By the way, in case you are wondering why it does this … the umls database that we use has roughly half a million cuis. Storing cuis in the various tables as longs takes up a lot less space than storing them as 8 character strings.
From: britt fitch [mailto:britt.fi...@wiredinformatics.com] Sent: Wednesday, July 08, 2015 2:23 PM To: dev@ctakes.apache.org Subject: dictionary-look-fast fails to handle alternative CUIs This is largely directed to Sean but open to other feedback as well. The current fast lookup using a BSV parses the first field as “C” and up to 7 numerals, padding with “0" as needed to reach that length when applicable [see CuiCodeUtil.getCuiCode(String)] The CUI string is then substring’d from 1 to len and parsed as a Long. This is producing issues with other related, but separate, ontologies (MedGen) where the bulk of concepts use UMLS CUIs but some additional concepts were created by the NCBI where no CUI previously existed. These MedGen-specific concepts are created with a prefix “CN” + 6 numerals, resulting in “N123456” failing to produce a Long. I wanted Sean’s thoughts on this and to get some feedback on if others are running into this issue and if the community wants a solution to providing a CUI format beyond the standard C + 7 numerals. I’m happy to make these edits and check them in whether that means updating the CuiCodeUtil class or creating an entirely new BSVConceptFactory if thats what makes the most sense. Thoughts? Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com
