Changelog¶

latest¶

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.