Tool for querying a local copy of the Phenoscape KB and generating an inferred presence-absence data matrix, for a given taxon and anatomy specification.
Switch branches/tags
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.settings
notebooks
project
sparql
src/main/scala/org/phenoscape/kb/matrix
.gitignore
.project
LICENSE
README.md
build.sbt

README.md

ontotrace

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.

Run

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 data
  • bigdata.properties—path to Bigdata properties file
  • bigdata.jnl—path to Phenoscape KB Bigdata journal database file
  • tbox.owl—path to Phenoscape KB tbox OWL file
  • anatomy.dl—path to text file containing input anatomy expression using OWL Manchester syntax
  • taxonomy.dl—path to text file containing input taxonomy expression using OWL Manchester syntax
  • result.xml—path for output file

Build

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.

Data

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.