[CTAKES-368] Allow alternate CUI formats in fast dictionary lookup module

• Type: Improvement
• Status: Closed
• Priority: Major
• Resolution: Fixed
• Affects Version/s: 3.2.2
• Fix Version/s: 3.2.3
• Component/s: ctakes-dictionary-lookup
• Assignee: Sean Finan
• Reporter: britt fitch
• Created: 09/Jul/15 19:23
• Updated: 10/Jul/15 21:28
• Resolved: 10/Jul/15 21:28

Description

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.