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From "Sean Finan (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-368) Allow alternate CUI formats in fast dictionary lookup module
Date Thu, 09 Jul 2015 19:43:05 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-368?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14621138#comment-14621138

Sean Finan commented on CTAKES-368:

Checked in code allowing custom cui prefixes.  Digit count for codes should remain constant
after prefixes.  For instance, "SPF001, SPF002, ... SPF999" and not "SPF1, SPF2, ... SPF999".

> Allow alternate CUI formats in fast dictionary lookup module
> ------------------------------------------------------------
>                 Key: CTAKES-368
>                 URL: https://issues.apache.org/jira/browse/CTAKES-368
>             Project: cTAKES
>          Issue Type: Improvement
>          Components: ctakes-dictionary-lookup
>    Affects Versions: 3.2.2
>            Reporter: britt fitch
>            Assignee: Sean Finan
>             Fix For: 3.2.3
> 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.
> It is preferred to allow alternative CUI formats.

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