Usage - $GoaParser->parse ( $FH, $map ) Returns - OBO::APO::GoaAssociationSet object Args - 1. indirect filehandle to a GOA associations file 2. ref to a hash { UniProtAC => UniProtID } or { GO ID => GO term name } to filter by, optional Function - converts a GOA associations file into a OBO::APO::GoaAssociationSet object
Usage - $GoaParser->work ( $ontology, $data, $up_map, $parent_protein_name ) # the last arg is optional Returns - a data structure with added proteins ( { NCBI_ID => {UP_AC => OBO::Core::Term object}} ) Args - 1. OBO::Core::Ontology object, 2. OBO::APO::GoaAssociationSet object, 3. parent term name for proteins ( string ), # to link new proteins to, e.g. 'gene regulation protein' Function - adds GO associations ( and optionally protein terms ) to ontology
OBO::Parser::GoaParser - A GOA associations to OBO translator.
Includes methods for adding information from GOA association files to ontologies GOA associations files can be obtained from http://www.ebi.ac.uk/GOA/proteomes.html
The method 'parse' parses the GOA association file and optioanlly filters data by a map
The method 'work' incorporates OBJ_SRC, OBJ_ID, OBJ_SYMB, SYNONYM, DESCRIPTION into the input ontology, writes the ontology into an OBO file, writes map files. This method assumes: - the ontology contains all and only the necessary GO terms. - the ontology contains the relationship types 'is_a', 'participates_in', 'has_participant'
Vladimir Mironov <vladimir.n.mironov@gmail.com>
Copyright (c) 2006-2015 by Vladimir Mironov. All rights reserved.
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.
To install OBO::Util::Set, copy and paste the appropriate command in to your terminal.
cpanm
cpanm OBO::Util::Set
CPAN shell
perl -MCPAN -e shell install OBO::Util::Set
For more information on module installation, please visit the detailed CPAN module installation guide.