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This is a list of questions that arose while PAINTing PTHR10373.

Questions for MOD curators

Molecular Function

Human LEF1

  • Question: Is the IMP to GO:0043027 "caspase inhibitor activity" in PMID 20360943 appropriate? Does the experiment really show a biochemical interaction between LEF1 and caspase, or is reduction of caspase activity a result of mutating LEF1? If the latter, shouldn't that be a BP annotation?
    • Curator answer: Insert answer here.
  • Question: Does LEF1 really bind estrogen, as the GO:0030284 "estrogen receptor activity" IDA from PMID 18794125 implies? How could LEF1 have both "estrogen receptor activity" and "estrogen receptor binding" activity (from the same paper)?
    • Curator answer: Insert answer here.

Biological Process

Mouse Lef1

  • Critical: Should the GO:0043586 "tongue development" annotation from PMID 17284610 , "Wnt signaling interacts with Shh to regulate taste papilla development," be to one of the child terms GO:0061193 "taste bud development" or GO:0061196 "fungiform papilla development"?
  • Is the annotation to GO:0050909 "sensory perception of taste" from PMID 17284610 really appropriate? The paper describes the role of Lef1 in taste bud development. Isn't taste perception a downstream effect?

Questions for ontology curators

Molecular Function

  • Based on the definition, shouldn't GO:0003705 "sequence-specific enhancer binding RNA polymerase II transcription factor activity" have some sort of relationship, either is_a or has_part, GO:0035326 "enhancer binding"?

Biological Process

  • The term GO:0071899 "negative regulation of estrogen receptor binding" is defined as "Any process that stops, prevents, or reduces the frequency, rate or extent of estrogen receptor binding, interacting selectively with an estrogen receptor." Binding to what? So, if protein X is annotated to 71899, does it mean that it prevents some other protein Y from binding to the estrogen receptor? If so, should protein Y be listed in the "with" column? Alternatively, does it mean that X prevents the estrogen receptor from binding DNA? Should those two scenarios (binding DNA vs. binding a protein) be separated into new child terms? Is this a general problem with all the "regulation of ___ binding" terms?
  • What is an appropriate taxonomic restriction for GO:0060710 "chorio-allantoic fusion"? There are annotations out to chicken.
  • GO:0019083 "viral transcription" is, through a series of intermediates, part_of GO:0016032 "viral reproduction," but there are plenty of example of viral gene transcription that is not directed toward viral reproduction. Genes involved in establishment of latency, for example, are specifically geared towards NOT producing virus particles, so anything involved in transcription of genes involved in establishment of latency should be annotated to 19083 but not 16032.