Taxon-GO Checks and Commentary - Part 1

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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. I Have written to Kimberly van Auken to ask if this is right.
  • 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.