Difference between revisions of "Taxon-GO Checks and Commentary - Part 1"

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  Jen  
 
  Jen  
  
 +
reply:
  
 +
Hi Jen,
 +
 +
In the past, I think the prevailing view was that nematodes didn't neatly
 +
fit into either the protostome or deuterostome classification, so they
 +
were kind of off on their own as 'pseudocoelomates'.  More recently,
 +
however,  a newer classification grouped nematodes, along with arthropods,
 +
as Ecdysozoa, a protostome superclade.  This more recent classification is
 +
what we've been following with these annotations.
 +
 +
Cheers,
 +
--Kimberly
 +
 +
I have written to suggest that we come up with a union_of taxon term that covers all the needed groups.
  
 
*'''nucleus''': 14 EcoCyc IEA annotations of E. coli gene products to 'nucleus' GO:0005634. Written to Jim Hu to ask about these.  
 
*'''nucleus''': 14 EcoCyc IEA annotations of E. coli gene products to 'nucleus' GO:0005634. Written to Jim Hu to ask about these.  

Revision as of 08:52, 28 August 2009

28th August 2009

I am looking through the file of errors that Chris Mungall's checking script has produced. It is called gaf-taxon-gaffes.txt and is in go/scratch/go-taxon.

Here are the things that I have found:

Annotation errors

  • Senescence: Human annotations to the plant senescence (GO:0010149) term. Senescence in plants is the process whereby cells die just before the shedding of an organ, whereas senscence in humans is the more general aging of cells that remain alive in the organism. We may need to make a new term for the human process, or add a synonym to the existing aging (GO:0007568) term. I have written to ask people, as I am not sure how much these processes differ, and whether we need separate terms.
    • 8 manual annotations by BHF-UCL to plant senescence. I have reported this to GOA, and they will liaise with BHF-UCL and send back any terms changes that need to be made.
    • 7 RGD ISO annotatations to the same term. Wrote to Simon Twigger.
    • organ senescence: 2 manual from RGD, 1 manual from MGI, 3 IEA from Ensembl. I have written to Harold Drabkin and Simon Twigger, but Emily will pass on the information to Ensembl later.
  • Lactation: Mammalian reproduction in chickens: There are 6 AgBase ISS annotations to GO:0001553 "luteinization" or GO:0007595 "lactation", which are both mammalian reproductive processes. Written to Fiona McCarthy.
  • phycobilisome: I will come back to phycobilisome GO:0030089 later as it needs some research.
  • gastrulation with mouth forming first: 67 WormBase annotations to 'gastrulation with mouth forming first' GO:0001703. All are IEA. The script objects to nematodes being on a term with only_in_taxon Protostomia. I Have written to Kimberly van Auken to ask if this is right.

Reply:

Hi Jen--

Thanks for asking about these annotations.

C. elegans is actually grouped with the protostomes, which means that with
respect to this basic phylogenetic division, their gastrulation is lumped
in the 'mouth forming first' category.

This categorization of gastrulation is probably a bit of an
oversimplification, as it's really the middle, or gut, that forms first in
elegans.  Nonetheless, I imagine we chose GO:0001703 'gastrulation with
mouth forming first' as the GO term for these IMP annotations to be sure
we annotated our genes to the 'protostome' gastrulation term so the
elegans annotations would be annotated to the same term as genes involved
in protostome gastrulation in other species.

Hope that rationale makes sense.

Cheers,
--Kimberly

I have then checked and this is the lineage of C. elegans in NCBI:

cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Pseudocoelomata; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis

C. elegans doesn't seem to be under Protostomia, so I sent this reply to Kimberly:

Hi Kimberly,

Thanks for getting back to me so swiftly.

How do you mean 'grouped with Protostomes'? It seems not to be under
protostomes in the NCBI classification. Should I be   marking this 
go term as intended for use with protostomes and some other taxonomic grouping as well?
 
Thanks,

Jen 

reply:

Hi Jen,

In the past, I think the prevailing view was that nematodes didn't neatly
fit into either the protostome or deuterostome classification, so they
were kind of off on their own as 'pseudocoelomates'.  More recently,
however,  a newer classification grouped nematodes, along with arthropods,
as Ecdysozoa, a protostome superclade.  This more recent classification is
what we've been following with these annotations.

Cheers,
--Kimberly

I have written to suggest that we come up with a union_of taxon term that covers all the needed groups.

  • nucleus: 14 EcoCyc IEA annotations of E. coli gene products to 'nucleus' GO:0005634. Written to Jim Hu to ask about these.
  • Emily is looking at the file too, and is making notes of the numbers of annotations errors found, and the fixes that she has applied. She is feeding this information back, along with any ontology errors that she finds.


Ontology errors

  • sensory perception GO:0007600 seems to be much less granular than its parent GO:0050890 cognition
    • I need a taxon link for neurological system process, which is the ancestor that indicates involvement of the brain. TODO
    • I need to add the cognitive part to the def of sensory perception. DONE

sensory perception
old def:The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal.

new def: The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.

cognition
def: The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.

  • nutrient reservoir activity: I have written to Tanya and Donghui about this term, as it has lots of TAIR annotations but an Arthropoda taxon link. I'm hoping they'll be able to shed light on what it means so we can improve the def and correct the taxon link.
GO:0045735
nutrient reservoir activity
def: Functions in the storage of nutritious substrates.