Structured comment name Pathogenicity in MIxS6

[ndheilly]

The term pathogenicity is problematic because an organism's pathogenicity depends on its virulence and on the host response. Organisms (bacteria, virus, fungus, helminths, ciliates, etc) can be pathogenic without being parasitic. They could be free-living and 'just' happen to be pathogenic when within a host. They can even be beneficial in some individuals, but pathogenic in an immunocompromised host. Parasites can be more or less pathogenic in different host species or different individuals within a given species. it depends on local adaptation of the host and parasite, and varies geographically and over time. Basically pathogenicity varies with host and parasite génotypes and can not be defined. Therefore, I think this term alone is useless and profoundly confusing. The definition 'to what is the entity pathogenic' does not help: do you mean what are the natural hosts? what about dead-end hosts? do you want the list of all hosts, or only the definitive hosts? and what about free-living organisms, that in fact do not have a host, but can be pathogenic if ingested? The parasite Microbiome Project Consortium has been working on the Parasite-associated package and maybe we should discuss together how to include some of the terms we develop into the core package. Hoping we can be of use. Best, Nolwenn

[only1chunts]

Just to help define this issue as a term update I have included the current details of the term Pathogenicity :

Current term details

Term name - known pathogenicity
Term ID - [if known]
Structured comment name - pathogenicity
Definition - To what is the entity pathogenic
Expected value - names of organisms that the entity is pathogenic to
Value syntax - {text} 
Example -human, animal, plant, fungi, bacteria
Preferred unit - 
Package(s) - core

Please can you (@ndheilly ) provide any suggestions for the definition and examples? Suggested update(s)

Term name -  known pathogenicity
Term ID - [if known]
Structured comment name - pathogenicity
Definition -??? Please list any individuals/species/genera/family that are known to be pathogenically affected by this specific sample. ???
Expected value - ???
Value syntax - {text}
Example - ???
Preferred unit - 
Package(s) - core

Alternatively, are you suggesting that the term be removed entirely?

Additional context It maybe useful to see examples of how this term has been used historically, the few examples I have found in NCBI are for MIGS samples and the values tend to be either "Pathogenic" or "non-pathogenic", which is not in line with the way it was originally defined anyway! @lschriml do you know how to pull usage of this term from the NCBI to see how its actually being used?

[mia-lgo]

Here is a couple of alternatives:

1. Leave the term as it is for the MIxS v6 release while beginning a thorough discussion with The parasite Microbiome Project Consortium for this and other terms that may derive from this and thus give specification to the issue of pathogenicity.

2. Changing the current term definition and the details as a consequence: The term can be left as only 'pathogenicity' and be defined as in PATO and other ontologies (such as phipo.owl, ms.owl, and flopo.owl).

In this case, the suggestion could be:

Term name -  pathogenicity
Term ID - [if known]
Structured comment name - pathogenicity
Definition -The ability of a pathogen to produce an infectious disease or disorder in an another organism.
Expected value -  text (with the description of the pathogenicity) and/or OBI or other relevant ontology
Value syntax - {text} or OBI/PATO {text}|{termLabel} {[termID]}
Example - 'responsible for mucosal infections, such as vaginitis or oral thrush, in otherwise healthy individuals' or 'human pathogenicity disposition [OBI:OBI_0000666]'
Preferred unit - 
Package(s) - core

However, we have to get back to 1 eventually to be able to split the term to provide more specific ones as suggested by the reporter. So I would prefer to go for option 1 at the moment.

What do you reckon?

[ndheilly]

I would suggest tha the term is removed entirely. The Symbiont-associated package that has been developped will answer all the questions raised above, and more, and allow everyone working with samples from pathogenic / non-pathogenic symbiotic organisms to provide metadata thta contextualize the sample.

[mia-lgo]

what are your thoughts @only1chunts ?

[only1chunts]

I think there is a need for more discussion on this, but it sounds like its not urgent and could be pushed back to be dealt with for v7 release in the future. So my suggestion is to leave it as-is for release v6.

[mia-lgo]

right, thank you. I will leave the issue open then.

[lschriml]

@mia-lgo - I have added the Label - discuss MIxS7.0

Searching in BioSample: pathogenicity[Attribute Name]

usage: Johne's disease pathogenic Chengdu non

I agree this needs to be revisited.

Cheers, Lynn

[only1chunts]

Thanks Lynn, I've removed the ticket from v6 Project