Phase: Bio_Entities
Input: Token SpaceToken Concept
Options: control = appelt

rule: BioConcept1
(
	(
		({Token.category == JJ} | {Token.category == JJR})
		{SpaceToken.kind == space}
	)*
	(
		({Token.category == NN} | {Token.category == NNS} | {Token.category == NNPS} | {Token.category == NNP})
		{SpaceToken.kind == space}
	)*
	({Token.string == cell} | {Token.string == neuron} | {Token.string == egg} |{Token.string == type} |{Token.string == types} | {Token.string == eggs} |{Token.string == lineage} |{Token.string == cells}|{Token.string == neurons}|{Token.string == glia} | {Token.string == glium})
):concept
-->
:concept.Concept = { rule = "BioConcept1" }

rule: BioConcept2
(
	(
		({Token.category == JJ} | {Token.category == JJR})
		{SpaceToken.kind == space}
	)*
	( 
		({Token.category == NNP} | {Token.category == NNPS} | {Token.category == NN} | {Token.category == NNS})	
		{SpaceToken.kind == space}
	)*
	({Token.category == NNP} | {Token.category == NNPS} | {Token.category == NN} | {Token.category == NNS}):noun
):concept
-->
{
	gate.AnnotationSet nouns = (gate.AnnotationSet)bindings.get( "noun" );
 	gate.AnnotationSet tokens = inputAS.get( nouns.firstNode().getOffset() ).get( "Token" );
	List tokensList = new ArrayList( tokens );
	Collections.sort( tokensList, new gate.util.OffsetComparator() );
	Iterator tokensIter = tokensList.iterator();
 	gate.Annotation token = (gate.Annotation)tokensIter.next();
 	String sToken = (String)token.getFeatures().get( "string" );
 	if( sToken.endsWith( "cyte" ) || sToken.endsWith( "blast" )  || sToken.endsWith("phage") 
		|| sToken.endsWith( "clast" )  || sToken.endsWith ( "glia" )
		|| sToken.endsWith( "clasts" ) || sToken.endsWith ( "blasts" )
		|| sToken.endsWith( "glium" )  || sToken.endsWith ( "phil" )
		|| sToken.endsWith( "gonia" )  || sToken.endsWith ( "gonium" )
 		|| sToken.endsWith( "cytes" )  || sToken.endsWith( "phages" ) )
 	{
 		try {
 			gate.AnnotationSet concept = (gate.AnnotationSet)bindings.get( "concept" );
 			outputAS.add( concept.firstNode().getOffset(), concept.lastNode().getOffset(), "Concept", Factory.newFeatureMap() );
 			gate.AnnotationSet concepts = inputAS.get( concept.firstNode().getOffset() ).get( "Concept" );
 			((gate.Annotation)concepts.iterator().next()).getFeatures().put( "rule", "BioConcept2" );
  		}
  		catch( InvalidOffsetException e ){
  			e.printStackTrace();
  		}
  	}
}

macro: BioConcept
(
	({BioConcept1}|{BioConcept2})
)