Hi Britt, I’ve got some code and tests to check in. Would you like to write the jira item?
From: britt fitch [mailto:britt.fi...@wiredinformatics.com] Sent: Thursday, July 09, 2015 8:55 AM To: dev@ctakes.apache.org Subject: Re: dictionary-look-fast fails to handle alternative CUIs I don’t think that is too much of a constraint, at least initially, to have all CUI values a consistent length for a given prefix. Thanks Sean, let me know if there is any part of this you’d like a hand with. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com On Jul 8, 2015, at 7:16 PM, Finan, Sean <sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu>> wrote: Hi Britt, You’ve got it exactly. I actually started working on this right before a meeting right before I left work right before I went to the store … but I’m now back to it and I’m going to move forward with the tiny bot that I’ve got. I don’t think that it will take too long … One reason that I like the “pair” idea is that something like “CN123456” won’t get converted to “CN0123456” by assuming that it is a seven digit numerical base. Likewise somebody could make a tiny dictionary with “SEAN01, SEAN02, SEAN03…” through 99. Then their output would still be formatted as “SEAN01 .. SEAN99”. They couldn’t mix in “SEAN1, SEAN2 …” though. Is that too much of a restraint? Hmmm. Well, I’m going to push forward with this idea. I’ll check in whatever I get done tonight. Cheers, Sean From: britt fitch [mailto:britt.fi...@wiredinformatics.com] Sent: Wednesday, July 08, 2015 4:21 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: dictionary-look-fast fails to handle alternative CUIs Thanks for the details Sean. I had assumed the conversion to Long was related to sort/search efficiency but that makes sense. I had been thinking of something similar with parsing out the non-numerals and converting them to 2-digit numeral values. i.e. “a” = 01, “z” = 26. Ultimately CN123456 would become 0314123456 but I don’t think its sophisticated enough to avoid issues with leading zeros. We could prepend a 9 to it to avoid losing digits and use something like: if(length>8 && begins with 9) discard 9 while (length > 8) convert first 2 numbers to a letter I think your suggestion sounds good to me. To run the example through: “NLM300" gets parsed to “NLM” + “300” Store Pair<Integer,String>(3, NLM) at Pair[0] Produce a Long of 0x10000000 + 300 = 300L Backtrack to the actual “CUI” floor(300/10000000) = 0L 300L - 0L = 300L Pair[0] = NLM CUI = NLM + 300 In that case, do we need to store it as a Pair at all or is just storing the prefix in a String[] sufficient? I’m happy to start working on this unless you have a preference for splitting it out into multiple tasks. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com<mailto:britt.fi...@wiredinformatics.com><mailto:britt.fi...@wiredinformatics.com> On Jul 8, 2015, at 2:54 PM, Finan, Sean <sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu><mailto:sean.fi...@childrens.harvard.edu>> wrote: 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<mailto:dev@ctakes.apache.org><mailto: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<http://wiredinformatics.com/> britt.fi...@wiredinformatics.com<mailto:britt.fi...@wiredinformatics.com><mailto:britt.fi...@wiredinformatics.com>
