To quickly get a larger mapping of ICD9 from all the SNOMED-CT codes that cTAKES finds I did a post processing step using the maps at: http://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html
-----Original Message----- From: Masanz, James J. [mailto:[email protected]] Sent: Wednesday, October 23, 2013 12:42 PM To: '[email protected]'; 'samir chabou' Subject: RE: Synonymous terms Maybe an example is best. There is a term in MeSH "Progeria-Like Syndrome" The CUI for that is C0009207 That term (using those words) does not appear in SNOMED-CT. But there is at least one SNOMED-CT term (Cockayne syndrome, with code 21086008) associated with that CUI within the UMLS metathesaurus. Therefore cTAKES will annotate "Progeria-Like Syndrome" with CUI C0009207and also cTAKES will list the SNOMED-CT codes that are associated with that CUI, even though none of the SNOMED-CT terms associated with the CUI C0009207 contain the word "like". However, the MeSH code (D003057) for "Progeria-Like Syndrome" will not be included within the CAS. Hope that helps -- James -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of samir chabou Sent: Tuesday, October 22, 2013 6:55 PM To: samir chabou; [email protected] Subject: Re: Synonymous terms sorry i'm having some problem with my e-mail correct me if i'm wrong. Based in what is said, when i do a lookup i'll get the term (entity, event for example) that can be from MeSH, ICD9 or NCI but the ontologyConceptArray will contains the codes synonyms in SNOMED-CT On Tuesday, October 22, 2013 12:23:06 PM, "Masanz, James J." <[email protected]> wrote: Just in case it wasn't clear, when I said it only contains SNOMED-CT codes, I pointing out that it doesn't have entries for ICD9 or MeSH or NCI Thesaurus, even though those are used when doing the dictionary lookup. I wasn't thinking about the codes vs. text part. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Chen, Pei Sent: Tuesday, October 22, 2013 11:17 AM To: [email protected]; 'samir chabou' Subject: RE: Synonymous terms > if I need to get term name do I have to do a lookup on umls ? FYI: I was proposing adding an additional attribute to store the description/preferredText(term) [1] since this information is already available in the dictionary lookup. I think most folks would find this useful in additional to just saving the CUI/Code. Otherwise, they would have to do another lookup further downstream to get the description of the CUI/Code. [1] https://issues.apache.org/jira/browse/CTAKES-224 --Pei > -----Original Message----- > From: Masanz, James J. [mailto:[email protected]] > Sent: Tuesday, October 22, 2013 10:57 AM > To: '[email protected]'; 'samir chabou' > Subject: RE: Synonymous terms > > > ontologyConceptArray only contains SNOMED-CT codes (except for > medications, where it contains RxNorm codes or CUIs) > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On > Behalf Of samir chabou > Sent: Monday, October 21, 2013 6:59 PM > To: [email protected] > Subject: Fw: Synonymous terms > > > > > > > On Monday, October 21, 2013 7:58:01 PM, samir chabou > <[email protected]> wrote: > > Synonymous > terms > > > > Given a C0001621 I need to get its synonyms terms for example in MeSH, > ICD, SNOMED (as shown bellow)…Is that possible ? > > > > Synonymous > terms Adrenal gland diseases MeSH D000307 Diseases of > the > adrenal glands SNOMED DB-70000 > ... > > Are the > synonyms kept in ontologyConceptArray ? If yes, then in the > ontologyConceptArray the information displayed is about identifier (code, > cui, tui, oid …) if I need to get term name do I have to do a lookup on umls ? > thanks > Samir IMPORTANT WARNING: Information contained in this email is intended for the use of the individual to whom it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is STRICTLY FORBIDDEN. If you have received this communication in error, please notify us immediately by return email and delete this document. Thank you.
