Dear Sir I updated the mail I sent before. On Tue, Aug 2, 2016 at 2:13 PM, Niraj Shrestha <[email protected]> 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 > > >
