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author jose-minyarro
date Mon, 19 Mar 2012 08:17:58 -0400
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<tool id="ncbo_resourceIndex" name="Search for resources matched up with terms in bio-ontologies depending on the given text" version="1.0.1">
	<description>Search for resources matched up with terms in bio-ontologies depending on the given text</description>
	<command>java -jar ${__tool_data_path__}/shared/jars/ncbo_resourceIndex_galaxy.jar $query $ontologyids $resourceId $mode $elementDetails $format $apikey > $output</command>
	<inputs>
		<param name="query" type="text" size="100" value="" label="Text to search for terms in the selected bio-ontologys"/>
		<param name="ontologyids" type="select" multiple="true" label="Indicates the list of ontologies to search for during the search process">
			<option value="all" selected="true">ALL</option>
			<option value="1394">Syndromic Surveillance Ontology</option>
			<option value="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
			<option value="1158">Cell Behavior Ontology</option>
			<option value="1033">NMR-instrument specific component of metabolomics investigations</option>
			<option value="1351">Medical Subject Headings</option>
			<option value="1146">Electrocardiography Ontology</option>
			<option value="1041">Protein modification</option>
			<option value="1058">SNP-Ontology</option>
			<option value="1099">African Traditional Medicine</option>
			<option value="1134">BioTop</option>
			<option value="1247">GeoSpecies Ontology</option>
			<option value="1024">Loggerhead nesting</option>
			<option value="1257">MeGO</option>
			<option value="1135">Pseudogene</option>
			<option value="1126">Family Health History Ontology</option>
			<option value="1108">Plant structure</option>
			<option value="1114">Bilateria anatomy</option>
			<option value="1100">Ontology for Genetic Interval</option>
			<option value="1044">Sample processing and separation techniques</option>
			<option value="1347">MedlinePlus Health Topics</option>
			<option value="1152">Minimal anatomical terminology</option>
			<option value="1063">Common Anatomy Reference Ontology</option>
			<option value="1089">BIRNLex</option>
			<option value="1116">Bleeding History Phenotype</option>
			<option value="1104">Biomedical Resource Ontology</option>
			<option value="1350">Logical Observation Identifier Names and Codes</option>
			<option value="1082">Gene Regulation Ontology</option>
			<option value="1047">Cereal plant development</option>
			<option value="1349">Physician Data Query</option>
			<option value="1190">Parasite Life Cycle</option>
			<option value="1192">Proteomics Pipeline Infrastructure for CPTAC</option>
			<option value="1352">National Drug File</option>
			<option value="1059">Computer-based Patient Record Ontology</option>
			<option value="1052">Protein Ontology</option>
			<option value="1341">COSTART</option>
			<option value="1344">International Classification of Primary Care</option>
			<option value="1061">Suggested Ontology for Pharmacogenomics</option>
			<option value="1353">SNOMED Clinical Terms</option>
			<option value="1224">Symptom Ontology</option>
			<option value="1013">eVOC (Expressed Sequence Annotation for Humans)</option>
			<option value="1149">DermLex: The Dermatology Lexicon</option>
			<option value="1311">Malaria Ontology</option>
			<option value="1335">Parasite Experiment Ontology</option>
			<option value="1370">Amphibian taxonomy</option>
			<option value="1354">WHO Adverse Reaction Terminology</option>
			<option value="1148">BioPortal Metadata</option>
			<option value="1038">Plant growth and developmental stage</option>
			<option value="1132">NCBI organismal classification</option>
			<option value="1328">Ontology of homology and related concepts in biology</option>
			<option value="1290">ABA Adult Mouse Brain</option>
			<option value="1055">Galen</option>
			<option value="1332">Basic Formal Ontology</option>
			<option value="1183">Lipid Ontology</option>
			<option value="1026">Multiple alignment</option>
			<option value="1130">Cancer Research and Management ACGT Master Ontology</option>
			<option value="1060">Epoch Clinical Trial Ontologies</option>
			<option value="1369">PhysicalFields</option>
			<option value="1086">Ontology for disease genetic investigation</option>
			<option value="1122">Skin Physiology Ontology</option>
			<option value="1142">Cardiac Electrophysiology Ontology</option>
			<option value="1128">Comparative Data Analysis Ontology</option>
			<option value="1088">MaHCO - An MHC Ontology</option>
			<option value="1249">Smoking Behavior Risk Ontology</option>
			<option value="1039">Proteomics data and process provenance</option>
			<option value="1040">Protein-protein interaction</option>
			<option value="1068">Subcellular Anatomy Ontology (SAO)</option>
			<option value="1087">Ontology of Geographical Region</option>
			<option value="1094">Pathogen transmission</option>
			<option value="1131">MGED Ontology</option>
			<option value="1106">Gene Regulation Ontology</option>
			<option value="1054">Amino Acid</option>
			<option value="1056">Basic Vertebrate Anatomy</option>
			<option value="1083">NanoParticle Ontology</option>
			<option value="1053">Foundational Model of Anatomy</option>
			<option value="1092">Infectious disease</option>
			<option value="1393">Information Artifact Ontology</option>
			<option value="1395">MDSS Mo</option>
			<option value="1397">Gazetteer</option>
			<option value="1398">Ontology of Language Disorder in Autism</option>
			<option value="1399">Pilot Ontology</option>
			<option value="1406">linkingkin2pep</option>
			<option value="1409">PKO_Re</option>
			<option value="1410">Kinetic Simulation Algorithm Ontology</option>
			<option value="1415">Common Terminology Criteria for Adverse Events</option>
			<option value="1418">TOK_Ontology</option>
			<option value="1419">Taxonomic rank vocabulary</option>
			<option value="1422">MedDRA</option>
			<option value="1424">National Drug Data File</option>
			<option value="1425">ICD-10-PCS</option>
			<option value="1426">Master Drug Data Base</option>
			<option value="1429">ICPC-2 PLUS</option>
			<option value="1430">AIR</option>
			<option value="1438">Breast tissue cell lines</option>
			<option value="1439">General Formal Ontology</option>
			<option value="1440">General Formal Ontology: Biology</option>
			<option value="1343">Health Level Seven</option>
			<option value="1484">International Classification of  External Causes of Injuries</option>
			<option value="1487">Body System</option>
			<option value="1490">Platynereis stage ontology</option>
			<option value="1491">IMGT-ONTOLOGY</option>
			<option value="1494">Tissue Microarray Ontology</option>
			<option value="1497">PMA 2010</option>
			<option value="1500">RNA ontology</option>
			<option value="1501">Neomark Oral Cancer-Centred Ontology</option>
			<option value="1504">Current Procedural Terminology</option>
			<option value="1505">Ontology for MicroRNA Target Prediction</option>
			<option value="1506">Gene Ontology Extension</option>
			<option value="1507">Cell Cycle Ontology</option>
			<option value="1509">ICPS Network</option>
			<option value="1510">Metathesaurus CPT Hierarchical Terms</option>
			<option value="1515">Interaction Network Ontology</option>
			<option value="1516">ICD10</option>
			<option value="1521">Neural Motor Recovery Ontology</option>
			<option value="1522">BioPAX</option>
			<option value="1523">OBOE SBC</option>
			<option value="1524">OBOE</option>
			<option value="1526">CRISP Thesaurus, 2006</option>
			<option value="1527">VANDF</option>
			<option value="1528">HUGO</option>
			<option value="1529">HCPCS</option>
			<option value="1530">Animal natural history and life history</option>
			<option value="1534">apollo-akesios</option>
			<option value="1537">Brucellosis Ontology</option>
			<option value="1538">Role Ontology</option>
			<option value="1539">Neural-Immune Gene Ontology</option>
			<option value="1540">Ontology for Drug Discovery Investigations</option>
			<option value="1541">Cell line ontology</option>
			<option value="1545">Wheat trait </option>
			<option value="1547">BRENDA tissue / enzyme source</option>
			<option value="1552">Reproductive traits ontology</option>
			<option value="1553">ICD10CM</option>
			<option value="1560">Cognitive Paradigm Ontology</option>
			<option value="1423">RxNORM</option>
			<option value="1517">Human developmental anatomy, abstract version, v2</option>
			<option value="1016">Drosophila development</option>
			<option value="1062">PRotein Ontology (PRO)</option>
			<option value="1000">Mouse adult gross anatomy</option>
			<option value="1065">Tick gross anatomy</option>
			<option value="1123">Ontology for Biomedical Investigations</option>
			<option value="1078">Spatial Ontology</option>
			<option value="1007">Chemical entities of biological interest</option>
			<option value="1049">C. elegans development</option>
			<option value="1070">Gene Ontology</option>
			<option value="1136">Experimental Factor Ontology</option>
			<option value="1141">Ontology of Physics for Biology</option>
			<option value="1005">BRENDA tissue / enzyme source</option>
			<option value="1321">Neural ElectroMagnetic Ontologies</option>
			<option value="1043">Physico-chemical process</option>
			<option value="1064">Fly taxonomy</option>
			<option value="1076">Ontology of Clinical Research (OCRe)</option>
			<option value="1110">Teleost Anatomy Ontology</option>
			<option value="1362">Hymenoptera Anatomy Ontology</option>
			<option value="1030">Mosquito gross anatomy</option>
			<option value="1029">Molecule role (INOH Protein name/family name ontology)</option>
			<option value="1144">Dendritic cell</option>
			<option value="1125">Human Phenotype Ontology</option>
			<option value="1023">Biological imaging methods</option>
			<option value="1021">Human developmental anatomy, abstract version</option>
			<option value="1046">Systems Biology</option>
			<option value="1051">Zebrafish anatomy and development</option>
			<option value="1037">Cereal plant trait</option>
			<option value="1107">Phenotypic quality</option>
			<option value="1081">Teleost taxonomy</option>
			<option value="1048">C. elegans gross anatomy</option>
			<option value="1050">Maize gross anatomy</option>
			<option value="1036">Plant environmental conditions</option>
			<option value="1109">Sequence types and features</option>
			<option value="1022">Human developmental anatomy, timed version</option>
			<option value="1095">Xenopus anatomy and development</option>
			<option value="1027">Medaka fish anatomy and development</option>
			<option value="1011">Event (INOH pathway ontology)</option>
			<option value="1010">Mouse gross anatomy and development</option>
			<option value="1015">Drosophila gross anatomy</option>
			<option value="1090">Amphibian gross anatomy</option>
			<option value="1019">Fungal gross anatomy</option>
			<option value="1067">C. elegans phenotype</option>
			<option value="1069">Environment Ontology</option>
			<option value="1112">Units of measurement</option>
			<option value="1091">Spider Ontology</option>
			<option value="1017">FlyBase Controlled Vocabulary</option>
			<option value="1348">Online Mendelian Inheritance in Man</option>
			<option value="1172">Vaccine Ontology</option>
			<option value="1222">Ascomycete phenotype ontology</option>
			<option value="1105">Mass spectrometry</option>
			<option value="1237">Situation-Based Access Control</option>
			<option value="1008">Dictyostelium discoideum anatomy</option>
			<option value="1150">Rat Strain Ontology</option>
			<option value="1101">International Classification of Diseases</option>
			<option value="1314">Cell Line Ontology</option>
			<option value="1009">Human disease</option>
			<option value="1084">NIFSTD</option>
			<option value="1025">Mammalian phenotype</option>
			<option value="1035">Pathway ontology</option>
			<option value="1012">Evidence codes</option>
			<option value="1115">Yeast phenotypes</option>
			<option value="1001">Cereal plant gross anatomy</option>
			<option value="1006">Cell type</option>
			<option value="1077">Mosquito insecticide resistance</option>
			<option value="1085">Ontology of Glucose Metabolism Disorder</option>
			<option value="1057">RadLex</option>
			<option value="1031">Mouse pathology</option>
			<option value="1032">NCI Thesaurus</option>
			<option value="1381">NIF Dysfunction</option>
			<option value="1401">International Classification for Nursing Practice</option>
			<option value="1402">NIF Cell</option>
			<option value="1404">Uber anatomy ontology</option>
			<option value="1407">Terminology for the Description of Dynamics</option>
			<option value="1411">International Classification of Functioning, Disability and Health (ICF)</option>
			<option value="1413">Software Ontology</option>
			<option value="1414">Ontology for General Medical Science</option>
			<option value="1444">Chemical Information Ontology</option>
			<option value="1461">Translational Medicine Ontology</option>
			<option value="1488">SysMO-JERM</option>
			<option value="1489">Adverse Event Ontology</option>
			<option value="1498">EDAM</option>
			<option value="1532">SemanticScience Integrated Ontology</option>
			<option value="1550">PHARE</option>
			<option value="1555">Vertebrate Anatomy Ontology</option>
			<option value="1565">Ontology of Medically Related Social Entities</option>
			<option value="1567">Pharmacovigilance Ontology</option>
			<option value="1568">Anatomical Entity Ontology</option>
			<option value="1569">Host Pathogen Interactions Ontology</option>
			<option value="1570">Traditional Medicine Constitution Value Set</option>
			<option value="1571">Traditional Medicine Other Factors Value Set</option>
			<option value="1572">Traditional Medicine Signs and Symptoms Value Set</option>
			<option value="1573">Traditional Medicine Meridian Value Sets</option>
			<option value="1574">vertebrate Homologous Organ Groups</option>
			<option value="1575">ExO</option>
			<option value="1576">FDA Medical Devices (2010)</option>
			<option value="1578">HOM_ElixhauserScores</option>
			<option value="1580">Adverse Event Reporting ontology</option>
			<option value="1581">HEALTH_INDICATORS</option>
			<option value="1582">COA</option>
			<option value="1583">Clinical Measurement Ontology</option>
			<option value="1584">Measurement Method Ontology</option>
			<option value="1585">Experimental Conditions Ontology</option>
			<option value="1587">Plant Ontology</option>
			<option value="1588">Ontology of General Purpose Datatypes</option>
			<option value="1596">MajDxCatgrs-DxRltdGrps</option>
			<option value="1613">Bone Dysplasia Ontology</option>
			<option value="1614">IxnO</option>
			<option value="1615">Systems Chemical Biology/Chemogenomics </option>
			<option value="1616">Phylogenetic Ontology</option>
			<option value="1621">Neuro Behavior Ontology</option>
		</param>
		<param name="resourceId" type="select" multiple="true" label="Indicates the list of resources Ids to search for during the Resource Index search process">
			<option value="all" selected="true">ALL</option>
			<option value="PGGE">PharmGKB [Gene]</option>
			<option value="BSM">Biositemaps</option>
			<option value="CDD">Conserved Domain Database (CDD)</option>
			<option value="CT">ClinicalTrials.gov</option>
			<option value="GM">ARRS GoldMiner</option>
			<option value="PC">Pathway Commons</option>
			<option value="DBK">DrugBank</option>
			<option value="AERS">Adverse Event Reporting System Data</option>
			<option value="PM">PubMed</option>
			<option value="MICAD">MICAD</option>
			<option value="OMIM">Online Mendelian Inheritance in Man</option>
			<option value="GAP">Database of Genotypes and Phenotypes</option>
			<option value="PCM">PubChem</option>
			<option value="PGDI">PharmGKB [Disease]</option>
			<option value="WP">WikiPathways</option>
			<option value="SMD">Stanford Microarray Database</option>
			<option value="AE">ArrayExpress</option>
			<option value="RXRD">ResearchCrossroads</option>
			<option value="GEO">Gene Expression Omnibus DataSets</option>
			<option value="REAC">Reactome</option>
			<option value="UPKB">UniProt KB</option>
			<option value="CANANO">caNanoLab</option>
			<option value="PGDR">PharmGKB [Drug]</option>
		</param>
		<param name="mode" type="select" label="Gets the union or intersection of the annotations done with the given text if we find more than one concept in the bio-ontologies	">
			<option value="unioin" selected="true">Union</option>
			<option value="intersection">Intersection</option>
		</param>
		<param name="elementDetails" type="boolean" value="true" label="Tick the box whether the returned resource elements should be detailled or not"/>
		<param name="format" type="select" label="Gets the results in a particular format">
			<option value="xml" selected="true">XML</option>
			<option value="text">Text</option>
			<option value="tabDelimited">Tab Delimited</option>
			<option value="rdf">RDF</option>
			<option value="owl">OWL</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="query"/>
			<param name="ontologyids"/>
			<param name="resouceId"/>
			<param name="apikey"/>
		</test>
	</tests>
	<help>

**Usage**
  Enter bioportal API key, a text, a list of bioontolgies Ids,a list of resources to search for, the mode, tick if you want detailed element and the format of the results, and the Resource Index interface retrieves the resources matched up with the bioontology terms associated with the text provided.
  Example of search text: Melanoma

**Contact**

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

  http://bioportal.bioontology.org

	</help>

</tool>