dependency
• phenol-annotations
  • Remodel HpoDisease, HpoAnnotation, HpoAssociationData, GeneIdentifiers, etc..
  • HpoDiseases has a version
  • Model temporal elements
  • Implement HGNCGeneIdentifierLoader for reading GeneIdentifiers from HGNC complete set archive.
  • Add new HpoOnset terms.
  • Consolidate hardcoded HPO constants (TermIds) into org.monarchinitiative.phenol.annotations.constants.hpo package
  • Standardize HPO annotations header, ensure the parsers can read the older releases.
  • Deprecate the code for parsing small files and move to hpoannotQC

v2.0.0-RC5

What's Changed

• Precalculate disease onset interval. by @ielis in #410
• Update deployment info by @ielis in #412
• Improve comparison and overlap of the temporal API by @ielis in #411
• Extended interface of AssociationContainer by new method by @pnrobinson in #413
• Add default HpoDiseaseAnnotation implementation with logic for querying number of patients presenting with the feature at a given time. by @ielis in #414
• Split HpoDisease loading by @ielis in #415
• Clarify alt ID meaning by @ielis in #416
• Offer versions in data containers/resource objects by @ielis in #418
• Make QC better, add tests by @iimpulse in #419

Full Changelog: v2.0.0-RC4...v2.0.0-RC5

v2.0.0-RC4

What's Changed

• further work on temporal API components
• drop non-modular curie-util dependency
• consolidate hardcoded HPO constants (TermIds) into org.monarchinitiative.phenol.annotations.constants.hpo package