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phenoscape-kb-ingest's Introduction

phenoscape-kb-ingest

Translations for data sources into Phenoscape Knowlegebase axioms.

Building

Install sbt on your system. For Mac OS X, it is easily done using Homebrew: brew install sbt

To build:

sbt compile

Using Eclipse

You must have the Scala IDE plugin installed in Eclipse.

You must have the sbteclipse plugin installed for sbt.

In the project directory, run sbt eclipse. In Eclipse, choose File > Import... > Existing Projects into Workspace. After any change to build.sbt, run sbt eclipse and refresh the project in Eclipse.

Obtaining the legacy history for this repository

The code in this repo was initially split off from the Phenoscape/phenoscape-owl-tools repository. The relevant legacy history of commits is archived in the tag legacy-history. It is also shared as a replacement of the initial commit, which unless suppressed yields a continuous history for all git commands, including log. To enable this, you must explicitly fetch the replacement:

git fetch origin 'refs/replace/*:refs/replace/*'

Replace origin with whatever you named your remote.

phenoscape-kb-ingest's People

Contributors

balhoff avatar calliem avatar hlapp avatar

Watchers

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Forkers

calliem

phenoscape-kb-ingest's Issues

Tests are lacking

Tests would seem to be particularly important for this repo, because for one, the structure of the axiom sets expected to come out of the translations are not particularly well defined or documented, yet will significantly influence the reasoning possible within the KB. So at the very least some basic assumptions about what axioms should (or should not) be there should be tested.

In addition to that, functioning tests can also greatly help with stepping through the code for debugging from a start and end point that are known to be good.

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