Re: Protoge 4 Question -- output all usage of an item within specific subclasses

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Re: Protoge 4 Question -- output all usage of an item within specific subclasses

Timothy Redmond
On 12/23/2013 12:29 PM, Lipori, Gigi wrote:
This worked great. Tried to add on  has_tc some 'Anti-emetic Agent [TC]’ to see if I could get a list of all the anti emetics, but that part didn’t work for me (just got the Anti-emetic class and not a list of drugs that map there). Any ideas on that one?

It may be because you phrased the query as

    has_tc some 'Anti-emetic Agent [TC]’

instead of

    has_TC some 'Anti-emetic Agent [TC]'


When I did the latter query I got exactly one class 'Antiemetic [EPC]'.

The tab character will give you completion options and this can be very useful.  It is particularly useful for me as I have no idea what the ontology means.  It is interesting because if I mention some of this to my wife she knows exactly what everything means.  (And gets the common-sense ideas like why you don't use an anti-psychotic to treat hiccups ;-)).

-Timothy



Sorry for my ignorance. Just learning. 

From: Timothy Redmond <[hidden email]>
Date: Sunday, December 22, 2013 at 2:15 AM
To: "Submit feedback for Protege 4.0 beta" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: FW: Protoge 4 Question -- output all usage of an item within specific subclasses

On 12/20/2013 09:17 AM, Lipori, Gigi Pflugfelder wrote:

From: <Lipori>, Gigi Lipori <[hidden email]>
Date: Friday, December 20, 2013 12:16 PM
To: "[hidden email]" <[hidden email]>
Subject: Protoge 4 Question -- output all usage of an item within specific subclasses

Using the NDF-RT ontology as an example, can I use the Protégé interface to export all drug names that may_treat or may_prevent nausea? By way of example in the screen below, I would want to show the usage of Nausea, but only for the drugs with the subclasses of may_prevent or may_treat, not those with a subclass of contraindicated_with. Truly appreciate any insights. 




This is not always pragmatic but the method I would like for this type of problem is to use a reasoner.  If you start a reasoner and go to the dl-query tab and enter:

      may_prevent some 'Nausea [Disease/Finding]' or may_treat some 'Nausea [Disease/Finding]'

and select "Direct sub-classes" you will get a list of things that treat or prevent nausea. 

The advantage of this is that the reasoner will figure out things that may require an extra step of inference which might be missed in a syntactic search.  A disadvantage of this approach is that inference can in some cases be expensive.

-Timothy


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