Welcome to the MeGO forum!

Discussions about the MGE ontology.

Moderator: raphael

Welcome to the MeGO forum!

Postby raphael » Thu Jan 31, 2008 1:48 pm

MeGO is a gene ontology dedicated to mobile genetic elements (MGE) functions. The terms defined in this ontology are or will be used to annotate MGE families in ACLAME.
The main MeGO page is available at http://aclame.ulb.ac.be/mego
You can download the ontology as an OBO formatted file or as a MySQL dump. The ontology can be browsed with the AmiGO interface.

Any comment on MeGO will be welcome.

Best regards,

the ACLAME team.
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Re: Welcome to the MeGO forum!

Postby jimhu » Mon Jan 26, 2009 8:06 pm

What's the relationship, if any, between MeGO and GO? From a quick look, it seemed like MeGO has terms that would fit in GO, SO, and neither(?). Is that right?

I'm wondering if we should be attaching MeGO terms to phage genes in EcoliWiki or if GO terms cover the MeGO annotations.
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Re: Welcome to the MeGO forum!

Postby ariane » Tue Jan 27, 2009 10:44 am

Hi Jim,
The exact status is a bit complicated. MeGO indeed contains terms to fit in GO and SO (that's why I keep the SO section in MeGO) and not in any of those (as "phage" and children since they contain both genes and proteins!). I also keep a list of ACLAME functions for other "things" that do not fit in GO or SO, mostly to help me keeping track on some features that I cannot enter in GO and for other people using the DB and who like to see protein families etc. In MeGO there are links to SO and GO when the term is in one of these ontologies. I just noticed that the SO links are no active, something we need to fix.
I am in contact with both GO and SO to try to harmonize the whole thing but it is slow, mostly because of my side! Normally, Jane Lomax at GO will start a discussion on virus terms in GO next spring. The situation is quite complicated because they already have herpes virus terms in GO, organized in a way they are not satisfied with. Combining those definitions with those in PhiGO is not obvious because they are almost the same but not exactly... due to differences in host cell stuctures etc... and of course there are lots of new terms related to other eukarotic viruses that need to be added in GO and which again will have to be harmonized with phage terms.
Any link you think may be useful to MeGO from E.coliHub is welcome for us. It is my hope that people will start using this ontology to annotate phage and plasmid genes so that there is wider input into it. A plasmid annotation platform should soon be up running, for which I hope we shall contribute with MeGO. Have a nice day. Best regards. Ariane.
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