INSTALL
=======
There are two typical ways:
Using CPAN.
==========
You'll want to use CPAN to install the modules by performing the
following steps:
From the root prompt on your server, invoke the CPAN shell:
# perl -MCPAN -e shell
Once the PERL interpreter has loaded (and been configured), you can
install modules by issuing the command install MODULENAME.
The first thing you should do is upgrade your CPAN:
cpan> install Bundle::CPAN
Once it's done, type:
cpan> reload cpan
Now, enter the following command to retrieve all of the required modules:
cpan> install OBO::Core::Ontology
Manually
========
By typing the following mantra:
perl Makefile.PL
make
make test
sudo make install
Other useful commands:
make clean
make distcheck
Documentation
=============
For more information about these modules, check:
- http://search.cpan.org/~easr/ONTO-PERL/
- http://www.cellcycleontology.org
- http://www.semantic-systems-biology.org
See also:
1. ONTO-PERL: An API supporting the development and analysis of bio-ontologies
Antezana E, Egana M, De Baets B, Kuiper M, Mironov V.
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
2. ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies,
Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.
BMC Bioinformatics 2010, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8
Citing ONTO-PERL
================
If you use ONTO-PERL in your work, you are kindly requested to cite:
ONTO-PERL: An API supporting the development and analysis of bio-ontologies
Antezana E, Egana M, De Baets B, Kuiper M, Mironov V.
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
Third part modules
==================
Required module:
1. Date::Manip (> v6.24) is used by the OBOParser (to check dates):
http://search.cpan.org/~sbeck/Date-Manip/
Optional modules:
1. XML::Parser (> v2.41) is used in format conversions (obo2owl and owl2obo):
http://search.cpan.org/~msergeant/XML-Parser/
2. XML::XPath (> v1.13) is used by the IntAct related modules:
http://search.cpan.org/~msergeant/XML-XPath/
3. SWISS Knife (> v1.67) is used by the 'UniProtParser':
ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/
Bugs/comments/questions/etc
===========================
We are regularly improving this API, please report any bugs
or send your comments to erick.antezana -@- gmail.com