That's the other weird thing. I don't see that either. Let me try to build the graph again.
-----Original Message----- From: Miller, Timothy [mailto:[email protected]] Sent: Friday, January 29, 2016 1:16 PM To: [email protected] Subject: Re: umls graph api I don't have 2015AA downloaded but I'll try to get it and see if I can reproduce. Before the test fails, do you see output from the other tests like: Ancestor (hypernym) is: C1304819 Ancestor (hypernym) is: C0346629 Ancestor (hypernym) is: C0009375 Ancestor (hypernym) is: C0009373 Ancestor (hypernym) is: C0006826 ... (many more lines like this) If so, it could be that it is indexing correctly but my test is 2015AB specific somehow. Tim On 01/29/2016 01:12 PM, Geise, Brandon D. wrote: > java.lang.AssertionError > at org.junit.Assert.fail(Assert.java:92) > at org.junit.Assert.assertTrue(Assert.java:43) > at org.junit.Assert.assertTrue(Assert.java:54) > at TestGraphFunctions.testHypernyms(TestGraphFunctions.java:38) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) > at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) > at java.lang.reflect.Method.invoke(Unknown Source) > at > org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:45) > at > org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15) > at > org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42) > at > org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20) > at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263) > at > org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:68) > at > org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:47) > at org.junit.runners.ParentRunner$3.run(ParentRunner.java:231) > at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:60) > at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:229) > at org.junit.runners.ParentRunner.access$000(ParentRunner.java:50) > at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:222) > at org.junit.runners.ParentRunner.run(ParentRunner.java:300) > at > org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:50) > at > org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38) > at > org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:459) > at > org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:675) > at > org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:382) > at > org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTest > Runner.java:192) > > -----Original Message----- > From: Miller, Timothy [mailto:[email protected]] > Sent: Friday, January 29, 2016 1:09 PM > To: [email protected] > Subject: Re: umls graph api > > 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_tmill >> s_umls-2Dgraph-2Dapi&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCo >> ppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6 >> 674h&m=VF6tEMHRXUuomFk3Rma04eOozJC4amQHvm7PfAsXqvw&s=J_kg_cPwEhOWJIDI >> 06-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. >> > >
