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From Niraj Shrestha <nshrest...@gmail.com>
Subject Re: ctakes concept and relation extraction
Date Tue, 02 Aug 2016 13:03:05 GMT
Dear Sir
I updated the mail I sent before.

On Tue, Aug 2, 2016 at 2:13 PM, Niraj Shrestha <nshresthan@gmail.com> wrote:

> Dear Sir
> I am trying to extract named entities and their relations from medical
> document. If I understood correctly concepts are basically entities.
> I have used two different analysis engines:
>      AggregatePlaintextFastUMLSProcessor.xml for concept extraction and
>      RelationExtractorAggregate for relation extraction.
>
> My first question is how can I combined both engine to obtain concept and
> relations in single file.
>
> If I understood correctly, If I need to extract all the entities
> (concepts) then I need to get all the nodes
> "org.apache.ctakes.typesystem.type.refsem.UmlsConcept" from output xml
> file. But how can I choose the single entities or concept from list of many
> concepts?
>
> and What is FSArray in which all concept ids are listed.
>
> I found some concepts are not mentioned on input data but it appeared in
> the output data for example, when I use following engine in "note.txt" file
>
> <import
> location="../analysis_engine/AggregatePlaintextFastUMLSProcessor.xml"/>
> output file is "note.txt4.xml" (attached here)
>
> One of the concept is following, where "kidney" is mentioned as
> preferredText. (Text delete here)
>
> <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="4503"
> codingScheme="SNOMEDCT" code="64033007" oid="64033007#SNOMEDCT" score="0.0"
> disambiguated="false" cui="C0022646" tui="T023" preferredText="Kidney"/>
>     <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="4493"
> codingScheme="SNOMEDCT" code="17373004" oid="17373004#SNOMEDCT" score="0.0"
> disambiguated="false" cui="C0227665" tui="T023" preferredText="Both
> kidneys"/>
>     <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="4483"
> codingScheme="SNOMEDCT" code="181414000" oid="181414000#SNOMEDCT"
> score="0.0" disambiguated="false" cui="C1278978" tui="T023"
> preferredText="Entire kidney"/>
>     <uima.cas.FSArray _id="4513" size="3">
>         <i>4483</i>
>         <i>4493</i>
>         <i>4503</i>
>     </uima.cas.FSArray>
>

If I need to choose one of the concept from above how can I choose one?

>
>
> ************************************
> My next query concern with relation extraction for which I use following
> engine.
>
> <import
> location="../../../ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml"/>
> output file is "note.txt_relation.xml" (attached here)
>
> I am not able to interpret the output file (note.txt_relation.xml) in
> which relation and their location is mentioned but could not figure out
> which entities and what relation between those entities in terms of words.
>
> For eg:
>
> <org.apache.ctakes.typesystem.type.relation.RelationArgument _indexed="1"
> _id="12422" id="0" _ref_argument="10680" role="Argument"/>
>     <org.apache.ctakes.typesystem.type.relation.RelationArgument
> _indexed="1" _id="12427" id="0" _ref_argument="10989" role="Related_to"/>
>     <org.apache.ctakes.typesystem.type.relation.RelationArgument
> _indexed="1" _id="12446" id="0" _ref_argument="10680" role="Argument"/>
> .
> .
> .
> .
> <org.apache.ctakes.typesystem.type.relation.RelationArgument _indexed="1"
> _id="12851" id="0" _ref_argument="12181" role="Related_to"/>
>     <org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
> _indexed="1" _id="12432" id="0" category="location_of"
> discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" _ref_arg1="12422" _ref_arg2="12427"/>
>     <org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
> _indexed="1" _id="12456" id="0" category="location_of"
> discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" _ref_arg1="12446" _ref_arg2="12451"/>
>     <org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
> _indexed="1" _id="12480" id="0" category="location_of"
> discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" _ref_arg1="12470" _ref_arg2="12475"/>
>     <org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
> _indexed="1" _id="12508" id="0" category="location_of"
> discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" _ref_arg1="12498" _ref_arg2="12503"/>
>
>
> Sorry for long and many queries at once.
>
> Thanks a lot in advance for your suggetions.
>
> With regards,
> Shrestha
>
>
>

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