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 traversalsphenol-io
- Dropping support for reading OBO/OWL ontologies - drop non-modular curie-util dependencyphenol-annotations
- RemodelHpoDisease
,HpoAnnotation
,HpoAssociationData
,GeneIdentifier``s, etc.. - ``HpoDiseases
has a version - Model temporal elements - ImplementHGNCGeneIdentifierLoader
for readingGeneIdentifiers
from HGNC complete set archive. - Add newHpoOnset
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 classOntologyAlgorithmTest
.
Implements functions to get children, parents, descendents and ancestors.
v0.3¶
xref
tags are now parsed and their content is available inTerm
. 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
andontolib-io
. - Adding
getPrimaryTermId()
inOntology
.
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
intoontology.algo
package.
v0.1¶
- Everything is new.