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CHANGELOG.rst

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Changelog

2.1.1

  • add Past medical history to Aspect enum

2.1.0

  • add HpoCategoryLookup to bin HPO terms into broad categories

2.0.5

  • extend OntologyGraph with convenience methods
  • audit calculation of Resnik similarity scores
  • use Jackson annotations to describe serialization of GeneIdentifier

2.0.4

Minor release, no breaking changes.

  • Fix broken implementation of MinimalOntology.subOntology method.
  • Simplify implementation of CSR adjacency matrix that backs OntologyGraph by default.
  • Improve OntologyGraph test coverage.
  • Add microbenchmark to benchmark the ontology loading.
  • Update dependencies, remove Guava usage.

2.0.3

Minor release, no breaking changes.

  • MinimalOntology is enough for the phenol-annotations functionality to work.

  • Add checks to see if the ontology meets the following: - we have `Term`s 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.

  • Improve Javadocs

2.0.2

Minor release, no breaking changes.

  • deprecate several MinimalOntology and Ontology methods (to be removed in v3.0.0), and introduction of the OntologyGraph API.
  • setup Javadoc & documentation deployment via CI

v2.0.1

Minor 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, GeneIdentifier``s, 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 (TermId``s) 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

v1.6.3

  • added class for efficient precalculation of Resnik scores for HPO
  • various bug fixes

v1.6.1

  • Fixed issue with parsing Orphanet en_product4.xml

v1.6.0

  • Simplified interface to GO overrepresentation analysis classes.
  • Parent-Child Gene Ontology overrepresentation analysis with unit tests
  • MGSA bugfix

v1.5.0

  • improved functions for display of upper level HPO categories

v1.4.3

  • fixing bug in parsing of MGI Genetic Marker file
  • fixing bug in parsing of orphanet genes file, en_product6.xml

v1.4.2

  • Prototype ingest of JSON ontology files
  • flexible handling of relation types
  • bug fix of previously incorrect handling of tRNA genes

v1.4.1

  • Added workaround for duplicated lines in Homo_sapiens_gene_info file
  • Added phenotype to gene extraction

v1.4.0

  • Added Orphanet inheritance parser
  • Aded several demonstration programs
  • refactored files for constructing the phenotype.hpoa file

v1.3.3

  • Various bug fixes
  • Orphanet inheritance XML file ingest
  • Adding additional demo app to show how to access Term information (hpdemo).

v1.3.0

  • refactored TermAnnotation interface to use TermId instead of String to identify objects being annotation
  • refactored GoGaf21Annotation class to use TermId internally instead of Strings for db and dbObjectId
  • refactored to use junit 5 (allowing legacy use of junit 4, will migrate completely in coming releases)

v1.2.5-SNAPSHOT

  • moving to SNAPSHOT version names to conform with maven standards
  • fixed bug in initialized association lists for Gene Ontology analysis.

v1.1.4

  • Adding parsing of onset, modifier, PMID/source to HpoAnnotation class
  • Adding all relation types relevant to MONDO

v1.1.3

  • Adding parsing of relations other than IS_A for Gene Ontology
  • Fixing calculation of frequency (double) from frequency category
  • allowing any valid curie as cross-ref

v1.1.2

  • Adding MP annotation parser for MGI_GenePheno.rst and MGI_Pheno_Sex.rst

v1.1.1

  • HPO Annotation parser now indexes diseases as a TermId representing the disease CURIE, e.g., MONDO:0000042.
  • HPO Annotation parser now uses new 'big-file' format (with updated treatment of biocuration field)

v1.0.3

  • refactored MP and GO parsing to use new OWLAPI-based parser
  • adding support for adding artificial root to ontologies such as GO with multiple root terms.
  • upgraded to obographs v0.1.1

v1.0.2

  • refactored TermId to remove superfluous interface and renamed ImmutableTermId to TermId
  • refactored TermSynonym to remove superfluous interface
  • adding support for alt term ids to Owl2OboTermFactory (class renamed from GenericOwlFactory)
  • adding support for database_cross_reference (usually PMID, ISBM, HPO, or MGI--added to term definitions)

v1.0.0

  • completed refactoring to use single Term/Relationship. The API is not backwards compatible with versions prior to v0.1.9.

v0.1.9

  • refactored to use just a single Term and Relationship instead of having separate types for each ontology. Simplified

classes that were templated to allow e.g., MpoTerm, MpoRelationship by hardcoding Term,Relationship and removing template.

v0.1.8

  • refactored HpoAnnotation from HpoTermId

v0.1.7

  • refactored phenol to use JGraphT library
  • Adding OWLAPI based parser
  • Refactoring HPO Disease annotation parser

v0.1.6

  • refactored HPO disease annotation parser (changed API)

v0.1.5

  • changed package and project name to phenol - Phenotype Ontology Library

v0.1.4

  • fix to GOA parser
  • added HPODiseaseWithMetaData parser
  • added functions to calculate Term relationships (sibling, subclass, related, not-related)

v0.1.2

  • refactored HpoFreqeuncy class to return frequencies (i.e., a number in [0,1]) rather than percentage
  • Added HpoOnset classes
  • Added HpoDiseaseWithMetadata class to encompass frequency and onset data

v0.4/v0.1.1

  • forked from ontolib
  • fixed mp.obo parse error
  • fixed subontology creation error (TermMap, TermRelation)
  • Adding Adding class OntologyAlgorithm with test class OntologyAlgorithmTest.

Implements functions to get children, parents, descendents and ancestors.

v0.3

  • xref tags are now parsed and their content is available in Term. Added appropriate classes for representation.
  • Added Ontology.getParent().
  • Removed JaccardIcWeightedSimilarity, JiangSimilarity, LinSimilarity, supporting code and tests.
  • Refactoring the code for object score I/O into ontolib-io package.
  • Adding support for score distribution reading and writing to H2 database files.
  • Ontology.getAncestorTermIds() now also resolves alternative term IDs.
  • Fixing dependency on slf4j components in ontolib-core and ontolib-io.
  • Adding getPrimaryTermId() in Ontology.

v0.2

  • Making date parser for HPO annotation files more robust. It works now for positive and negative associations.
  • Small bug fix in HPO OBO parser.
  • Adding ontolib-cli package that allows score distribution precomputation from the command line.
  • Removed some dead code.
  • Added various tests, minor internal refactoring.
  • Moved OntologyTerms into ontology.algo package.

v0.1

  • Everything is new.