Function-Process Use Cases

Execution of function is one of the building blocks required to complete a process

See slide 3 from Media:F-P-stcroix.ppt for details

Consider:

 MF GO:0004397 histidine ammonia-lyase activity
 BP GO:0006548 histidine catabolic process

It is the case that every execution of the function is part of the process. It is also the case that every time the process unfolds, the function is executed (in this case, at the start of the process, but we do not capture this)

• F implies P? YES
• P implies F? YES

Contrast with:

 MF GO:0030409 glutamate formimidoyltransferase activity
 BP GO:0006548 histidine catabolic process

In some species, the unfolding of the process does not require execution of the function. Is every execution of the function necessarily a part of the process? Not clear from slide. It appears to be the case for known genes (see amigo)

• F implies P? UNKNOWN
• P implies F? NO

If F implies P is false, this means we should not do this:

 GO:0006548 histidine catabolic process
 --[?] GO:0030409 glutamate formimidoyltransferase activity

Because we read ALL-SOME statements up the graph

More examples

Electron transport

The respiratory electron transport chain and photosynthetic electron transport chains are particularly good examples of situations where function and process terms meet. These chains are long processes that are composed of a series of very well characterized molecular functions.

Glycolysis

See Glycolysis Process-Function Links for initial considerations (hjd)

TCA Cycle

See TCA_Cycle_Process-Function_Links for initial thoughts (hjd)

Process and function closely correspond

 [i]transmembrane transport process (process ontology)
 ---[?]transmembrane transporter activity (function ontology)

Regulation of function

 [i]transmembrane transport process (process ontology)
 ---[?]regulation of transmembrane transporter activity (process  ontology)

See regulates pages (link?)

Question:

• do we use the same relation for RoBP as for RoMF? Probably not
  • suggestion: regulates_process, regulates_function

Low Hanging Fruit

There are a number of potential links that are (a) easy to create, because they involve basic biological knowledge and (b) deliver high value to annotators and users. The following list is incomplete - this is a scratch area, feel free to add:

Phosphorylation and Kinase Activity

• GO:0016310 ! phosphorylation - 3640 genes
• GO:0016301 ! kinase activity - 6053 genes

There are currently only 2230 annotated to both

this means:

• p( phosphorylation GIVEN kinase activity ) = 0.3684
• p( kinase activity GIVEN phosphorylation ) = 0.6126

Should the correlation not be higher?

Transcription factor activity & regulation of transcription

...

Using links to drive displays

https://sourceforge.net/tracker2/?func=detail&aid=2152300&group_id=36855&atid=494390