CamEds Ontology meeting 2012-10-24

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Are we ok with adding transcription terms that refer to very specific types of RNA?

Stemming from this SF request: https://sourceforge.net/tracker/?func=detail&aid=3579162&group_id=36855&atid=440764

The Sequence Ontology doesn't have any term more specific than 'telomeric repeat' (under 'telomere'). Therefore no term outside of GO that Antonia could use in annotation extensions. I'd opt for adding all her requested terms, but I vaguely remember that there was a discussion on sequence-related terms and I can't find it on the wiki. [Paola]


Taxon constraints

I need to add a couple of taxon constraints stemming from SF requests.

Chris added to last week's editors call wiki:

'to add a new one, first request an ID range for tax rules'

(http://wiki.geneontology.org/index.php/Ontology_meeting_2012-10-18#Question:_Taxon_triggers)

There's this file with instructions in svn:

/go-trunk/quality_control/annotation_checks/taxon_checks/x-taxon-idranges.owl

According to it, my GOTAX ID range should be (if I'm reading this correctly):


Datatype: idrange:3

Annotations: allocatedto: "GOC:pr"

EquivalentTo: xsd:integer[> 2001 , <= 3000]


I've tried to add a taxon rule using the assign-relation-ids.pl script. The resulting stanzas are as follows (I'm copying both the last one, i.e. the one I've just added, and the second-last stanza, a constraint I actually added back in July):


[Term]

id: GO:0097347

name: TAM protein secretion complex

relationship: only_in_taxon NCBITaxon:2 {id="GOTAX:0000536"} ! Bacteria


[Term]

id: GO:0097387

name: capitate projection

relationship: only_in_taxon NCBITaxon:7203 {id="GOTAX:0010015"} ! Brachycera


So the new GOTAX ID is 0010015. Does this look ok? It's not really in the range 2001-3000, but it's a much higher number than 0000536...

Have Tanya or David tried this already? Should we discuss it at the editors call tomorrow?

[Paola]