Get All Gene Ontology (Molecular Function) Parents For A Go Term Using Perl

Question

[sayonidas03]

Hi,

I would be very grateful to you if anyone can point me towards the answer as to how to get all parent GO terms in thee Molecular Function Gene Ontology tree for a particular GO term using Perl. I came some ways to do it using python and R in this forum, however, I am still trying to get that done using perl. Any help is appreciated. Thanks in advance!

Answer 1

[David Westergaard]

Use GO::Parser. It's a somewhat complex module, but it gets the job done. You are probably interested in get_recursive_parent_terms or get_recursive_parent_terms

Answer 2

[sjcarbon]

Honestly, if it's a one-off in that you're only really interested in ancestor, you should probably just use DBI mysql against one of the public GO mirrors:

http://www.geneontology.org/GO.database.shtml#avail

There is also example SQL up for the various things you might try, which makes getting something working quickly rather easy, and you don't have to worry about keeping things up to date at your end:

http://wiki.geneontology.org/index.php/Example_LEAD_Queries

Again, coming from a online database perspective, you might want to check out the libraries that are consumed by AmiGO. Either go-dev or gobo-dbic, depending on your use case:

http://wiki.geneontology.org/index.php/AmiGO_Manual:_Installation_1.8

You can also keep in mind that you can get direct help from the GO Consortium at:

http://www.geneontology.org/GO.contacts.shtml

They could probably put you into contact with one of their programmers if you're still having problems (hi!).

Answer 3

[EagleEye]

GeneSCF is perl based tool where you can reterive complete GO (CURRENT) into simple tab-seperated table format (GOID GOTERM GENES). But without the tree information (LEVEL).

Example :

Downloading current available database for Mus Musculus from Gene Ontology

./prepare_database -db=GO_all -org=mgi

The above command downloads complete GO db as simple text file in following location, 'geneSCF-tool/class/lib/db/mgi/'.