dbgap_to_owl

Convert the dbGaP XML Schema to an ISO 11179-3 compliant OWL representation

Requirements

• python3 (ideally >= 3.5, but any 3.x version will do). You can determine whether you have python on your machine and its version by:
  • python -v -- if 3.x you are ready to go, otherwise...
  • python3 -v -- if this works you are also ready to go
• virtualenv -- if this isn't on your machine, see http://pythoncentral.io/how-to-install-virtualenv-python/
• java -- we need version 1.7 or greater

Installation

Set up a python3 virtual environment:

> virtualenv dbgaptoowl -p python3
> . dbgaptoowl/bin/activate
(dbgaptoowl) > pip install dbgap-to-owl

Clone the modified PyXB executable

In an appropriate temporary directory:

> (dbgaptoowl) > cd temp
> (dbgaptoowl) > git clone https://github.com/crDDI/pyxb.git
> (dbgaptoowl) > cd pyxb
> (dbgaptoowl) > python setup.py install
...
changing mode of [...]dbgaptoowl/bin/pyxbwsdl to 755
running install_egg_info
Writing [...]/dbgaptoowl/lib/python3.5/site-packages/PyXB-1.2.5_DEV-py3.5.egg-info
> (dbgaptoowl) > (cd back to working directory)

Note that the git clone step may take a while (we will see whether we can't merge this with the official PyXB branch at some point in the future)

Run the conversion

Convert dbGaPEx2.1.5.xsd starting at the GaPExchange element, placing the output in dbGapEx2.1.5.ttl

(dbgaptoowl) > dbgaptoowl -i ftp://ftp.ncbi.nlm.nih.gov/dbgap/xsl/dbGaPEx2.1.5.xsd -o data/dbGapEx2.1.5.ttl -e GaPExchange
Attribute None.groupNum-REF renamed to groupNum_REF
Attribute DAC.dac-fax renamed to dac_fax
(dbgaptoowl) >