What is the exact meaning of 'penetration structure'?

[jseager7]

There's a sub-branch of PHIPO that describes terms related to a pathogen's 'penetration structure'. The root of the branch is the term 'abnormal formation of pathogen penetration structure' (PHIPO:0000032), and the definition is as follows:

A single species pathogen growth phenotype in which the formation of the pathogen penetration structure is abnormal (i.e different than wild-type) when assessed for penetration ability on a given experimental substance/membrane.

I need to apply a uPheno pattern to this term. The definition suggests an abnormal biological process, but there is no process in GO that seems to exactly relate to the formation of a 'penetration structure'. These are the closest terms:

• formation of host infection structure
  • penetration hypha formation
  • penetration peg formation

It's not entirely clear whether the infection structures defined by 'formation of host infection structure' are restricted to structures that involve penetration (the term definition does not preclude non-penetrating structures), so that term might be too broad. The latter two terms are specific examples of penetration structures, so they're too narrow.

So, is PHIPO actually describing a more specific example of a penetration structure (like hypha), or is this a limitation of GO's current term definitions and/or hierarchy?

[ValWood]

@CuzickA are infection structure and penetration structure interchangeable? Which is preferred?

[CuzickA]

I think 'infection structure' and 'penetration structure' are interchangeable. We could have them as Synonyms. I'm not sure which is preferable to the wider community but in PHI-base we have used 'penetration'.

We have used 'penetration structure' in both the single species and PHI branches of PHIPO as we wanted this to be a grouping term for penetration hyphae, penetration peg, appressorium formation etc rather than making all the individual terms.

[jseager7]

We have used 'penetration structure' in both the single species and PHI branches of PHIPO as we wanted this to be a grouping term for penetration hyphae, penetration peg, appressorium formation etc rather than making all the individual terms.

It sounds like the concept of a penetration structure is synonymous to an infection structure in this case. I'd recommend either adding synonyms to the penetration structure terms, or changing the labels to follow GO's terminology.

[ValWood]

We should also get synonyms added to the GO term. I will open a ticket for this.

[CuzickA]

Can we close this ticket now?

[jseager7]

Can we close this ticket now?

Yes, since it sounds like I can use the GO term 'formation of host infection structure' for the pattern mapping. Closing.