Mercurial > repos > mikel-egana-aranguren > ncbo_services
diff NCBO_services/ncbo_annotator.xml @ 17:fc4c8a9b3152
branch merge
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Wed, 18 Jan 2012 11:06:11 +0100 |
| parents | ff87703d9c85 |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/ncbo_annotator.xml Wed Jan 18 11:06:11 2012 +0100 @@ -0,0 +1,704 @@ +<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> \ No newline at end of file