sml-xmlconf.xml

<sglib>
	<opt  threads = "10"  />

	<namespaces>
		<nm prefix="GO" ref="http://purl.org/obo/owl/GO#" />
	</namespaces>

	<graphs>    
		<graph uri="http://bio/"  >    
			<data>
				<file format="OBO"   path="data/external/go-basic-2017-10-04.obo"/>    
				<file format="GAF2"   path="data/external/goa_human-2017-09-26.gaf"/>    
			</data>

			<actions>
				<action type="VERTICES_REDUCTION" root_uri="http://purl.org/obo/owl/GO#0008150" />
				<action type="TRANSITIVE_REDUCTION" target="CLASSES" />
				<action type="TRANSITIVE_REDUCTION" target="INSTANCES" />
			</actions>
		</graph>    
	</graphs>

	<filters>
		<filter
			id = "filter_gaf_2"
			type = "GAF2"
			remove_ec="ISS,ISO,ISA,ISM,IGC,IBA,IBD,IKR,KRD,RCA,TAS,NAS,HTP,HDA,HMP,HGI,HEP"
		/>
	</filters>
	<sml module="sm" graph="http://bio/" >

		<opt_module threads="10" 	quiet = "true"
/>


		<ics>
			<ic id   = "resnik" flag = "IC_ANNOT_RESNIK_1995"  />
			<ic id   = "ic_prob_propagatted" flag = "ICI_PROB_OCCURENCE_PROPAGATED"  />
		</ics>

		<measures type = "pairwise">
			<measure   id   = "schlicker" flag = "SIM_PAIRWISE_DAG_NODE_SCHLICKER_2006"  ic = "resnik"  ic_prob = "ic_prob_propagatted" />
		</measures>

		<measures type = "groupwise">
			<measure   id   = "bma" flag = "SIM_GROUPWISE_BMA"  pairwise_measure = "schlicker"  />
		</measures>

		<queries id= "query" 
			type    = "oTOo" 
			file    = "tmp/kinome-all-vs-all.tsv" 
			output  = "out/go-bp-sem-sim-uniprot.tsv" 
			noAnnots = "set=-1"
			notFound = "set=-1"
			uri_prefix = "http://bio/"
			output_basename = "false" 
		/>
	</sml>
</sglib>