I was using 2015AB. Can you copy/paste the error trace that junit gives you? Thanks Tim
On 01/29/2016 01:04 PM, Geise, Brandon D. wrote: > Very cool. > > I started going through your instructions. Everything seemed to be working > except for the GraphFunction Junit test fails on the first assertion. I'm > using 2015AA and it doesn't appear that the isa relationship holds true, > unless I messed something up. What UMLS version did you test with? > > Thanks, > Brandon > > -----Original Message----- > From: Miller, Timothy [mailto:[email protected]] > Sent: Tuesday, January 26, 2016 2:59 PM > To: [email protected] > Subject: umls graph api > > I've been working on some code for easy querying of the UMLS relation graph > that I think might be useful in ctakes. The repo is here: > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tmills_umls-2Dgraph-2Dapi&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=VF6tEMHRXUuomFk3Rma04eOozJC4amQHvm7PfAsXqvw&s=J_kg_cPwEhOWJIDI06-lORddJf83jmbb_I-MwkC_3Zg&e= > > > If you point it at your umls download you can build the db in about 5 minutes > (45 MB). Then the API has a class GraphFunctions with the following methods: > > public static List<String> getHypernyms(String cui); > public static List<String> getHyponyms(String cui); > public static boolean isa(String cui1, String cui2); > > These make use of just the "isa" relation in the MRREL file, and could tell > you, for example, that > > isa("C0007102", "C3662248") is true (colon cancer is a finding) but that > isa("C3662248", "C0007102") is not true. > > If people find it useful enough we may wish to add it to ctakes and perhaps > we could redistribute this view of the UMLS subject to the same username > checking we do now for the dictionary. We may wish to include other relations > and ontologies as well -- right now just SNOMED. But this is the skeleton and > I think with this starting point adding new capabilities will be pretty easy. > > Tim > > > > IMPORTANT WARNING: The information in this message (and the documents > attached to it, if any) is confidential and may be legally privileged. It is > intended solely for the addressee. Access to this message by anyone else is > unauthorized. If you are not the intended recipient, any disclosure, copying, > distribution or any action taken, or omitted to be taken, in reliance on it > is prohibited and may be unlawful. If you have received this message in > error, please delete all electronic copies of this message (and the documents > attached to it, if any), destroy any hard copies you may have created and > notify me immediately by replying to this email. Thank you. > > Geisinger Health System utilizes an encryption process to safeguard Protected > Health Information and other confidential data contained in external e-mail > messages. If email is encrypted, the recipient will receive an e-mail > instructing them to sign on to the Geisinger Health System Secure E-mail > Message Center to retrieve the encrypted e-mail. >
