owlapi_wrapper 1.5.0

What's Changed

• Ci/codecov integration by @alexskr in #23
• Fix: Mixed ontology level annotations by @syphax-bouazzouni in #20
• Ontoportal lirmm/bugfix/ontology level annotations by @mdorf and @syphax-bouazzouni in #28
• add GitHub release workflow and update pom.xml for external versioning by @alexskr in #27

New Contributors

• @alexskr made their first contribution in #23

Full Changelog: v1.4.2...v1.5.0

v1.4.2 for Nucleic Acids Research

This tag corresponds to the code used in our Nucleic Acids Research publication:

ID: NAR-00680-Web-S-2025.R1
BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies
Vendetti, Jennifer; Harris, Nomi; Dorf, Michael; Skrenchuk, Alex; Caufield, J. Harry; Gonçalves, Rafael S; Graybeal, John B; Hegde, Harshad; Redmond, Timothy; Mungall, Christopher; Musen, Mark A.

Archived via Zenodo for reproducibility and citation. DOI: https://doi.org/10.5281/zenodo.15284525.

owlapi_wrapper 1.4.2

What's Changed

• Add an IRI mapper for the SKOS Core Vocabulary to resolve missing import errors (#22)
• Bump commons-csv from 1.9.0 to 1.10.0
• Bump logback-classic from 1.2.11 to 1.4.11
• Clean up outdated information in the Maven POM file

Full Changelog: v1.4.1...v1.4.2

owlapi_wrapper 1.4.1

What's Changed

• Preserve ontology IDs in processed ontologies. Previously, ontology IDs were dropped and all processed ontologies were anonymous. Thanks go to @syphax-bouazzouni for the contribution (#17).
• Set the logging level to info for the metrics package (#19)
• Bumped logback-classic from 1.2.10 to 1.2.11

New Contributors

• @syphax-bouazzouni made their first contribution in #17

Full Changelog: v1.4.0...v1.4.1

owlapi_wrapper 1.4.0

• Added new code to calculate the maximum depth of an ontology
• Refactored the package names to be cleaner

Full Changelog: v1.3.8...v1.4.0

owlapi_wrapper 1.3.8

• Explicity banned the TriX parser to ease debugging of some RDF ontologies (owlcs/owlapi#1045)
• Moved the import handling strategy to a properties file
• Refactored some unit test code

Full Changelog: v1.3.7...v1.3.8

owlapi_wrapper 1.3.7

• Upgraded to version 4.5.18 of the OWL API.
• Added jaxb-api dependency to prevent NoClassDefFoundError exceptions during parsing of some ontologies (#16).
• Upgraded various plugins to latest versions (maven-compiler-plugin, maven-surefire-plugin, maven-shade-plugin).
• Upgraded various dependencies to latest versions (junit, commons-csv, commons-cli, logback-classic).
• Fixed commons-csv deprecation warnings.

owlapi_wrapper 1.3.6

• Upgraded to version 4.5.17 of the OWL API.
• Expanded the list of allowed suffixes for ontology files to include .n3, .nt, .nq, .skos, .rdf, and .rdfs. Thanks go to @jlamarque34 for the contribution (#13).
• Upgraded the commons-csv and junit dependencies to latest versions.

owlapi_wrapper 1.3.5

• Upgraded to OpenJDK 11.0.4.
• Upgraded to version 4.5.13 of the OWL API.
• Upgraded maven-compiler-plugin and commons-csv dependencies to latest versions.
• Added "TTL" as a supported filename extension for ontology files. Allows BioPortal to parse ontologies submitted by end users with the TTL extension, e.g., the SWEET ontology.

owlapi_wrapper 1.3.4

• Replaced the Maven Assembly Plugin with the Maven Shade Plugin for generating the uber-jar. Fixes an issue with missing content in the META-INF/services directory. See owlcs/owlapi#842 for details.
• Removed an IRI mapping to an NCBO-maintained version of the BFO ontology. See ncbo/bfo#1 for details.
• Upgraded commons-csv dependency to latest version.
• Minor code refactors for readability and easier debugging.