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Continuous integration
Authors and contributors:
- Chris Mungall (author)
- Heiko Dietze (contributor)
Date: 2012
Document Type: metadata_description
In software engineering, continuous integration (CI) implements continuous processes of applying quality control - small pieces of effort, applied frequently. The same techniques can be applied to ontology engineering - this is especially important for integrative ontologies, where changes in one ontology can have effects on other ontologies.
Classes in Uberon subsume classes in species-specific anatomy ontologies. In addition, Uberon is interconnected with other ontologies such as CL, GO and phenotype ontologies. These ontologies are developed in an asynchronous manner by different distributed groups. With this type of development, there is the possibility of inconsistencies arising between ontologies.
Integration tests verify that two or more ontologies are compatible - i.e. combining them in an import chain together with bridging axioms does not produce any unsatisfiable classes. For example, if MA were to accidentally place 'styloopod' as a part of a forelimb, a reasoner would find an unsatisfiable class in the integrated ontology set, because in uberon fore and hindlimbs are spatially disjoint.
Integration tests can be time consuming to debug and resolve. The software engineering principle of Continuous Integration (CI) holds that integration tests should be done as far upstream as possible in the development cycle. This means problems can be detected and resolved immediately, rather than building up over time.
The OBO CI system uses the Jenkins CI server to perform integration tests over multiple OBO ontologies.
The system consists of a set of jobs, each performing a particular set of tests. These jobs are typically triggered by a commit to a Version Control System (VCS) such as SVN.
For example, whenever an Uberon editor commits to the core github repository, the build-uberon job is queued. This job executes a number of scripts and runs Oort to perform a build. If a problem is found, Jenkins will email the committer.
In addition, cross-anatomy builds are triggered whenever an external AO commits (currently just ZFA, MA and EHDAA2). This checks that the union of Uberon and this AO plus bridging axioms is satisfiable.
The following Jobs involve Uberon:
- build-uberon
- build-go-xp-uberon
- check-uberon-ehdaa2
- check-uberon-ma
- check-uberon-zfa
- build-phenoscape
Currently Jenkins is only used as a verification step for Uberon - the build process requires multiple steps governed by a complex Makefile, the components of which are currently being migrated to Jenkins.
In the future we intend to add additional cross-species Jobs.
Uberon is a multi-species anatomy ontology and knowledge base, find out more on the home page