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infectious agent - organisms only #18

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Prions are normally included as infectious agents. IDO does not seem to
allow for that.

Original issue reported on code.google.com by bjoern.p...@gmail.com on 27 Oct 2009 at 2:24

GoogleCodeExporter commented 9 years ago 
we had prions originally but took them out, although i don't remember what the 
problems were.  i will make an 
note to add them again.

Original comment by lindsay....@utsouthwestern.edu on 27 Oct 2009 at 4:04

GoogleCodeExporter commented 9 years ago

Original comment by lindsay....@utsouthwestern.edu on 4 Nov 2010 at 3:52

GoogleCodeExporter commented 9 years ago 
Hi Lindsay,

When we just looked into the IDO definition, both the logical and textual still 
only refer to organism: 
http://www.ontobee.org/browser/rdf.php?o=IDO&iri=http://purl.obolibrary.org/obo/
IDO_0000596

Original comment by bjoern.p...@gmail.com on 6 May 2013 at 4:58

GoogleCodeExporter commented 9 years ago 
Hi Bjoern,

Thanks for your note.  This has been one of those hotbed issues where we go 
back and forth between "organism" and "material entity" to allow or disallow 
the inclusion of prions (and all sorts of other things).  No matter which way 
we go, someone is up in arms (I'm sure you have that experience with OBI).

For the record, when we use organism, prions are excluded, as you point out.  
When we use material entity, prions are included, which some people object to, 
but the primary complaint is that other kinds of things are then also allowed, 
such as the tasmanian devil face "cancer".

I think excluding prions will cause more problems for users and IDO 
compatibility with other resources than allowing tasmanian face cancers, so I 
will put revising the relevant terms in my queue.  

If anyone strongly objects let me know.

Thanks,

Lindsay

Original comment by lindsay....@utsouthwestern.edu on 6 May 2013 at 5:24

GoogleCodeExporter commented 9 years ago 
What's wrong with including the tasmanian devil face "cancer"?

On Mon, May 6, 2013 at 1:24 PM,
<infectious-disease-ontology@googlecode.com>wrote:

Original comment by alanruttenberg@gmail.com on 6 May 2013 at 9:29