[GMOD-devel] Re: references for terms

[Chris M. <cj...@fr...>]

On Fri, 20 May 2005, Hilmar Lapp wrote:

> There's no full-blown representation of literature references for
> ontology terms on go-perl, unless I'm missing something (I may well be
> - don't hesitate to set me straight).
>
> Is this intentional or a possible oversight? I.e., will OBO-style
> ontologies generally not have references along the lines of
> Bio::Annotation::Reference (as an example; i.e., with authors, title,
> etc), but only dbxrefs?

Hi Hilmar

Yes, this is correct, and intentional. From the point of view of an OBO
ontology, a supporting publication is just a dbxref. The obo file format
and the go-perl objects won't go any deeper than that.

Of course, this means you won't have the syntactic convenience of being
able to say

 $term->definion_dbxref->author_list

Instead you would have to say something like

 $pub_handle->get_pub($term->definition_dbxref)->author_list

But this decoupling of object models is a good thing in my book

> If yes, do you anticipate that those dbxrefs will include references to
> medline or pubmed which obviously in reality are literature refs? If
> so, is there a special attribute to query for whether this is in
> reality a publication ref, or does one have to rely on the
> $xref->xref_dbname property matching certain names.

Yes, one could use the metadata about each db name to guess the kind of
publication, although sometimes it is obvious from the calling context

> 	-hilmar
>
> (if this is not the right place to ask about this please forgive me, I
> think go-dev is down)
>