Documentation: understanding ontology basics

[suzialeksander]

We had a user write in with a series of ontology questions that do not appear to be addressed in our help docs. They include:

• My questions is the product of two "regulates" relations produce
  something unsure. Would you please help me understand it?
  "regulates ○ regulates → ?"

• How to reason with has_part?
  Would you please show me how has_part should be reasoned with the
  other 5 relation types?

  • i: is a
  • P: part of
  • R: regulates
  • R+: positive regulates
  • R-: negative regulates

• Why a GO term can be both "is_a" and "part_of" another GO term?
  I see GO:0098882 is both "is_a" and "part_of" GO:0099181. This
  doesn't quite make sense to me. I think a GO term can be either "is_a"
  or "part_of" another GO term but not both. Is this an error in GO?
  [Term]
  id: GO:0098882
  ...
  is_a: GO:0099181 ! structural constituent of presynapse
  ...
  intersection_of: part_of GO:0099181 ! structural constituent of presynapse
  ...
  relationship: part_of GO:0099181 ! structural constituent of presynapse

• Where is the corresponding high-throughput code for IPI? It says "Each of the experimental evidence code have a corresponding ‘high throughput’ evidence code (HTP)." on the following URL. But I don't see the high-throughput code for IPI. Is this an error in
  the above statement?
  http://geneontology.org/docs/guide-go-evidence-codes/

• part_of vs is_a in BP
  I am trying to understand the difference between part_of and is_a.
  As shown on QuickGO, GO:0033955 is "part_of" GO:0000266 and "is_a" GO:0000002.
  I can understand "part_of" when it is used in CC. I still don't quite
  understand the subtle difference between "part_of" and "is_a" when
  they are used in BP. Would you please help me understand the
  difference between "part_of" and "is_a" in this example? Thanks.
  mitochondrial DNA inheritance
  Definition: The process in which copies of the mitochondrial genome
  are distributed into daughter mitochondria upon mitochondrial fission.
  https://www.ebi.ac.uk/QuickGO/term/GO:0033955
  mitochondrial fission
  Definition: The division of a mitochondrion within a cell to form two
  or more separate mitochondrial compartments. PMID:11038192
  https://www.ebi.ac.uk/QuickGO/term/GO:0000266
  mitochondrial genome maintenance
  Definition: The maintenance of the structure and integrity of the
  mitochondrial genome; includes replication and segregation of the
  mitochondrial chromosome.
  https://www.ebi.ac.uk/QuickGO/term/GO:0000002