taxon restrictions on nevous system processes

[pgaudet]

Hello,

I came across
GO:0042063 gliogenesis
The use of this term should conform to the following taxon constraints:
Ancestor GO ID Ancestor GO Term Name Relationship Taxon ID Taxon Reference(s)
GO:0032501 multicellular organismal process never_in_taxon 4896 Schizosaccharomyces pombe
GO:0032501 multicellular organismal process never_in_taxon 4932 Saccharomyces cerevisiae
GO:0032501 multicellular organismal process only_in_taxon 2759 Eukaryota

I am not an expert in neurobiology, but wikipedia claims that the nervous system evolved in metazoa (https://en.wikipedia.org/wiki/Evolution_of_nervous_systems). I suggest that all descendants of
GO:0007399 nervous system development and GO:0050877 neurological system process be minimally limited to metazoa.

Thanks, Pascale

[tberardini]

Leaving open for a few days for comments. If there are none, I will add restrictions to GO:0007399 nervous system development and GO:0050877 neurological system process for only in metazoa.

[paolaroncaglia]

@cmungall
This may be a question for UBERON.
GO ‘nervous system development’ points to UBERON ‘nervous system’. The latter doesn’t have a formal taxon constraint, but says, consistently with Pascale’s comment:
“homology_notes: Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]”
see
http://www.ontobee.org/ontology/UBERON?iri=http://purl.obolibrary.org/obo/UBERON_0001016
Should UBERON_0001016 ‘nervous system’ be limited to Metazoa (or Eumetazoa)?

@pgaudet @tberardini
GO:0050877 neurological system process is already restricted to only in taxon Metazoa.

[dosumis]

Bigger question: Don't we need a plan for turning the inheritance of taxon restriction from Uberon back on ?

I believe it was turned off because of the number of things that needed fixing (I thought there was a ticket with details of progress but can't seem to find it). It's not a massive amount of work, we just need to schedule a time when we (myself + Chris & @ukemi ?) can commit to doing it.

[paolaroncaglia]

@dosumis , I added to the agenda for today's editors call. Not sure we'll get there, though...

[tberardini]

Didn't get to this during yesterday's call so will wait till next week.

[dosumis]

Covered in editor's call. Suggest we add taxon constraints to Uberon, from where they will soon be imported:

'nervous system' only_in_taxon Metazoa

I don't think this will be sufficient for the constraint on gliogenesis (if it was, we couldn't have terms for phylogenetically restricted parts of nervous systems). For that, I think we would need a taxon restriction on CL and imports from there. @cmungall is this possible, or should we add in GO for now?

[tberardini]

Is there an action item for this issue or can all the issues be addressed by changes to Uberon and CL?

[dosumis]

Nervous system constraint can come from Uberon. Only a few issues to fix
before we turn Uberon taxon imports back on.
On 4 May 2016 23:26, "Tanya Berardini" notifications@github.com wrote:

Is there an action item for this issue or can all the issues be addressed
by changes to Uberon and CL?

—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
#12411 (comment)

[tberardini]

Ok, I will leave this issue open until Uberon taxon imports are back on and we can verify that the taxon constraints have been propagated as we hope.

[cmungall]

blocked on #12223

[dosumis]

All taxon restrictions on anatomical structures on anatomical structures are now inherited from Uberon. This ticket therefore belongs on the Uberon tracker.

(This may be handy https://github-issue-mover.appspot.com/)

[tberardini]

@cmungall, @dosumis - can I close this now that the linked issue #12223 has been resolved? Do I need to open a ticket on the Uberon tracker for adding a taxon constraint to UBERON_0001016? Thanks.

[cmungall]

we already have

id: UBERON:0001016
name: nervous system
...
relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa
relationship: never_in_taxon NCBITaxon:6040 ! Porifera

this is now propagated to any GO terms that existentially depend on a nervous system over the appropriate relations. I'll close this ticket. Assuming no one thinks plants have nervous systems

http://phenomena.nationalgeographic.com/2015/12/15/can-a-plant-remember-this-one-seems-to-heres-the-evidence/

[tberardini]

CLOSE this issue. In fact, I'll just do that.

Plants don't have nervous systems.