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@jamesaoverton jamesaoverton released this Mar 15, 2019 · 1 commit to master since this release

This release adds the rename command (see #419), allowing you to replace lists of old IRIs with new IRIs. It also adds SPARQL Update support (#352), for adding and removing triples from ontologies using SPARQL. This feature builds on Apache Jena, but note the warning in the 'Update' section of the documentation at http://robot.obolibrary.org/query.

Other improvements include:

  • new --annotate-with-source option for extract (#392)
  • new --intermediates option for extract (#441)
  • new --individuals option for extract (#385)
  • improvements to the built-in reports (#438)
  • new selectors for remove and filter: domain and range (#427), ontology (#452)
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@jamesaoverton jamesaoverton released this Jan 18, 2019 · 86 commits to master since this release

This release of ROBOT introduces the explain command, contributed by Jim Balhoff, which finds explanations for axioms inferred by a reasoner. See http://robot.obolibrary.org/explain

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@jamesaoverton jamesaoverton released this Dec 6, 2018 · 127 commits to master since this release

This release of ROBOT introduces the remove and filter commands, which allow you to remove selected axioms from an ontology. See http://robot.obolibrary.org/remove.

Breaking Change: We have upgraded from Apache Jena 2.13.0 to 3.8.0 (#314), which involves the renaming of several packages and changes to the return types of QueryOperation. One other change we've noted is that the new Jena adds fewer xsd:string datatypes than the previous version.

Other changes:

  • --use-graphs true option for query allows queries over imports as named graphs, #158
  • upgrade to OWLAPI 4.5.6 sometimes changes the ordering of elements in RDFXML format, causing spurious differences in line order when comparing output from previous versions of ROBOT. But note that Protege5.5 uses the same version of the OWLAPI so orderings should be consistent between the two.
  • add --labels option to diff command, #363
  • add support for gzipped files, #371
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Pre-release

@jamesaoverton jamesaoverton released this Aug 4, 2018 · 250 commits to master since this release

This is a development release of ROBOT that adds the remove command and updates the filter command.

remove and filter allow you to remove selected axioms from an ontology. See http://robot.obolibrary.org/remove. These commands may change in future development releases!

Breaking Change: We have upgraded from Apache Jena 2.13.0 to 3.8.0 (#314), which involves the renaming of several packages and changes to the return types of QueryOperation. One other change we've noted is that the new Jena adds fewer xsd:string datatypes than the previous version.

Other changes:

  • --use-graphs true option for query allows queries over imports as named graphs, #158
Assets 3

@jamesaoverton jamesaoverton released this Aug 4, 2018 · 322 commits to master since this release

This release of ROBOT includes the new report command and a number of other improvements.

report runs a series of quality control checks (SPARQL queries) over the input ontology and generates a TSV or YAML report file based on the results. We will add and revise these checks with input from the OBO community. See http://robot.obolibrary.org/report.

Other changes:

  • --collapse-import-closure option for merge: When true (the default) all imports will be merged and all owl:import statements will be removed. Possible breaking change: In previous versions of ROBOT, owl:import statements were not removed. #275
  • improved error messages, linking to ROBOT website #246
  • global --catalog FILE option #274
  • --check option for convert allows conversion of more OBO-format files
  • --include-annotations option for merge allows better control of ontology annotations #277
  • --copy-ontology-annotations option for extract, #319
  • --dump-unsatisfiable option for reason, #174
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@jamesaoverton jamesaoverton released this Feb 8, 2018 · 491 commits to master since this release

First official release of ROBOT!

We are pleased to announce the release of version 1.0.0 of ROBOT. ROBOT is a command-line tool for working with OWL ontologies, especially ontologies in the Open Biological and Biomedical Ontologies (OBO) community. While graphical editors such as Protégé are great for editing ontologies interactively, ROBOT is for automating ontology development tasks such as importing terms, building terms from templates, converting between file formats, merging OWL files, reasoning, and testing ontologies. ROBOT helps to bridge the gap between ontology development and software engineering.

ROBOT is currently used in the development and release of GO, ENVO, ECO, RO, OBI, MRO, and a number of other ontologies in the OBO Library (http://obofoundry.org).

We have a new website http://robot.obolibrary.org, and are actively improving the documentation based on user feedback.

ROBOT is used in the ontology starter kit (https://github.com/INCATools/ontology-starter-kit/) which will create an ontology repository with pieces in place for running ROBOT-based workflows.

There are two main parts to ROBOT:

  1. robot-core is a library of common ontology operations, building on OWLAPI
  2. robot-command is a command-line interface for robot-core

ROBOT is written in Java and distributed from Maven Central (https://mvnrepository.com/artifact/org.obolibrary.robot). It can be used with any language that runs on the Java Virtual Machine, so you can use robot-core operations in your own code. See the JavaDocs at https://www.javadoc.io/doc/org.obolibrary.robot/robot-core/.

The project is hosted on GitHub and shared under a BSD license. We welcome all suggestions for improvements, including additional documentation and training material https://github.com/ontodev/robot/issues.

Acknowledgments

ROBOT development has been supported by NIH grant 1 R24 HG010032-01, “Services to support the OBO foundry standards” to C. Mungall and B. Peters. The initial version of ROBOT was funded by the Gene Ontology Consortium. We thank the numerous developers for their contributions and users for their feedback

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