Issue 42 in infectious-disease-ontology: biological vector role

[infectious-di...@googlecode.com]

Status: New
Owner: alanrut...@gmail.com
Labels: Type-Enhancement Priority-Medium

New issue 42 by zhengj2...@gmail.com: biological vector role
https://code.google.com/p/infectious-disease-ontology/issues/detail?id=42

OBI deprecated 'biological vector role'
(http://purl.obolibrary.org/obo/OBI_0000109). The term is defined as
subClassOf 'material to be added role' with subClass 'cloning vector role'.

The modeling of 'biological vector role' is outside of the scope of OBI if
it is meant to cover disease vectors in the wild and the current modeling
is incorrect as the only realization of this role would be in protocols,
but the definition implies that this could also happen in the wild.

The term seems in the IDO scope since 'vector organism' as relevant to
infectious diseases.

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Comment #1 on issue 42 by zhengj2...@gmail.com: biological vector role
https://code.google.com/p/infectious-disease-ontology/issues/detail?id=42

Related OBI tracker is:
https://sourceforge.net/p/obi/obi-terms/102/

[infectious-di...@googlecode.com]

Comment #2 on issue 42 by lindsay....@utsouthwestern.edu: biological vector
role
https://code.google.com/p/infectious-disease-ontology/issues/detail?id=42

If the term "biological vector role" from OBI is intended to cover the uses
of vectors in assays (like reporter vectors), then it may be quite
different from the relevant vector terms currently in IDO. I will start by
describing those so we can discuss possible changes that may be needed for
IDO or OBI.

Currently in IDO, we have the term "infectious agent vector role"
(http://purl.obolibrary.org/obo/IDO_0000417), which is defined as "An
infectious agent transporter role that is borne by an organism active in
the transfer of an infectious agent to an organism of another Species and
in which the agent is infectious." We include the following clarifying
comment: "The role is realized in a transmission process. A bearer of a
vector role is also a bearer of a host role."

For reference, the parent term, "infectious agent transporter role"
(http://purl.obolibrary.org/obo/IDO_0000417) is defined as "A role borne by
a material entity in virtue of the fact that an infectious agent is located
in or on the entity and the entity has the capability to transfer (either
actively or passively) the infectious agent from one location to another."
We include the following clarifying comment: "The role is realized in a
process that transfers an infectious organism from one location to another."

Also for reference, "transmission process", as referred to in the
clarifying comment associated with "infectious agent vector role", is a
term from the Transmission Ontology and is defined as follows "A process
that is the means during which the pathogen is transmitted directly or
indirectly from its natural reservoir, a susceptible host or source to a
new host."

Based on http://purl.obolibrary.org/obo/OBI_0000109, it sounds as if this
may be a term which could have the IDO term "infectious agent transporter
role" as a subtype, and then an OBI term corresponding to cloning vectors
etc also as a subtype. If others agree, the question is, where does the
parent term reside.

Thank you for raising the issue.

Lindsay

[infectious-di...@googlecode.com]

Comment #3 on issue 42 by zhengj2...@gmail.com: biological vector role
https://code.google.com/p/infectious-disease-ontology/issues/detail?id=42

Thanks for quick response. I will bring it back to OBI developers.

Jie