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