Ontotrace is a tool for querying a local copy of the Phenoscape Knowledgebase and generating an inferred presence/absence data matrix, for a given taxon and anatomy specification.
To run Ontotrace you must have a working installation of Java (7 or higher). You can download a prebuilt Ontotrace package from the GitHub Releases page. Start Ontotrace by running ./ontotrace
within the bin
folder. You will need to provide seven arguments in this order:
--informative
|--all
—output only variable characters or all characters with either presence or absence databigdata.properties
—path to Bigdata properties filebigdata.jnl
—path to Phenoscape KB Bigdata journal database filetbox.owl
—path to Phenoscape KB tbox OWL fileanatomy.dl
—path to text file containing input anatomy expression using OWL Manchester syntaxtaxonomy.dl
—path to text file containing input taxonomy expression using OWL Manchester syntaxresult.xml
—path for output file
Ontotrace is written in Scala. To build it you must first have SBT installed. If you are using Homebrew on Mac OS X, simply run brew install sbt
. Otherwise, follow the instructions on the SBT website.
To build a packaged version containing a runnable script and all dependencies, run sbt stage
. This will create a relocatable folder at target/universal/stage
which has executable scripts within bin
and library dependencies within lib
.
To create an archive for release, run sbt universal:packageZipTarball
. The archive will be created within target/universal
.
Phenoscape Knowledgebase data dumps can be downloaded from DataHub. Before using Ontotrace you will need to load all the triples into Bigdata and provide the Bigdata journal file as an argument.