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From "Geise, Brandon D." <bdge...@geisinger.edu>
Subject RE: umls graph api
Date Fri, 29 Jan 2016 18:17:41 GMT
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:Timothy.Miller@childrens.harvard.edu] 
Sent: Friday, January 29, 2016 1:16 PM
To: dev@ctakes.apache.org
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

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.


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:Timothy.Miller@childrens.harvard.edu]
> Sent: Friday, January 29, 2016 1:09 PM
> To: dev@ctakes.apache.org
> 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:Timothy.Miller@childrens.harvard.edu]
>> Sent: Tuesday, January 26, 2016 2:59 PM
>> To: dev@ctakes.apache.org
>> 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
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