[Go] addition of localization specific process terms ?

[Karen Christie]

Hi,

In last week's Reference Genomes annotation jamboree, a question came
up about whether/when it is appropriate to add localization specific
process terms. We'd like clarification of the GOC's current practice
on this issue. More details are below.

thanks,

-Karen



We were discussing the appropriate process terms for the LONP1 group
of genes, which are involved in proteolysis of proteins in the
mitochondrial matrix. The question came up regarding whether it would
be appropriate to have a specific term for mitochondrial proteolysis,
considering that we already have terms like:

- ER-associated protein catabolic process (GO:0030433)
- mitochondrial translation (GO:0032543)

At one time, the philosophy on this was to have one term representing
the basic process, and to indicate localizations using the component
annotations. However, more recently, terms such as the two listed
above have been added to GO.


Arguments in favor of localization specific process terms included:

-- 1. the fact that a different set of genes is involved in a given
"process", e.g. mitochondrial translation versus cytoplasmic
translation

-- 2. being able to look for terms enriched in a process such as
"mitochondrial translation", without having to also use a component
term to narrow the search to the mitochondrial genes (this is
apparently not possible in many tools)


Arguments against having localization specific process terms included:

-- 1. unnecessary proliferation of terms in the ontology, since the
localization can be obtained via the component annotations


So, for going forwards, we'd like clarification of when it is or is
not appropriate to request localization specific process terms and on
the guiding principles for deciding when/if such terms are appropriate.

thanks,

-Karen