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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Building a dictionary from ontologies [EXTERNAL]
Date Tue, 23 Jan 2018 22:21:26 GMT
Hi Erick,

Each synonym gets a single line in the bsv file.  So:

OWL00770 | TOOO | Right parietal lobe
OWL00770 | TOOO | parietal lobe, right
OWL00770 | TOOO | parietal lobe on the right

If you don't have a tui then you can simplify the lines by leaving the second column empty:

OWL00770 | | Right parietal lobe
OWL00770 | | parietal lobe, right
OWL00770 | | parietal lobe on the right


Sean

-----Original Message-----
From: Erick Velazquez [mailto:erick.lerouge@gmail.com] 
Sent: Tuesday, January 23, 2018 5:15 PM
To: dev@ctakes.apache.org
Subject: Re: Building a dictionary from ontologies [EXTERNAL]

Hi Sean,

Thank you for your answer!

I would like to show you my results. As an example, I got this:

 

OWL00770 | TOOO | Right parietal lobe

 

The third column is the text.

You suggested to me to use the uri but what I get from the ontology is only a web link. Then,
I don’t use the preferred text option.

When you say that text should also contain synonyms what do you mean? That means that every
token in the text column is considered as a synonym? Then in my example, right would be interpreted
as a synonym of parietal and lob?

 

Kind regards,

 

Erick Velazquez 


> On Jan 22, 2018, at 2:47 PM, Finan, Sean <Sean.Finan@childrens.harvard.edu> wrote:
> 
> Hi Erick,
> 
> There is a fourth option that should work
> 
> cui | tui | text | preferredText
> 
> I would create an importer that creates a -fake- cui.  The cui need not (in this case
should not) start with 'C'.  So, I would import per-owl uri using something like OWL00001.
 
> 
> tui can be empty, in which case "T000" will be used, =forcing ctakes to create annotations
of unknown semantic type.  
> 
> text(s) should contain your synonym(s).
> 
> preferredText can be your owl uri.
> 
> This should allow you to fake it with an imported owl.  Upon deconstruction of the cas
you will want to look at the preferredTerm for each annotation and ignore the cui and tui.
> 
> Sean 
> 
> ________________________________________
> From: Erick Velazquez <erick.lerouge@gmail.com>
> Sent: Monday, January 22, 2018 11:14 AM
> To: dev@ctakes.apache.org
> Subject: Building a dictionary from ontologies  [EXTERNAL]
> 
> Hello,
> 
> I’m building a dictionary from an ontology (OWL), but there is no CUI, neither TUI
in the information. Since the format of a dictionary in cTAKES is CUI | TUI | TEXT, or CUI
| TEXT, is there any specification to create CUIs for terms?
> Thanks,
> 
> Erick

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