Hi Sean, Thanks for your help. So now I got my BSV file, but I don’t find the documentation that explains how to include it into the cTAKES analysis. Is there any document that can help me? Kind regards,
Erick > On Jan 23, 2018, at 5:21 PM, Finan, Sean <[email protected]> > wrote: > > 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:[email protected]] > Sent: Tuesday, January 23, 2018 5:15 PM > To: [email protected] > 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 <[email protected]> >> 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 <[email protected]> >> Sent: Monday, January 22, 2018 11:14 AM >> To: [email protected] >> 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 >
