Pattern for traits, where the trait is related to a biological process that can be linked to a molecular function

[rays22]

How to define a biological process related trait when no appropriate biological process component term exist?

Problem: there is a trend of biological processes going obsolete:

Source: https://geneontology.org/stats.html

Look for examples here:

• Obsoletion notices.
• Obsoletion requests

Example

• Biological process term: obsolete DNA methylation Definition: The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
• Related molecular function: GO:0009008 DNA-methyltransferase activity Definition: Catalysis of the transfer of a methyl group to a DNA molecule.

Proposed solution

If there is a molecular function, for example GO:0009008 DNA-methyltransferase activity in the case of obsolete DNA methylation, then create an OBA trait pattern where a anonymous biological function is used in the logical definition (EQ):

quality and (
  characteristic_of some (
    biological_process and 
    (has_participant some some molecular_function)
  ) and (occurs_in some independent_continuant)
)

In the case of DNA methylation:

quality and (
  characteristic_of some (
    'GO:0006304 DNA modification' and 
    (has_participant some some 'GO:0009008 DNA-methyltransferase activity')
  ) and (occurs_in some 'CL:0000000 cell')
)

Limitations

This strategy will not work for complex biological processes that does not involve one defined molecular function or involve multiple molecular functions. For example, GO:0031668 obsolete cellular response to extracellular stimulus would not fit the approach suggested above.

[rays22]

I have just realised that GO:0003674 molecular_function is a BFO:0000015 process and NOT a BFO:0000034 function. :blush: This results in a more simple EQ:

process_quality and (characteristic_of some molecular_function)

For the case of DNA methylation:

process_quality and (characteristic_of some 'GO:0009008 DNA-methyltransferase activity')

As these EQs fit the existing entity_attribute pattern, there is no need to create a new one. In summary, the GO molecular_function process terms can be used in a subset of cases as replacement components when a GO biological_process term becomes obsolete.