WBPaper00038523 GO linking comments

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doi10.1534/genetics.111.130450 00038523

Comments concerning GO linking of this paper


  • authors discuss many types of 'aging', which are all linking to one GO term "aging"- the authors are setting out to distinguish aging events that occur in different tissues, so the global linking of all instances of 'aging' throughout this paper is counter to the point the author is trying to make.
  • non-informative links -- in most of these cases, it would be good if there were GO terms that actually could capture the whole phrase
    • regulation
    • aging when referring to 'reproductive aging', 'somatic aging', 'human aging', 'C. elegans aging'
    • kinase as part of phosphatidylinositol-3-kinase
    • reproduction as part of 'late reproduction', 'early reproduction'
    • insulin-like growth factor in 'insulin-like growth factor-1'
    • growth in 'nematode growth media'
    • development in 'dauer development'
    • receptor and kinase in 'receptor tyrosine kinase'
    • fertilization in 'self-fertilization'
    • formation in 'dauer formation'
    • mating is not an informative link here, the GO definition is too cellular-based to capture the essence of how mating is used here.
    • signaling is obsolete? it doesn't exist in wormbase GO
    • gametogenesis seems like a good link but the use of gametophyte in the GO definition is non-animals centered
    • cell in 'germ cell'
    • ovulation -the GO term definition does not seem broad enough
    • reflex this does not match the meaning of the GO term


  • Several instances of the word "aging" are not linked, I presume because one or all of the letters are capitalized.
  • The term "signaling" links to a non-specific search page
  • "Insulin-like growth factor" links to "insulin-like growth factor receptor binding"; do we want to keep this?
  • The abbreviation "LS", intended to represent "Lifespan" is linked to "lipoate synthase activity"
  • The abbreviation "FPS", intended to represent "Fast Pharyngeal Pumping Span" is linked to "sn-glycerol-3-phosphate 2-alpha-galactosyltransferase activity"
  • The term "formation" in reference to "Dauer formation" links to the GO term "biosynthetic process", which has the more biochemical connotation of "formation"
  • The term "reflex" in reference to the physical bending/turning of the gonad arm in C. elegans links to the GO term "reflex" referring to muscle or gland response to stimulus
  • The term "PDK1" in reference to phosphoinositide-dependent protein kinase links to the GO term for "pyruvate dehydrogenase (acetyl-transferring) kinase activity"


Same comments as Karen and Chris


Overall: 195 total links

  • CORRECT, as is ~40.5%
  • CORRECT meaning, but part of another entity ~50.8%
  • NO - ~5.6%

Time consideration: 50 minutes