<tool id="ncbo_annotator" name="Annotates a text with bio-ontology terms" version="1.0.1">
	<description>Annotates biological texts with the terms of the bio-ontologies from BioPortal</description>
	<command>java -jar ${__tool_data_path__}/shared/jars/ncbo_annotator_galaxy.jar $longestOnly $wholeWordOnly $filterNumber $stopWords $withDefaultStopWords $isTopWordsCaseSensitive $mintermSize $scored $withSynonyms $ontologiesToExpand $ontologiesToKeepInResult $semanticTypes $levelMax $mappingTypes $textToAnnotate $format $apikey > $output </command>
	<inputs>
		<param name="longestOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only the longest word"/>
		<param name="wholeWordOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only whole words"/>
		<param name="filterNumber" type="boolean" value="true" label="Tick the box if the Annotator should filter numbers before annotating the text"/>
		<param name="stopWords" type="text" value="" size="100" label="List the words that the Annotator should omit from the text"/>
		<param name="withDefaultStopWords" type="boolean" value="true" label="Tick the box if the Annotator should use the default list of stop words"/>
		<param name="isTopWordsCaseSensitive" type="boolean" value="false" label="Tick the box whether the stop words are case sensitive or not"/>
		<param name="mintermSize" type="integer" value="3" min="0" max="100" label="Indicates the minimum length for the terms to annotate"/>
		<param name="scored" type="boolean" value="true" label="Tick the box whether the Annotator should assign a numeric accuracy to each annotation or not"/>
		<param name="withSynonyms" type="boolean" value="true" label="Tick the box if the Annotator should use synonyms in the direct annotation"/>
		<param name="ontologiesToExpand" type="select" multiple="true" label="Indicates the list of ontologies to use with the mapping semantic expansion component">
			<option value="e-all" selected="true">ALL</option>
			<option value="e-1394">Syndromic Surveillance Ontology</option>
			<option value="e-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
			<option value="e-1158">Cell Behavior Ontology</option>
			<option value="e-1033">NMR-instrument specific component of metabolomics investigations</option>
			<option value="e-1351">Medical Subject Headings</option>
			<option value="e-1146">Electrocardiography Ontology</option>
			<option value="e-1041">Protein modification</option>
			<option value="e-1058">SNP-Ontology</option>
			<option value="e-1099">African Traditional Medicine</option>
			<option value="e-1134">BioTop</option>
			<option value="e-1247">GeoSpecies Ontology</option>
			<option value="e-1024">Loggerhead nesting</option>
			<option value="e-1257">MeGO</option>
			<option value="e-1135">Pseudogene</option>
			<option value="e-1126">Family Health History Ontology</option>
			<option value="e-1108">Plant structure</option>
			<option value="e-1114">Bilateria anatomy</option>
			<option value="e-1100">Ontology for Genetic Interval</option>
			<option value="e-1044">Sample processing and separation techniques</option>
			<option value="e-1347">MedlinePlus Health Topics</option>
			<option value="e-1152">Minimal anatomical terminology</option>
			<option value="e-1063">Common Anatomy Reference Ontology</option>
			<option value="e-1089">BIRNLex</option>
			<option value="e-1116">Bleeding History Phenotype</option>
			<option value="e-1104">Biomedical Resource Ontology</option>
			<option value="e-1350">Logical Observation Identifier Names and Codes</option>
			<option value="e-1082">Gene Regulation Ontology</option>
			<option value="e-1047">Cereal plant development</option>
			<option value="e-1349">Physician Data Query</option>
			<option value="e-1190">Parasite Life Cycle</option>
			<option value="e-1192">Proteomics Pipeline Infrastructure for CPTAC</option>
			<option value="e-1352">National Drug File</option>
			<option value="e-1059">Computer-based Patient Record Ontology</option>
			<option value="e-1052">Protein Ontology</option>
			<option value="e-1341">COSTART</option>
			<option value="e-1344">International Classification of Primary Care</option>
			<option value="e-1061">Suggested Ontology for Pharmacogenomics</option>
			<option value="e-1353">SNOMED Clinical Terms</option>
			<option value="e-1224">Symptom Ontology</option>
			<option value="e-1013">eVOC (Expressed Sequence Annotation for Humans)</option>
			<option value="e-1149">DermLex: The Dermatology Lexicon</option>
			<option value="e-1311">Malaria Ontology</option>
			<option value="e-1335">Parasite Experiment Ontology</option>
			<option value="e-1370">Amphibian taxonomy</option>
			<option value="e-1354">WHO Adverse Reaction Terminology</option>
			<option value="e-1148">BioPortal Metadata</option>
			<option value="e-1038">Plant growth and developmental stage</option>
			<option value="e-1132">NCBI organismal classification</option>
			<option value="e-1328">Ontology of homology and related concepts in biology</option>
			<option value="e-1290">ABA Adult Mouse Brain</option>
			<option value="e-1055">Galen</option>
			<option value="e-1332">Basic Formal Ontology</option>
			<option value="e-1183">Lipid Ontology</option>
			<option value="e-1026">Multiple alignment</option>
			<option value="e-1130">Cancer Research and Management ACGT Master Ontology</option>
			<option value="e-1060">Epoch Clinical Trial Ontologies</option>
			<option value="e-1369">PhysicalFields</option>
			<option value="e-1086">Ontology for disease genetic investigation</option>
			<option value="e-1122">Skin Physiology Ontology</option>
			<option value="e-1142">Cardiac Electrophysiology Ontology</option>
			<option value="e-1128">Comparative Data Analysis Ontology</option>
			<option value="e-1088">MaHCO - An MHC Ontology</option>
			<option value="e-1249">Smoking Behavior Risk Ontology</option>
			<option value="e-1039">Proteomics data and process provenance</option>
			<option value="e-1040">Protein-protein interaction</option>
			<option value="e-1068">Subcellular Anatomy Ontology (SAO)</option>
			<option value="e-1087">Ontology of Geographical Region</option>
			<option value="e-1094">Pathogen transmission</option>
			<option value="e-1131">MGED Ontology</option>
			<option value="e-1106">Gene Regulation Ontology</option>
			<option value="e-1054">Amino Acid</option>
			<option value="e-1056">Basic Vertebrate Anatomy</option>
			<option value="e-1083">NanoParticle Ontology</option>
			<option value="e-1053">Foundational Model of Anatomy</option>
			<option value="e-1092">Infectious disease</option>
			<option value="e-1393">Information Artifact Ontology</option>
			<option value="e-1395">MDSS Mo</option>
			<option value="e-1397">Gazetteer</option>
			<option value="e-1398">Ontology of Language Disorder in Autism</option>
			<option value="e-1399">Pilot Ontology</option>
			<option value="e-1406">linkingkin2pep</option>
			<option value="e-1409">PKO_Re</option>
			<option value="e-1410">Kinetic Simulation Algorithm Ontology</option>
			<option value="e-1415">Common Terminology Criteria for Adverse Events</option>
			<option value="e-1418">TOK_Ontology</option>
			<option value="e-1419">Taxonomic rank vocabulary</option>
			<option value="e-1422">MedDRA</option>
			<option value="e-1424">National Drug Data File</option>
			<option value="e-1425">ICD-10-PCS</option>
			<option value="e-1426">Master Drug Data Base</option>
			<option value="e-1429">ICPC-2 PLUS</option>
			<option value="e-1430">AIR</option>
			<option value="e-1438">Breast tissue cell lines</option>
			<option value="e-1439">General Formal Ontology</option>
			<option value="e-1440">General Formal Ontology: Biology</option>
			<option value="e-1343">Health Level Seven</option>
			<option value="e-1484">International Classification of  External Causes of Injuries</option>
			<option value="e-1487">Body System</option>
			<option value="e-1490">Platynereis stage ontology</option>
			<option value="e-1491">IMGT-ONTOLOGY</option>
			<option value="e-1494">Tissue Microarray Ontology</option>
			<option value="e-1497">PMA 2010</option>
			<option value="e-1500">RNA ontology</option>
			<option value="e-1501">Neomark Oral Cancer-Centred Ontology</option>
			<option value="e-1504">Current Procedural Terminology</option>
			<option value="e-1505">Ontology for MicroRNA Target Prediction</option>
			<option value="e-1506">Gene Ontology Extension</option>
			<option value="e-1507">Cell Cycle Ontology</option>
			<option value="e-1509">ICPS Network</option>
			<option value="e-1510">Metathesaurus CPT Hierarchical Terms</option>
			<option value="e-1515">Interaction Network Ontology</option>
			<option value="e-1516">ICD10</option>
			<option value="e-1521">Neural Motor Recovery Ontology</option>
			<option value="e-1522">BioPAX</option>
			<option value="e-1523">OBOE SBC</option>
			<option value="e-1524">OBOE</option>
			<option value="e-1526">CRISP Thesaurus, 2006</option>
			<option value="e-1527">VANDF</option>
			<option value="e-1528">HUGO</option>
			<option value="e-1529">HCPCS</option>
			<option value="e-1530">Animal natural history and life history</option>
			<option value="e-1534">apollo-akesios</option>
			<option value="e-1537">Brucellosis Ontology</option>
			<option value="e-1538">Role Ontology</option>
			<option value="e-1539">Neural-Immune Gene Ontology</option>
			<option value="e-1540">Ontology for Drug Discovery Investigations</option>
			<option value="e-1541">Cell line ontology</option>
			<option value="e-1545">Wheat trait </option>
			<option value="e-1547">BRENDA tissue / enzyme source</option>
			<option value="e-1552">Reproductive traits ontology</option>
			<option value="e-1553">ICD10CM</option>
			<option value="e-1560">Cognitive Paradigm Ontology</option>
			<option value="e-1423">RxNORM</option>
			<option value="e-1517">Human developmental anatomy, abstract version, v2</option>
			<option value="e-1016">Drosophila development</option>
			<option value="e-1062">PRotein Ontology (PRO)</option>
			<option value="e-1000">Mouse adult gross anatomy</option>
			<option value="e-1065">Tick gross anatomy</option>
			<option value="e-1123">Ontology for Biomedical Investigations</option>
			<option value="e-1078">Spatial Ontology</option>
			<option value="e-1007">Chemical entities of biological interest</option>
			<option value="e-1049">C. elegans development</option>
			<option value="e-1070">Gene Ontology</option>
			<option value="e-1136">Experimental Factor Ontology</option>
			<option value="e-1141">Ontology of Physics for Biology</option>
			<option value="e-1005">BRENDA tissue / enzyme source</option>
			<option value="e-1321">Neural ElectroMagnetic Ontologies</option>
			<option value="e-1043">Physico-chemical process</option>
			<option value="e-1064">Fly taxonomy</option>
			<option value="e-1076">Ontology of Clinical Research (OCRe)</option>
			<option value="e-1110">Teleost Anatomy Ontology</option>
			<option value="e-1362">Hymenoptera Anatomy Ontology</option>
			<option value="e-1030">Mosquito gross anatomy</option>
			<option value="e-1029">Molecule role (INOH Protein name/family name ontology)</option>
			<option value="e-1144">Dendritic cell</option>
			<option value="e-1125">Human Phenotype Ontology</option>
			<option value="e-1023">Biological imaging methods</option>
			<option value="e-1021">Human developmental anatomy, abstract version</option>
			<option value="e-1046">Systems Biology</option>
			<option value="e-1051">Zebrafish anatomy and development</option>
			<option value="e-1037">Cereal plant trait</option>
			<option value="e-1107">Phenotypic quality</option>
			<option value="e-1081">Teleost taxonomy</option>
			<option value="e-1048">C. elegans gross anatomy</option>
			<option value="e-1050">Maize gross anatomy</option>
			<option value="e-1036">Plant environmental conditions</option>
			<option value="e-1109">Sequence types and features</option>
			<option value="e-1022">Human developmental anatomy, timed version</option>
			<option value="e-1095">Xenopus anatomy and development</option>
			<option value="e-1027">Medaka fish anatomy and development</option>
			<option value="e-1011">Event (INOH pathway ontology)</option>
			<option value="e-1010">Mouse gross anatomy and development</option>
			<option value="e-1015">Drosophila gross anatomy</option>
			<option value="e-1090">Amphibian gross anatomy</option>
			<option value="e-1019">Fungal gross anatomy</option>
			<option value="e-1067">C. elegans phenotype</option>
			<option value="e-1069">Environment Ontology</option>
			<option value="e-1112">Units of measurement</option>
			<option value="e-1091">Spider Ontology</option>
			<option value="e-1017">FlyBase Controlled Vocabulary</option>
			<option value="e-1348">Online Mendelian Inheritance in Man</option>
			<option value="e-1172">Vaccine Ontology</option>
			<option value="e-1222">Ascomycete phenotype ontology</option>
			<option value="e-1105">Mass spectrometry</option>
			<option value="e-1237">Situation-Based Access Control</option>
			<option value="e-1008">Dictyostelium discoideum anatomy</option>
			<option value="e-1150">Rat Strain Ontology</option>
			<option value="e-1101">International Classification of Diseases</option>
			<option value="e-1314">Cell Line Ontology</option>
			<option value="e-1009">Human disease</option>
			<option value="e-1084">NIFSTD</option>
			<option value="e-1025">Mammalian phenotype</option>
			<option value="e-1035">Pathway ontology</option>
			<option value="e-1012">Evidence codes</option>
			<option value="e-1115">Yeast phenotypes</option>
			<option value="e-1001">Cereal plant gross anatomy</option>
			<option value="e-1006">Cell type</option>
			<option value="e-1077">Mosquito insecticide resistance</option>
			<option value="e-1085">Ontology of Glucose Metabolism Disorder</option>
			<option value="e-1057">RadLex</option>
			<option value="e-1031">Mouse pathology</option>
			<option value="e-1032">NCI Thesaurus</option>
			<option value="e-1381">NIF Dysfunction</option>
			<option value="e-1401">International Classification for Nursing Practice</option>
			<option value="e-1402">NIF Cell</option>
			<option value="e-1404">Uber anatomy ontology</option>
			<option value="e-1407">Terminology for the Description of Dynamics</option>
			<option value="e-1411">International Classification of Functioning, Disability and Health (ICF)</option>
			<option value="e-1413">Software Ontology</option>
			<option value="e-1414">Ontology for General Medical Science</option>
			<option value="e-1444">Chemical Information Ontology</option>
			<option value="e-1461">Translational Medicine Ontology</option>
			<option value="e-1488">SysMO-JERM</option>
			<option value="e-1489">Adverse Event Ontology</option>
			<option value="e-1498">EDAM</option>
			<option value="e-1532">SemanticScience Integrated Ontology</option>
			<option value="e-1550">PHARE</option>
			<option value="e-1555">Vertebrate Anatomy Ontology</option>
			<option value="e-1565">Ontology of Medically Related Social Entities</option>
			<option value="e-1567">Pharmacovigilance Ontology</option>
			<option value="e-1568">Anatomical Entity Ontology</option>
			<option value="e-1569">Host Pathogen Interactions Ontology</option>
			<option value="e-1570">Traditional Medicine Constitution Value Set</option>
			<option value="e-1571">Traditional Medicine Other Factors Value Set</option>
			<option value="e-1572">Traditional Medicine Signs and Symptoms Value Set</option>
			<option value="e-1573">Traditional Medicine Meridian Value Sets</option>
			<option value="e-1574">vertebrate Homologous Organ Groups</option>
			<option value="e-1575">ExO</option>
			<option value="e-1576">FDA Medical Devices (2010)</option>
			<option value="e-1578">HOM_ElixhauserScores</option>
			<option value="e-1580">Adverse Event Reporting ontology</option>
			<option value="e-1581">HEALTH_INDICATORS</option>
			<option value="e-1582">COA</option>
			<option value="e-1583">Clinical Measurement Ontology</option>
			<option value="e-1584">Measurement Method Ontology</option>
			<option value="e-1585">Experimental Conditions Ontology</option>
			<option value="e-1587">Plant Ontology</option>
			<option value="e-1588">Ontology of General Purpose Datatypes</option>
			<option value="e-1596">MajDxCatgrs-DxRltdGrps</option>
			<option value="e-1613">Bone Dysplasia Ontology</option>
			<option value="e-1614">IxnO</option>
			<option value="e-1615">Systems Chemical Biology/Chemogenomics </option>
			<option value="e-1616">Phylogenetic Ontology</option>
			<option value="e-1621">Neuro Behavior Ontology</option>
		</param>
		<param name="ontologiesToKeepInResult" type="select" multiple="true" label="Indicates the list of ontologies to keep in the result of the annotation process">
			<option value="k-all" selected="true">ALL</option>
			<option value="k-1394">Syndromic Surveillance Ontology</option>
			<option value="k-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
			<option value="k-1158">Cell Behavior Ontology</option>
			<option value="k-1033">NMR-instrument specific component of metabolomics investigations</option>
			<option value="k-1351">Medical Subject Headings</option>
			<option value="k-1146">Electrocardiography Ontology</option>
			<option value="k-1041">Protein modification</option>
			<option value="k-1058">SNP-Ontology</option>
			<option value="k-1099">African Traditional Medicine</option>
			<option value="k-1134">BioTop</option>
			<option value="k-1247">GeoSpecies Ontology</option>
			<option value="k-1024">Loggerhead nesting</option>
			<option value="k-1257">MeGO</option>
			<option value="k-1135">Pseudogene</option>
			<option value="k-1126">Family Health History Ontology</option>
			<option value="k-1108">Plant structure</option>
			<option value="k-1114">Bilateria anatomy</option>
			<option value="k-1100">Ontology for Genetic Interval</option>
			<option value="k-1044">Sample processing and separation techniques</option>
			<option value="k-1347">MedlinePlus Health Topics</option>
			<option value="k-1152">Minimal anatomical terminology</option>
			<option value="k-1063">Common Anatomy Reference Ontology</option>
			<option value="k-1089">BIRNLex</option>
			<option value="k-1116">Bleeding History Phenotype</option>
			<option value="k-1104">Biomedical Resource Ontology</option>
			<option value="k-1350">Logical Observation Identifier Names and Codes</option>
			<option value="k-1082">Gene Regulation Ontology</option>
			<option value="k-1047">Cereal plant development</option>
			<option value="k-1349">Physician Data Query</option>
			<option value="k-1190">Parasite Life Cycle</option>
			<option value="k-1192">Proteomics Pipeline Infrastructure for CPTAC</option>
			<option value="k-1352">National Drug File</option>
			<option value="k-1059">Computer-based Patient Record Ontology</option>
			<option value="k-1052">Protein Ontology</option>
			<option value="k-1341">COSTART</option>
			<option value="k-1344">International Classification of Primary Care</option>
			<option value="k-1061">Suggested Ontology for Pharmacogenomics</option>
			<option value="k-1353">SNOMED Clinical Terms</option>
			<option value="k-1224">Symptom Ontology</option>
			<option value="k-1013">eVOC (Expressed Sequence Annotation for Humans)</option>
			<option value="k-1149">DermLex: The Dermatology Lexicon</option>
			<option value="k-1311">Malaria Ontology</option>
			<option value="k-1335">Parasite Experiment Ontology</option>
			<option value="k-1370">Amphibian taxonomy</option>
			<option value="k-1354">WHO Adverse Reaction Terminology</option>
			<option value="k-1148">BioPortal Metadata</option>
			<option value="k-1038">Plant growth and developmental stage</option>
			<option value="k-1132">NCBI organismal classification</option>
			<option value="k-1328">Ontology of homology and related concepts in biology</option>
			<option value="k-1290">ABA Adult Mouse Brain</option>
			<option value="k-1055">Galen</option>
			<option value="k-1332">Basic Formal Ontology</option>
			<option value="k-1183">Lipid Ontology</option>
			<option value="k-1026">Multiple alignment</option>
			<option value="k-1130">Cancer Research and Management ACGT Master Ontology</option>
			<option value="k-1060">Epoch Clinical Trial Ontologies</option>
			<option value="k-1369">PhysicalFields</option>
			<option value="k-1086">Ontology for disease genetic investigation</option>
			<option value="k-1122">Skin Physiology Ontology</option>
			<option value="k-1142">Cardiac Electrophysiology Ontology</option>
			<option value="k-1128">Comparative Data Analysis Ontology</option>
			<option value="k-1088">MaHCO - An MHC Ontology</option>
			<option value="k-1249">Smoking Behavior Risk Ontology</option>
			<option value="k-1039">Proteomics data and process provenance</option>
			<option value="k-1040">Protein-protein interaction</option>
			<option value="k-1068">Subcellular Anatomy Ontology (SAO)</option>
			<option value="k-1087">Ontology of Geographical Region</option>
			<option value="k-1094">Pathogen transmission</option>
			<option value="k-1131">MGED Ontology</option>
			<option value="k-1106">Gene Regulation Ontology</option>
			<option value="k-1054">Amino Acid</option>
			<option value="k-1056">Basic Vertebrate Anatomy</option>
			<option value="k-1083">NanoParticle Ontology</option>
			<option value="k-1053">Foundational Model of Anatomy</option>
			<option value="k-1092">Infectious disease</option>
			<option value="k-1393">Information Artifact Ontology</option>
			<option value="k-1395">MDSS Mo</option>
			<option value="k-1397">Gazetteer</option>
			<option value="k-1398">Ontology of Language Disorder in Autism</option>
			<option value="k-1399">Pilot Ontology</option>
			<option value="k-1406">linkingkin2pep</option>
			<option value="k-1409">PKO_Re</option>
			<option value="k-1410">Kinetic Simulation Algorithm Ontology</option>
			<option value="k-1415">Common Terminology Criteria for Adverse Events</option>
			<option value="k-1418">TOK_Ontology</option>
			<option value="k-1419">Taxonomic rank vocabulary</option>
			<option value="k-1422">MedDRA</option>
			<option value="k-1424">National Drug Data File</option>
			<option value="k-1425">ICD-10-PCS</option>
			<option value="k-1426">Master Drug Data Base</option>
			<option value="k-1429">ICPC-2 PLUS</option>
			<option value="k-1430">AIR</option>
			<option value="k-1438">Breast tissue cell lines</option>
			<option value="k-1439">General Formal Ontology</option>
			<option value="k-1440">General Formal Ontology: Biology</option>
			<option value="k-1343">Health Level Seven</option>
			<option value="k-1484">International Classification of  External Causes of Injuries</option>
			<option value="k-1487">Body System</option>
			<option value="k-1490">Platynereis stage ontology</option>
			<option value="k-1491">IMGT-ONTOLOGY</option>
			<option value="k-1494">Tissue Microarray Ontology</option>
			<option value="k-1497">PMA 2010</option>
			<option value="k-1500">RNA ontology</option>
			<option value="k-1501">Neomark Oral Cancer-Centred Ontology</option>
			<option value="k-1504">Current Procedural Terminology</option>
			<option value="k-1505">Ontology for MicroRNA Target Prediction</option>
			<option value="k-1506">Gene Ontology Extension</option>
			<option value="k-1507">Cell Cycle Ontology</option>
			<option value="k-1509">ICPS Network</option>
			<option value="k-1510">Metathesaurus CPT Hierarchical Terms</option>
			<option value="k-1515">Interaction Network Ontology</option>
			<option value="k-1516">ICD10</option>
			<option value="k-1521">Neural Motor Recovery Ontology</option>
			<option value="k-1522">BioPAX</option>
			<option value="k-1523">OBOE SBC</option>
			<option value="k-1524">OBOE</option>
			<option value="k-1526">CRISP Thesaurus, 2006</option>
			<option value="k-1527">VANDF</option>
			<option value="k-1528">HUGO</option>
			<option value="k-1529">HCPCS</option>
			<option value="k-1530">Animal natural history and life history</option>
			<option value="k-1534">apollo-akesios</option>
			<option value="k-1537">Brucellosis Ontology</option>
			<option value="k-1538">Role Ontology</option>
			<option value="k-1539">Neural-Immune Gene Ontology</option>
			<option value="k-1540">Ontology for Drug Discovery Investigations</option>
			<option value="k-1541">Cell line ontology</option>
			<option value="k-1545">Wheat trait </option>
			<option value="k-1547">BRENDA tissue / enzyme source</option>
			<option value="k-1552">Reproductive traits ontology</option>
			<option value="k-1553">ICD10CM</option>
			<option value="k-1560">Cognitive Paradigm Ontology</option>
			<option value="k-1423">RxNORM</option>
			<option value="k-1517">Human developmental anatomy, abstract version, v2</option>
			<option value="k-1016">Drosophila development</option>
			<option value="k-1062">PRotein Ontology (PRO)</option>
			<option value="k-1000">Mouse adult gross anatomy</option>
			<option value="k-1065">Tick gross anatomy</option>
			<option value="k-1123">Ontology for Biomedical Investigations</option>
			<option value="k-1078">Spatial Ontology</option>
			<option value="k-1007">Chemical entities of biological interest</option>
			<option value="k-1049">C. elegans development</option>
			<option value="k-1070">Gene Ontology</option>
			<option value="k-1136">Experimental Factor Ontology</option>
			<option value="k-1141">Ontology of Physics for Biology</option>
			<option value="k-1005">BRENDA tissue / enzyme source</option>
			<option value="k-1321">Neural ElectroMagnetic Ontologies</option>
			<option value="k-1043">Physico-chemical process</option>
			<option value="k-1064">Fly taxonomy</option>
			<option value="k-1076">Ontology of Clinical Research (OCRe)</option>
			<option value="k-1110">Teleost Anatomy Ontology</option>
			<option value="k-1362">Hymenoptera Anatomy Ontology</option>
			<option value="k-1030">Mosquito gross anatomy</option>
			<option value="k-1029">Molecule role (INOH Protein name/family name ontology)</option>
			<option value="k-1144">Dendritic cell</option>
			<option value="k-1125">Human Phenotype Ontology</option>
			<option value="k-1023">Biological imaging methods</option>
			<option value="k-1021">Human developmental anatomy, abstract version</option>
			<option value="k-1046">Systems Biology</option>
			<option value="k-1051">Zebrafish anatomy and development</option>
			<option value="k-1037">Cereal plant trait</option>
			<option value="k-1107">Phenotypic quality</option>
			<option value="k-1081">Teleost taxonomy</option>
			<option value="k-1048">C. elegans gross anatomy</option>
			<option value="k-1050">Maize gross anatomy</option>
			<option value="k-1036">Plant environmental conditions</option>
			<option value="k-1109">Sequence types and features</option>
			<option value="k-1022">Human developmental anatomy, timed version</option>
			<option value="k-1095">Xenopus anatomy and development</option>
			<option value="k-1027">Medaka fish anatomy and development</option>
			<option value="k-1011">Event (INOH pathway ontology)</option>
			<option value="k-1010">Mouse gross anatomy and development</option>
			<option value="k-1015">Drosophila gross anatomy</option>
			<option value="k-1090">Amphibian gross anatomy</option>
			<option value="k-1019">Fungal gross anatomy</option>
			<option value="k-1067">C. elegans phenotype</option>
			<option value="k-1069">Environment Ontology</option>
			<option value="k-1112">Units of measurement</option>
			<option value="k-1091">Spider Ontology</option>
			<option value="k-1017">FlyBase Controlled Vocabulary</option>
			<option value="k-1348">Online Mendelian Inheritance in Man</option>
			<option value="k-1172">Vaccine Ontology</option>
			<option value="k-1222">Ascomycete phenotype ontology</option>
			<option value="k-1105">Mass spectrometry</option>
			<option value="k-1237">Situation-Based Access Control</option>
			<option value="k-1008">Dictyostelium discoideum anatomy</option>
			<option value="k-1150">Rat Strain Ontology</option>
			<option value="k-1101">International Classification of Diseases</option>
			<option value="k-1314">Cell Line Ontology</option>
			<option value="k-1009">Human disease</option>
			<option value="k-1084">NIFSTD</option>
			<option value="k-1025">Mammalian phenotype</option>
			<option value="k-1035">Pathway ontology</option>
			<option value="k-1012">Evidence codes</option>
			<option value="k-1115">Yeast phenotypes</option>
			<option value="k-1001">Cereal plant gross anatomy</option>
			<option value="k-1006">Cell type</option>
			<option value="k-1077">Mosquito insecticide resistance</option>
			<option value="k-1085">Ontology of Glucose Metabolism Disorder</option>
			<option value="k-1057">RadLex</option>
			<option value="k-1031">Mouse pathology</option>
			<option value="k-1032">NCI Thesaurus</option>
			<option value="k-1381">NIF Dysfunction</option>
			<option value="k-1401">International Classification for Nursing Practice</option>
			<option value="k-1402">NIF Cell</option>
			<option value="k-1404">Uber anatomy ontology</option>
			<option value="k-1407">Terminology for the Description of Dynamics</option>
			<option value="k-1411">International Classification of Functioning, Disability and Health (ICF)</option>
			<option value="k-1413">Software Ontology</option>
			<option value="k-1414">Ontology for General Medical Science</option>
			<option value="k-1444">Chemical Information Ontology</option>
			<option value="k-1461">Translational Medicine Ontology</option>
			<option value="k-1488">SysMO-JERM</option>
			<option value="k-1489">Adverse Event Ontology</option>
			<option value="k-1498">EDAM</option>
			<option value="k-1532">SemanticScience Integrated Ontology</option>
			<option value="k-1550">PHARE</option>
			<option value="k-1555">Vertebrate Anatomy Ontology</option>
			<option value="k-1565">Ontology of Medically Related Social Entities</option>
			<option value="k-1567">Pharmacovigilance Ontology</option>
			<option value="k-1568">Anatomical Entity Ontology</option>
			<option value="k-1569">Host Pathogen Interactions Ontology</option>
			<option value="k-1570">Traditional Medicine Constitution Value Set</option>
			<option value="k-1571">Traditional Medicine Other Factors Value Set</option>
			<option value="k-1572">Traditional Medicine Signs and Symptoms Value Set</option>
			<option value="k-1573">Traditional Medicine Meridian Value Sets</option>
			<option value="k-1574">vertebrate Homologous Organ Groups</option>
			<option value="k-1575">ExO</option>
			<option value="k-1576">FDA Medical Devices (2010)</option>
			<option value="k-1578">HOM_ElixhauserScores</option>
			<option value="k-1580">Adverse Event Reporting ontology</option>
			<option value="k-1581">HEALTH_INDICATORS</option>
			<option value="k-1582">COA</option>
			<option value="k-1583">Clinical Measurement Ontology</option>
			<option value="k-1584">Measurement Method Ontology</option>
			<option value="k-1585">Experimental Conditions Ontology</option>
			<option value="k-1587">Plant Ontology</option>
			<option value="k-1588">Ontology of General Purpose Datatypes</option>
			<option value="k-1596">MajDxCatgrs-DxRltdGrps</option>
			<option value="k-1613">Bone Dysplasia Ontology</option>
			<option value="k-1614">IxnO</option>
			<option value="k-1615">Systems Chemical Biology/Chemogenomics </option>
			<option value="k-1616">Phylogenetic Ontology</option>
			<option value="k-1621">Neuro Behavior Ontology</option>
		</param>
		<param name="semanticTypes" type="select" multiple="true" label="Indicates the list of semantic types to use in the annotation process">
			<option value="T-all" selected="true">ALL</option>
			<option value="T000">UMLS concept</option>
			<option value="T998">Jax Mouse/Human Gene dictionary concept</option>
			<option value="T999">NCBO BioPortal concept</option>
			<option value="T116">Amino Acid, Peptide, or Protein</option>
			<option value="T121">Pharmacologic Substance</option>
			<option value="T130">Indicator, Reagent, or Diagnostic Aid</option>
			<option value="T119">Lipid</option>
			<option value="T126">Enzyme</option>
			<option value="T123">Biologically Active Substance</option>
			<option value="T109">Organic Chemical</option>
			<option value="T131">Hazardous or Poisonous Substance</option>
			<option value="T110">Steroid</option>
			<option value="T125">Hormone</option>
			<option value="T114">Nucleic Acid, Nucleoside, or Nucleotide</option>
			<option value="T111">Eicosanoid</option>
			<option value="T118">Carbohydrate</option>
			<option value="T124">Neuroreactive Substance or Biogenic Amine</option>
			<option value="T127">Vitamin</option>
			<option value="T195">Antibiotic</option>
			<option value="T129">Immunologic Factor</option>
			<option value="T024">Tissue</option>
			<option value="T115">Organophosphorus Compound</option>
			<option value="T073">Manufactured Object</option>
			<option value="T081">Quantitative Concept</option>
			<option value="T170">Intellectual Product</option>
			<option value="T029">Body Location or Region</option>
			<option value="T184">Sign or Symptom</option>
			<option value="T033">Finding</option>
			<option value="T037">Injury or Poisoning</option>
			<option value="T191">Neoplastic Process</option>
			<option value="T023">Body Part, Organ, or Organ Component</option>
			<option value="T005">Virus</option>
			<option value="T047">Disease or Syndrome</option>
			<option value="T019">Congenital Abnormality</option>
			<option value="T169">Functional Concept</option>
			<option value="T190">Anatomical Abnormality</option>
			<option value="T022">Body System</option>
			<option value="T018">Embryonic Structure</option>
			<option value="T101">Patient or Disabled Group</option>
			<option value="T093">Health Care Related Organization</option>
			<option value="T089">Regulation or Law</option>
			<option value="T061">Therapeutic or Preventive Procedure</option>
			<option value="T062">Research Activity</option>
			<option value="T046">Pathologic Function</option>
			<option value="T041">Mental Process</option>
			<option value="T055">Individual Behavior</option>
			<option value="T004">Fungus</option>
			<option value="T060">Diagnostic Procedure</option>
			<option value="T070">Natural Phenomenon or Process</option>
			<option value="T197">Inorganic Chemical</option>
			<option value="T057">Occupational Activity</option>
			<option value="T083">Geographic Area</option>
			<option value="T074">Medical Device</option>
			<option value="T002">Plant</option>
			<option value="T065">Educational Activity</option>
			<option value="T092">Organization</option>
			<option value="T009">Invertebrate</option>
			<option value="T025">Cell</option>
			<option value="T196">Element, Ion, or Isotope</option>
			<option value="T067">Phenomenon or Process</option>
			<option value="T080">Qualitative Concept</option>
			<option value="T102">Group Attribute</option>
			<option value="T098">Population Group</option>
			<option value="T040">Organism Function</option>
			<option value="T034">Laboratory or Test Result</option>
			<option value="T201">Clinical Attribute</option>
			<option value="T097">Professional or Occupational Group</option>
			<option value="T064">Governmental or Regulatory Activity</option>
			<option value="T054">Social Behavior</option>
			<option value="T003">Alga</option>
			<option value="T007">Bacterium</option>
			<option value="T044">Molecular Function</option>
			<option value="T053">Behavior</option>
			<option value="T069">Environmental Effect of Humans</option>
			<option value="T042">Organ or Tissue Function</option>
			<option value="T103">Chemical</option>
			<option value="T122">Biomedical or Dental Material</option>
			<option value="T015">Mammal</option>
			<option value="T020">Acquired Abnormality</option>
			<option value="T030">Body Space or Junction</option>
			<option value="T026">Cell Component</option>
			<option value="T043">Cell Function</option>
			<option value="T059">Laboratory Procedure</option>
			<option value="T052">Activity</option>
			<option value="T056">Daily or Recreational Activity</option>
			<option value="T079">Temporal Concept</option>
			<option value="T091">Biomedical Occupation or Discipline</option>
			<option value="T192">Receptor</option>
			<option value="T031">Body Substance</option>
			<option value="T048">Mental or Behavioral Dysfunction</option>
			<option value="T058">Health Care Activity</option>
			<option value="T120">Chemical Viewed Functionally</option>
			<option value="T100">Age Group</option>
			<option value="T104">Chemical Viewed Structurally</option>
			<option value="T171">Language</option>
			<option value="T032">Organism Attribute</option>
			<option value="T095">Self-help or Relief Organization</option>
			<option value="T078">Idea or Concept</option>
			<option value="T090">Occupation or Discipline</option>
			<option value="T167">Substance</option>
			<option value="T068">Human-caused Phenomenon or Process</option>
			<option value="T168">Food</option>
			<option value="T028">Gene or Genome</option>
			<option value="T014">Reptile</option>
			<option value="T050">Experimental Model of Disease</option>
			<option value="T045">Genetic Function</option>
			<option value="T011">Amphibian</option>
			<option value="T013">Fish</option>
			<option value="T094">Professional Society</option>
			<option value="T087">Amino Acid Sequence</option>
			<option value="T066">Machine Activity</option>
			<option value="T185">Classification</option>
			<option value="T006">Rickettsia or Chlamydia</option>
			<option value="T049">Cell or Molecular Dysfunction</option>
			<option value="T008">Animal</option>
			<option value="T051">Event</option>
			<option value="T038">Biologic Function</option>
			<option value="T194">Archaeon</option>
			<option value="T086">Nucleotide Sequence</option>
			<option value="T039">Physiologic Function</option>
			<option value="T012">Bird</option>
			<option value="T063">Molecular Biology Research Technique</option>
			<option value="T017">Anatomical Structure</option>
			<option value="T082">Spatial Concept</option>
			<option value="T088">Carbohydrate Sequence</option>
			<option value="T099">Family Group</option>
			<option value="T001">Organism</option>
			<option value="T075">Research Device</option>
			<option value="T096">Group</option>
			<option value="T016">Human</option>
			<option value="T072">Physical Object</option>
			<option value="T071">Entity</option>
			<option value="T200">Clinical Drug</option>
			<option value="T085">Molecular Sequence</option>
			<option value="T077">Conceptual Entity</option>
			<option value="T010">Vertebrate</option>
			<option value="T203">Drug Delivery Device</option>
			<option value="T021">Fully Formed Anatomical Structure</option>
			<option value="T204">Eukaryote</option>
		</param>
		<param name="levelMax" type="integer" value="0" min="0" label="Indicates the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step"/>
		<param name="mappingTypes" type="select" multiple="true" label="the list of mapping type to use during the mapping expansion step">
			<option value="m-all" selected="true">ALL</option>
			<option value="m-null">None</option>
			<option value="m-Automatic">Automatic</option>
			<option value="m-Manual">Manual</option>
		</param>
		<param name="textToAnnotate" type="text" size="100" value="" label="Text to annotate"/>
		<param name="format" type="select" label="File output format">
			<option value="xml" selected="true">XML</option>
			<option value="text">Text</option>
			<option value="tabDelimited">Tab Delimited</option>
		</param>
		<param name="apikey" type="text" size="100" value="" label="BioPortal API key"/>
	</inputs>
	<outputs>
		<data format="text" name="output" />
	</outputs>
	<tests>
		<test>
			<param name="longestOnly"/>
			<param name="wholeWordOnly"/>
			<param name="filterNumber"/>
			<param name="stopWords"/>
			<param name="withDefaultStopWords"/>
			<param name="isTopWordsCaseSensitive"/>
			<param name="mintermSize"/>
			<param name="scored"/>
			<param name="withSynony"/>
			<param name="ontologiesToExpand"/>
			<param name="ontologiesToKeepInResult"/>
			<param name="semanticTypes"/>
			<param name="levelMax"/>
			<param name="mappintTypes"/>
			<param name="textToAnnotate"/>
			<param name="format"/>
			<param name="apikey"/>
		</test>
	</tests>
	<help>

**Usage**
  Enter bioportal API key, a text to annotate and specify the parameters, and the annotations will be retrieved.

**Contact**

  Please send any request or comment to jose.minyarro@um.es
  
**More information**

  http://bioportal.bioontology.org

	</help>

</tool>