Mercurial > repos > mikel-egana-aranguren > ncbo_services
comparison NCBO_services/ncbo_annotator.xml @ 26:354aa87772e0
Uploaded
| author | jose-minyarro |
|---|---|
| date | Mon, 19 Mar 2012 08:25:59 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 25:c324108a12ce | 26:354aa87772e0 |
|---|---|
| 1 <tool id="ncbo_annotator" name="Annotates a text with bio-ontology terms" version="1.0.1"> | |
| 2 <description>Annotates biological texts with the terms of the bio-ontologies from BioPortal</description> | |
| 3 <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> | |
| 4 <inputs> | |
| 5 <param name="longestOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only the longest word"/> | |
| 6 <param name="wholeWordOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only whole words"/> | |
| 7 <param name="filterNumber" type="boolean" value="true" label="Tick the box if the Annotator should filter numbers before annotating the text"/> | |
| 8 <param name="stopWords" type="text" value="" size="100" label="List the words that the Annotator should omit from the text"/> | |
| 9 <param name="withDefaultStopWords" type="boolean" value="true" label="Tick the box if the Annotator should use the default list of stop words"/> | |
| 10 <param name="isTopWordsCaseSensitive" type="boolean" value="false" label="Tick the box whether the stop words are case sensitive or not"/> | |
| 11 <param name="mintermSize" type="integer" value="3" min="0" max="100" label="Indicates the minimum length for the terms to annotate"/> | |
| 12 <param name="scored" type="boolean" value="true" label="Tick the box whether the Annotator should assign a numeric accuracy to each annotation or not"/> | |
| 13 <param name="withSynonyms" type="boolean" value="true" label="Tick the box if the Annotator should use synonyms in the direct annotation"/> | |
| 14 <param name="ontologiesToExpand" type="select" multiple="true" label="Indicates the list of ontologies to use with the mapping semantic expansion component"> | |
| 15 <option value="e-all" selected="true">ALL</option> | |
| 16 <option value="e-1394">Syndromic Surveillance Ontology</option> | |
| 17 <option value="e-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> | |
| 18 <option value="e-1158">Cell Behavior Ontology</option> | |
| 19 <option value="e-1033">NMR-instrument specific component of metabolomics investigations</option> | |
| 20 <option value="e-1351">Medical Subject Headings</option> | |
| 21 <option value="e-1146">Electrocardiography Ontology</option> | |
| 22 <option value="e-1041">Protein modification</option> | |
| 23 <option value="e-1058">SNP-Ontology</option> | |
| 24 <option value="e-1099">African Traditional Medicine</option> | |
| 25 <option value="e-1134">BioTop</option> | |
| 26 <option value="e-1247">GeoSpecies Ontology</option> | |
| 27 <option value="e-1024">Loggerhead nesting</option> | |
| 28 <option value="e-1257">MeGO</option> | |
| 29 <option value="e-1135">Pseudogene</option> | |
| 30 <option value="e-1126">Family Health History Ontology</option> | |
| 31 <option value="e-1108">Plant structure</option> | |
| 32 <option value="e-1114">Bilateria anatomy</option> | |
| 33 <option value="e-1100">Ontology for Genetic Interval</option> | |
| 34 <option value="e-1044">Sample processing and separation techniques</option> | |
| 35 <option value="e-1347">MedlinePlus Health Topics</option> | |
| 36 <option value="e-1152">Minimal anatomical terminology</option> | |
| 37 <option value="e-1063">Common Anatomy Reference Ontology</option> | |
| 38 <option value="e-1089">BIRNLex</option> | |
| 39 <option value="e-1116">Bleeding History Phenotype</option> | |
| 40 <option value="e-1104">Biomedical Resource Ontology</option> | |
| 41 <option value="e-1350">Logical Observation Identifier Names and Codes</option> | |
| 42 <option value="e-1082">Gene Regulation Ontology</option> | |
| 43 <option value="e-1047">Cereal plant development</option> | |
| 44 <option value="e-1349">Physician Data Query</option> | |
| 45 <option value="e-1190">Parasite Life Cycle</option> | |
| 46 <option value="e-1192">Proteomics Pipeline Infrastructure for CPTAC</option> | |
| 47 <option value="e-1352">National Drug File</option> | |
| 48 <option value="e-1059">Computer-based Patient Record Ontology</option> | |
| 49 <option value="e-1052">Protein Ontology</option> | |
| 50 <option value="e-1341">COSTART</option> | |
| 51 <option value="e-1344">International Classification of Primary Care</option> | |
| 52 <option value="e-1061">Suggested Ontology for Pharmacogenomics</option> | |
| 53 <option value="e-1353">SNOMED Clinical Terms</option> | |
| 54 <option value="e-1224">Symptom Ontology</option> | |
| 55 <option value="e-1013">eVOC (Expressed Sequence Annotation for Humans)</option> | |
| 56 <option value="e-1149">DermLex: The Dermatology Lexicon</option> | |
| 57 <option value="e-1311">Malaria Ontology</option> | |
| 58 <option value="e-1335">Parasite Experiment Ontology</option> | |
| 59 <option value="e-1370">Amphibian taxonomy</option> | |
| 60 <option value="e-1354">WHO Adverse Reaction Terminology</option> | |
| 61 <option value="e-1148">BioPortal Metadata</option> | |
| 62 <option value="e-1038">Plant growth and developmental stage</option> | |
| 63 <option value="e-1132">NCBI organismal classification</option> | |
| 64 <option value="e-1328">Ontology of homology and related concepts in biology</option> | |
| 65 <option value="e-1290">ABA Adult Mouse Brain</option> | |
| 66 <option value="e-1055">Galen</option> | |
| 67 <option value="e-1332">Basic Formal Ontology</option> | |
| 68 <option value="e-1183">Lipid Ontology</option> | |
| 69 <option value="e-1026">Multiple alignment</option> | |
| 70 <option value="e-1130">Cancer Research and Management ACGT Master Ontology</option> | |
| 71 <option value="e-1060">Epoch Clinical Trial Ontologies</option> | |
| 72 <option value="e-1369">PhysicalFields</option> | |
| 73 <option value="e-1086">Ontology for disease genetic investigation</option> | |
| 74 <option value="e-1122">Skin Physiology Ontology</option> | |
| 75 <option value="e-1142">Cardiac Electrophysiology Ontology</option> | |
| 76 <option value="e-1128">Comparative Data Analysis Ontology</option> | |
| 77 <option value="e-1088">MaHCO - An MHC Ontology</option> | |
| 78 <option value="e-1249">Smoking Behavior Risk Ontology</option> | |
| 79 <option value="e-1039">Proteomics data and process provenance</option> | |
| 80 <option value="e-1040">Protein-protein interaction</option> | |
| 81 <option value="e-1068">Subcellular Anatomy Ontology (SAO)</option> | |
| 82 <option value="e-1087">Ontology of Geographical Region</option> | |
| 83 <option value="e-1094">Pathogen transmission</option> | |
| 84 <option value="e-1131">MGED Ontology</option> | |
| 85 <option value="e-1106">Gene Regulation Ontology</option> | |
| 86 <option value="e-1054">Amino Acid</option> | |
| 87 <option value="e-1056">Basic Vertebrate Anatomy</option> | |
| 88 <option value="e-1083">NanoParticle Ontology</option> | |
| 89 <option value="e-1053">Foundational Model of Anatomy</option> | |
| 90 <option value="e-1092">Infectious disease</option> | |
| 91 <option value="e-1393">Information Artifact Ontology</option> | |
| 92 <option value="e-1395">MDSS Mo</option> | |
| 93 <option value="e-1397">Gazetteer</option> | |
| 94 <option value="e-1398">Ontology of Language Disorder in Autism</option> | |
| 95 <option value="e-1399">Pilot Ontology</option> | |
| 96 <option value="e-1406">linkingkin2pep</option> | |
| 97 <option value="e-1409">PKO_Re</option> | |
| 98 <option value="e-1410">Kinetic Simulation Algorithm Ontology</option> | |
| 99 <option value="e-1415">Common Terminology Criteria for Adverse Events</option> | |
| 100 <option value="e-1418">TOK_Ontology</option> | |
| 101 <option value="e-1419">Taxonomic rank vocabulary</option> | |
| 102 <option value="e-1422">MedDRA</option> | |
| 103 <option value="e-1424">National Drug Data File</option> | |
| 104 <option value="e-1425">ICD-10-PCS</option> | |
| 105 <option value="e-1426">Master Drug Data Base</option> | |
| 106 <option value="e-1429">ICPC-2 PLUS</option> | |
| 107 <option value="e-1430">AIR</option> | |
| 108 <option value="e-1438">Breast tissue cell lines</option> | |
| 109 <option value="e-1439">General Formal Ontology</option> | |
| 110 <option value="e-1440">General Formal Ontology: Biology</option> | |
| 111 <option value="e-1343">Health Level Seven</option> | |
| 112 <option value="e-1484">International Classification of External Causes of Injuries</option> | |
| 113 <option value="e-1487">Body System</option> | |
| 114 <option value="e-1490">Platynereis stage ontology</option> | |
| 115 <option value="e-1491">IMGT-ONTOLOGY</option> | |
| 116 <option value="e-1494">Tissue Microarray Ontology</option> | |
| 117 <option value="e-1497">PMA 2010</option> | |
| 118 <option value="e-1500">RNA ontology</option> | |
| 119 <option value="e-1501">Neomark Oral Cancer-Centred Ontology</option> | |
| 120 <option value="e-1504">Current Procedural Terminology</option> | |
| 121 <option value="e-1505">Ontology for MicroRNA Target Prediction</option> | |
| 122 <option value="e-1506">Gene Ontology Extension</option> | |
| 123 <option value="e-1507">Cell Cycle Ontology</option> | |
| 124 <option value="e-1509">ICPS Network</option> | |
| 125 <option value="e-1510">Metathesaurus CPT Hierarchical Terms</option> | |
| 126 <option value="e-1515">Interaction Network Ontology</option> | |
| 127 <option value="e-1516">ICD10</option> | |
| 128 <option value="e-1521">Neural Motor Recovery Ontology</option> | |
| 129 <option value="e-1522">BioPAX</option> | |
| 130 <option value="e-1523">OBOE SBC</option> | |
| 131 <option value="e-1524">OBOE</option> | |
| 132 <option value="e-1526">CRISP Thesaurus, 2006</option> | |
| 133 <option value="e-1527">VANDF</option> | |
| 134 <option value="e-1528">HUGO</option> | |
| 135 <option value="e-1529">HCPCS</option> | |
| 136 <option value="e-1530">Animal natural history and life history</option> | |
| 137 <option value="e-1534">apollo-akesios</option> | |
| 138 <option value="e-1537">Brucellosis Ontology</option> | |
| 139 <option value="e-1538">Role Ontology</option> | |
| 140 <option value="e-1539">Neural-Immune Gene Ontology</option> | |
| 141 <option value="e-1540">Ontology for Drug Discovery Investigations</option> | |
| 142 <option value="e-1541">Cell line ontology</option> | |
| 143 <option value="e-1545">Wheat trait </option> | |
| 144 <option value="e-1547">BRENDA tissue / enzyme source</option> | |
| 145 <option value="e-1552">Reproductive traits ontology</option> | |
| 146 <option value="e-1553">ICD10CM</option> | |
| 147 <option value="e-1560">Cognitive Paradigm Ontology</option> | |
| 148 <option value="e-1423">RxNORM</option> | |
| 149 <option value="e-1517">Human developmental anatomy, abstract version, v2</option> | |
| 150 <option value="e-1016">Drosophila development</option> | |
| 151 <option value="e-1062">PRotein Ontology (PRO)</option> | |
| 152 <option value="e-1000">Mouse adult gross anatomy</option> | |
| 153 <option value="e-1065">Tick gross anatomy</option> | |
| 154 <option value="e-1123">Ontology for Biomedical Investigations</option> | |
| 155 <option value="e-1078">Spatial Ontology</option> | |
| 156 <option value="e-1007">Chemical entities of biological interest</option> | |
| 157 <option value="e-1049">C. elegans development</option> | |
| 158 <option value="e-1070">Gene Ontology</option> | |
| 159 <option value="e-1136">Experimental Factor Ontology</option> | |
| 160 <option value="e-1141">Ontology of Physics for Biology</option> | |
| 161 <option value="e-1005">BRENDA tissue / enzyme source</option> | |
| 162 <option value="e-1321">Neural ElectroMagnetic Ontologies</option> | |
| 163 <option value="e-1043">Physico-chemical process</option> | |
| 164 <option value="e-1064">Fly taxonomy</option> | |
| 165 <option value="e-1076">Ontology of Clinical Research (OCRe)</option> | |
| 166 <option value="e-1110">Teleost Anatomy Ontology</option> | |
| 167 <option value="e-1362">Hymenoptera Anatomy Ontology</option> | |
| 168 <option value="e-1030">Mosquito gross anatomy</option> | |
| 169 <option value="e-1029">Molecule role (INOH Protein name/family name ontology)</option> | |
| 170 <option value="e-1144">Dendritic cell</option> | |
| 171 <option value="e-1125">Human Phenotype Ontology</option> | |
| 172 <option value="e-1023">Biological imaging methods</option> | |
| 173 <option value="e-1021">Human developmental anatomy, abstract version</option> | |
| 174 <option value="e-1046">Systems Biology</option> | |
| 175 <option value="e-1051">Zebrafish anatomy and development</option> | |
| 176 <option value="e-1037">Cereal plant trait</option> | |
| 177 <option value="e-1107">Phenotypic quality</option> | |
| 178 <option value="e-1081">Teleost taxonomy</option> | |
| 179 <option value="e-1048">C. elegans gross anatomy</option> | |
| 180 <option value="e-1050">Maize gross anatomy</option> | |
| 181 <option value="e-1036">Plant environmental conditions</option> | |
| 182 <option value="e-1109">Sequence types and features</option> | |
| 183 <option value="e-1022">Human developmental anatomy, timed version</option> | |
| 184 <option value="e-1095">Xenopus anatomy and development</option> | |
| 185 <option value="e-1027">Medaka fish anatomy and development</option> | |
| 186 <option value="e-1011">Event (INOH pathway ontology)</option> | |
| 187 <option value="e-1010">Mouse gross anatomy and development</option> | |
| 188 <option value="e-1015">Drosophila gross anatomy</option> | |
| 189 <option value="e-1090">Amphibian gross anatomy</option> | |
| 190 <option value="e-1019">Fungal gross anatomy</option> | |
| 191 <option value="e-1067">C. elegans phenotype</option> | |
| 192 <option value="e-1069">Environment Ontology</option> | |
| 193 <option value="e-1112">Units of measurement</option> | |
| 194 <option value="e-1091">Spider Ontology</option> | |
| 195 <option value="e-1017">FlyBase Controlled Vocabulary</option> | |
| 196 <option value="e-1348">Online Mendelian Inheritance in Man</option> | |
| 197 <option value="e-1172">Vaccine Ontology</option> | |
| 198 <option value="e-1222">Ascomycete phenotype ontology</option> | |
| 199 <option value="e-1105">Mass spectrometry</option> | |
| 200 <option value="e-1237">Situation-Based Access Control</option> | |
| 201 <option value="e-1008">Dictyostelium discoideum anatomy</option> | |
| 202 <option value="e-1150">Rat Strain Ontology</option> | |
| 203 <option value="e-1101">International Classification of Diseases</option> | |
| 204 <option value="e-1314">Cell Line Ontology</option> | |
| 205 <option value="e-1009">Human disease</option> | |
| 206 <option value="e-1084">NIFSTD</option> | |
| 207 <option value="e-1025">Mammalian phenotype</option> | |
| 208 <option value="e-1035">Pathway ontology</option> | |
| 209 <option value="e-1012">Evidence codes</option> | |
| 210 <option value="e-1115">Yeast phenotypes</option> | |
| 211 <option value="e-1001">Cereal plant gross anatomy</option> | |
| 212 <option value="e-1006">Cell type</option> | |
| 213 <option value="e-1077">Mosquito insecticide resistance</option> | |
| 214 <option value="e-1085">Ontology of Glucose Metabolism Disorder</option> | |
| 215 <option value="e-1057">RadLex</option> | |
| 216 <option value="e-1031">Mouse pathology</option> | |
| 217 <option value="e-1032">NCI Thesaurus</option> | |
| 218 <option value="e-1381">NIF Dysfunction</option> | |
| 219 <option value="e-1401">International Classification for Nursing Practice</option> | |
| 220 <option value="e-1402">NIF Cell</option> | |
| 221 <option value="e-1404">Uber anatomy ontology</option> | |
| 222 <option value="e-1407">Terminology for the Description of Dynamics</option> | |
| 223 <option value="e-1411">International Classification of Functioning, Disability and Health (ICF)</option> | |
| 224 <option value="e-1413">Software Ontology</option> | |
| 225 <option value="e-1414">Ontology for General Medical Science</option> | |
| 226 <option value="e-1444">Chemical Information Ontology</option> | |
| 227 <option value="e-1461">Translational Medicine Ontology</option> | |
| 228 <option value="e-1488">SysMO-JERM</option> | |
| 229 <option value="e-1489">Adverse Event Ontology</option> | |
| 230 <option value="e-1498">EDAM</option> | |
| 231 <option value="e-1532">SemanticScience Integrated Ontology</option> | |
| 232 <option value="e-1550">PHARE</option> | |
| 233 <option value="e-1555">Vertebrate Anatomy Ontology</option> | |
| 234 <option value="e-1565">Ontology of Medically Related Social Entities</option> | |
| 235 <option value="e-1567">Pharmacovigilance Ontology</option> | |
| 236 <option value="e-1568">Anatomical Entity Ontology</option> | |
| 237 <option value="e-1569">Host Pathogen Interactions Ontology</option> | |
| 238 <option value="e-1570">Traditional Medicine Constitution Value Set</option> | |
| 239 <option value="e-1571">Traditional Medicine Other Factors Value Set</option> | |
| 240 <option value="e-1572">Traditional Medicine Signs and Symptoms Value Set</option> | |
| 241 <option value="e-1573">Traditional Medicine Meridian Value Sets</option> | |
| 242 <option value="e-1574">vertebrate Homologous Organ Groups</option> | |
| 243 <option value="e-1575">ExO</option> | |
| 244 <option value="e-1576">FDA Medical Devices (2010)</option> | |
| 245 <option value="e-1578">HOM_ElixhauserScores</option> | |
| 246 <option value="e-1580">Adverse Event Reporting ontology</option> | |
| 247 <option value="e-1581">HEALTH_INDICATORS</option> | |
| 248 <option value="e-1582">COA</option> | |
| 249 <option value="e-1583">Clinical Measurement Ontology</option> | |
| 250 <option value="e-1584">Measurement Method Ontology</option> | |
| 251 <option value="e-1585">Experimental Conditions Ontology</option> | |
| 252 <option value="e-1587">Plant Ontology</option> | |
| 253 <option value="e-1588">Ontology of General Purpose Datatypes</option> | |
| 254 <option value="e-1596">MajDxCatgrs-DxRltdGrps</option> | |
| 255 <option value="e-1613">Bone Dysplasia Ontology</option> | |
| 256 <option value="e-1614">IxnO</option> | |
| 257 <option value="e-1615">Systems Chemical Biology/Chemogenomics </option> | |
| 258 <option value="e-1616">Phylogenetic Ontology</option> | |
| 259 <option value="e-1621">Neuro Behavior Ontology</option> | |
| 260 </param> | |
| 261 <param name="ontologiesToKeepInResult" type="select" multiple="true" label="Indicates the list of ontologies to keep in the result of the annotation process"> | |
| 262 <option value="k-all" selected="true">ALL</option> | |
| 263 <option value="k-1394">Syndromic Surveillance Ontology</option> | |
| 264 <option value="k-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> | |
| 265 <option value="k-1158">Cell Behavior Ontology</option> | |
| 266 <option value="k-1033">NMR-instrument specific component of metabolomics investigations</option> | |
| 267 <option value="k-1351">Medical Subject Headings</option> | |
| 268 <option value="k-1146">Electrocardiography Ontology</option> | |
| 269 <option value="k-1041">Protein modification</option> | |
| 270 <option value="k-1058">SNP-Ontology</option> | |
| 271 <option value="k-1099">African Traditional Medicine</option> | |
| 272 <option value="k-1134">BioTop</option> | |
| 273 <option value="k-1247">GeoSpecies Ontology</option> | |
| 274 <option value="k-1024">Loggerhead nesting</option> | |
| 275 <option value="k-1257">MeGO</option> | |
| 276 <option value="k-1135">Pseudogene</option> | |
| 277 <option value="k-1126">Family Health History Ontology</option> | |
| 278 <option value="k-1108">Plant structure</option> | |
| 279 <option value="k-1114">Bilateria anatomy</option> | |
| 280 <option value="k-1100">Ontology for Genetic Interval</option> | |
| 281 <option value="k-1044">Sample processing and separation techniques</option> | |
| 282 <option value="k-1347">MedlinePlus Health Topics</option> | |
| 283 <option value="k-1152">Minimal anatomical terminology</option> | |
| 284 <option value="k-1063">Common Anatomy Reference Ontology</option> | |
| 285 <option value="k-1089">BIRNLex</option> | |
| 286 <option value="k-1116">Bleeding History Phenotype</option> | |
| 287 <option value="k-1104">Biomedical Resource Ontology</option> | |
| 288 <option value="k-1350">Logical Observation Identifier Names and Codes</option> | |
| 289 <option value="k-1082">Gene Regulation Ontology</option> | |
| 290 <option value="k-1047">Cereal plant development</option> | |
| 291 <option value="k-1349">Physician Data Query</option> | |
| 292 <option value="k-1190">Parasite Life Cycle</option> | |
| 293 <option value="k-1192">Proteomics Pipeline Infrastructure for CPTAC</option> | |
| 294 <option value="k-1352">National Drug File</option> | |
| 295 <option value="k-1059">Computer-based Patient Record Ontology</option> | |
| 296 <option value="k-1052">Protein Ontology</option> | |
| 297 <option value="k-1341">COSTART</option> | |
| 298 <option value="k-1344">International Classification of Primary Care</option> | |
| 299 <option value="k-1061">Suggested Ontology for Pharmacogenomics</option> | |
| 300 <option value="k-1353">SNOMED Clinical Terms</option> | |
| 301 <option value="k-1224">Symptom Ontology</option> | |
| 302 <option value="k-1013">eVOC (Expressed Sequence Annotation for Humans)</option> | |
| 303 <option value="k-1149">DermLex: The Dermatology Lexicon</option> | |
| 304 <option value="k-1311">Malaria Ontology</option> | |
| 305 <option value="k-1335">Parasite Experiment Ontology</option> | |
| 306 <option value="k-1370">Amphibian taxonomy</option> | |
| 307 <option value="k-1354">WHO Adverse Reaction Terminology</option> | |
| 308 <option value="k-1148">BioPortal Metadata</option> | |
| 309 <option value="k-1038">Plant growth and developmental stage</option> | |
| 310 <option value="k-1132">NCBI organismal classification</option> | |
| 311 <option value="k-1328">Ontology of homology and related concepts in biology</option> | |
| 312 <option value="k-1290">ABA Adult Mouse Brain</option> | |
| 313 <option value="k-1055">Galen</option> | |
| 314 <option value="k-1332">Basic Formal Ontology</option> | |
| 315 <option value="k-1183">Lipid Ontology</option> | |
| 316 <option value="k-1026">Multiple alignment</option> | |
| 317 <option value="k-1130">Cancer Research and Management ACGT Master Ontology</option> | |
| 318 <option value="k-1060">Epoch Clinical Trial Ontologies</option> | |
| 319 <option value="k-1369">PhysicalFields</option> | |
| 320 <option value="k-1086">Ontology for disease genetic investigation</option> | |
| 321 <option value="k-1122">Skin Physiology Ontology</option> | |
| 322 <option value="k-1142">Cardiac Electrophysiology Ontology</option> | |
| 323 <option value="k-1128">Comparative Data Analysis Ontology</option> | |
| 324 <option value="k-1088">MaHCO - An MHC Ontology</option> | |
| 325 <option value="k-1249">Smoking Behavior Risk Ontology</option> | |
| 326 <option value="k-1039">Proteomics data and process provenance</option> | |
| 327 <option value="k-1040">Protein-protein interaction</option> | |
| 328 <option value="k-1068">Subcellular Anatomy Ontology (SAO)</option> | |
| 329 <option value="k-1087">Ontology of Geographical Region</option> | |
| 330 <option value="k-1094">Pathogen transmission</option> | |
| 331 <option value="k-1131">MGED Ontology</option> | |
| 332 <option value="k-1106">Gene Regulation Ontology</option> | |
| 333 <option value="k-1054">Amino Acid</option> | |
| 334 <option value="k-1056">Basic Vertebrate Anatomy</option> | |
| 335 <option value="k-1083">NanoParticle Ontology</option> | |
| 336 <option value="k-1053">Foundational Model of Anatomy</option> | |
| 337 <option value="k-1092">Infectious disease</option> | |
| 338 <option value="k-1393">Information Artifact Ontology</option> | |
| 339 <option value="k-1395">MDSS Mo</option> | |
| 340 <option value="k-1397">Gazetteer</option> | |
| 341 <option value="k-1398">Ontology of Language Disorder in Autism</option> | |
| 342 <option value="k-1399">Pilot Ontology</option> | |
| 343 <option value="k-1406">linkingkin2pep</option> | |
| 344 <option value="k-1409">PKO_Re</option> | |
| 345 <option value="k-1410">Kinetic Simulation Algorithm Ontology</option> | |
| 346 <option value="k-1415">Common Terminology Criteria for Adverse Events</option> | |
| 347 <option value="k-1418">TOK_Ontology</option> | |
| 348 <option value="k-1419">Taxonomic rank vocabulary</option> | |
| 349 <option value="k-1422">MedDRA</option> | |
| 350 <option value="k-1424">National Drug Data File</option> | |
| 351 <option value="k-1425">ICD-10-PCS</option> | |
| 352 <option value="k-1426">Master Drug Data Base</option> | |
| 353 <option value="k-1429">ICPC-2 PLUS</option> | |
| 354 <option value="k-1430">AIR</option> | |
| 355 <option value="k-1438">Breast tissue cell lines</option> | |
| 356 <option value="k-1439">General Formal Ontology</option> | |
| 357 <option value="k-1440">General Formal Ontology: Biology</option> | |
| 358 <option value="k-1343">Health Level Seven</option> | |
| 359 <option value="k-1484">International Classification of External Causes of Injuries</option> | |
| 360 <option value="k-1487">Body System</option> | |
| 361 <option value="k-1490">Platynereis stage ontology</option> | |
| 362 <option value="k-1491">IMGT-ONTOLOGY</option> | |
| 363 <option value="k-1494">Tissue Microarray Ontology</option> | |
| 364 <option value="k-1497">PMA 2010</option> | |
| 365 <option value="k-1500">RNA ontology</option> | |
| 366 <option value="k-1501">Neomark Oral Cancer-Centred Ontology</option> | |
| 367 <option value="k-1504">Current Procedural Terminology</option> | |
| 368 <option value="k-1505">Ontology for MicroRNA Target Prediction</option> | |
| 369 <option value="k-1506">Gene Ontology Extension</option> | |
| 370 <option value="k-1507">Cell Cycle Ontology</option> | |
| 371 <option value="k-1509">ICPS Network</option> | |
| 372 <option value="k-1510">Metathesaurus CPT Hierarchical Terms</option> | |
| 373 <option value="k-1515">Interaction Network Ontology</option> | |
| 374 <option value="k-1516">ICD10</option> | |
| 375 <option value="k-1521">Neural Motor Recovery Ontology</option> | |
| 376 <option value="k-1522">BioPAX</option> | |
| 377 <option value="k-1523">OBOE SBC</option> | |
| 378 <option value="k-1524">OBOE</option> | |
| 379 <option value="k-1526">CRISP Thesaurus, 2006</option> | |
| 380 <option value="k-1527">VANDF</option> | |
| 381 <option value="k-1528">HUGO</option> | |
| 382 <option value="k-1529">HCPCS</option> | |
| 383 <option value="k-1530">Animal natural history and life history</option> | |
| 384 <option value="k-1534">apollo-akesios</option> | |
| 385 <option value="k-1537">Brucellosis Ontology</option> | |
| 386 <option value="k-1538">Role Ontology</option> | |
| 387 <option value="k-1539">Neural-Immune Gene Ontology</option> | |
| 388 <option value="k-1540">Ontology for Drug Discovery Investigations</option> | |
| 389 <option value="k-1541">Cell line ontology</option> | |
| 390 <option value="k-1545">Wheat trait </option> | |
| 391 <option value="k-1547">BRENDA tissue / enzyme source</option> | |
| 392 <option value="k-1552">Reproductive traits ontology</option> | |
| 393 <option value="k-1553">ICD10CM</option> | |
| 394 <option value="k-1560">Cognitive Paradigm Ontology</option> | |
| 395 <option value="k-1423">RxNORM</option> | |
| 396 <option value="k-1517">Human developmental anatomy, abstract version, v2</option> | |
| 397 <option value="k-1016">Drosophila development</option> | |
| 398 <option value="k-1062">PRotein Ontology (PRO)</option> | |
| 399 <option value="k-1000">Mouse adult gross anatomy</option> | |
| 400 <option value="k-1065">Tick gross anatomy</option> | |
| 401 <option value="k-1123">Ontology for Biomedical Investigations</option> | |
| 402 <option value="k-1078">Spatial Ontology</option> | |
| 403 <option value="k-1007">Chemical entities of biological interest</option> | |
| 404 <option value="k-1049">C. elegans development</option> | |
| 405 <option value="k-1070">Gene Ontology</option> | |
| 406 <option value="k-1136">Experimental Factor Ontology</option> | |
| 407 <option value="k-1141">Ontology of Physics for Biology</option> | |
| 408 <option value="k-1005">BRENDA tissue / enzyme source</option> | |
| 409 <option value="k-1321">Neural ElectroMagnetic Ontologies</option> | |
| 410 <option value="k-1043">Physico-chemical process</option> | |
| 411 <option value="k-1064">Fly taxonomy</option> | |
| 412 <option value="k-1076">Ontology of Clinical Research (OCRe)</option> | |
| 413 <option value="k-1110">Teleost Anatomy Ontology</option> | |
| 414 <option value="k-1362">Hymenoptera Anatomy Ontology</option> | |
| 415 <option value="k-1030">Mosquito gross anatomy</option> | |
| 416 <option value="k-1029">Molecule role (INOH Protein name/family name ontology)</option> | |
| 417 <option value="k-1144">Dendritic cell</option> | |
| 418 <option value="k-1125">Human Phenotype Ontology</option> | |
| 419 <option value="k-1023">Biological imaging methods</option> | |
| 420 <option value="k-1021">Human developmental anatomy, abstract version</option> | |
| 421 <option value="k-1046">Systems Biology</option> | |
| 422 <option value="k-1051">Zebrafish anatomy and development</option> | |
| 423 <option value="k-1037">Cereal plant trait</option> | |
| 424 <option value="k-1107">Phenotypic quality</option> | |
| 425 <option value="k-1081">Teleost taxonomy</option> | |
| 426 <option value="k-1048">C. elegans gross anatomy</option> | |
| 427 <option value="k-1050">Maize gross anatomy</option> | |
| 428 <option value="k-1036">Plant environmental conditions</option> | |
| 429 <option value="k-1109">Sequence types and features</option> | |
| 430 <option value="k-1022">Human developmental anatomy, timed version</option> | |
| 431 <option value="k-1095">Xenopus anatomy and development</option> | |
| 432 <option value="k-1027">Medaka fish anatomy and development</option> | |
| 433 <option value="k-1011">Event (INOH pathway ontology)</option> | |
| 434 <option value="k-1010">Mouse gross anatomy and development</option> | |
| 435 <option value="k-1015">Drosophila gross anatomy</option> | |
| 436 <option value="k-1090">Amphibian gross anatomy</option> | |
| 437 <option value="k-1019">Fungal gross anatomy</option> | |
| 438 <option value="k-1067">C. elegans phenotype</option> | |
| 439 <option value="k-1069">Environment Ontology</option> | |
| 440 <option value="k-1112">Units of measurement</option> | |
| 441 <option value="k-1091">Spider Ontology</option> | |
| 442 <option value="k-1017">FlyBase Controlled Vocabulary</option> | |
| 443 <option value="k-1348">Online Mendelian Inheritance in Man</option> | |
| 444 <option value="k-1172">Vaccine Ontology</option> | |
| 445 <option value="k-1222">Ascomycete phenotype ontology</option> | |
| 446 <option value="k-1105">Mass spectrometry</option> | |
| 447 <option value="k-1237">Situation-Based Access Control</option> | |
| 448 <option value="k-1008">Dictyostelium discoideum anatomy</option> | |
| 449 <option value="k-1150">Rat Strain Ontology</option> | |
| 450 <option value="k-1101">International Classification of Diseases</option> | |
| 451 <option value="k-1314">Cell Line Ontology</option> | |
| 452 <option value="k-1009">Human disease</option> | |
| 453 <option value="k-1084">NIFSTD</option> | |
| 454 <option value="k-1025">Mammalian phenotype</option> | |
| 455 <option value="k-1035">Pathway ontology</option> | |
| 456 <option value="k-1012">Evidence codes</option> | |
| 457 <option value="k-1115">Yeast phenotypes</option> | |
| 458 <option value="k-1001">Cereal plant gross anatomy</option> | |
| 459 <option value="k-1006">Cell type</option> | |
| 460 <option value="k-1077">Mosquito insecticide resistance</option> | |
| 461 <option value="k-1085">Ontology of Glucose Metabolism Disorder</option> | |
| 462 <option value="k-1057">RadLex</option> | |
| 463 <option value="k-1031">Mouse pathology</option> | |
| 464 <option value="k-1032">NCI Thesaurus</option> | |
| 465 <option value="k-1381">NIF Dysfunction</option> | |
| 466 <option value="k-1401">International Classification for Nursing Practice</option> | |
| 467 <option value="k-1402">NIF Cell</option> | |
| 468 <option value="k-1404">Uber anatomy ontology</option> | |
| 469 <option value="k-1407">Terminology for the Description of Dynamics</option> | |
| 470 <option value="k-1411">International Classification of Functioning, Disability and Health (ICF)</option> | |
| 471 <option value="k-1413">Software Ontology</option> | |
| 472 <option value="k-1414">Ontology for General Medical Science</option> | |
| 473 <option value="k-1444">Chemical Information Ontology</option> | |
| 474 <option value="k-1461">Translational Medicine Ontology</option> | |
| 475 <option value="k-1488">SysMO-JERM</option> | |
| 476 <option value="k-1489">Adverse Event Ontology</option> | |
| 477 <option value="k-1498">EDAM</option> | |
| 478 <option value="k-1532">SemanticScience Integrated Ontology</option> | |
| 479 <option value="k-1550">PHARE</option> | |
| 480 <option value="k-1555">Vertebrate Anatomy Ontology</option> | |
| 481 <option value="k-1565">Ontology of Medically Related Social Entities</option> | |
| 482 <option value="k-1567">Pharmacovigilance Ontology</option> | |
| 483 <option value="k-1568">Anatomical Entity Ontology</option> | |
| 484 <option value="k-1569">Host Pathogen Interactions Ontology</option> | |
| 485 <option value="k-1570">Traditional Medicine Constitution Value Set</option> | |
| 486 <option value="k-1571">Traditional Medicine Other Factors Value Set</option> | |
| 487 <option value="k-1572">Traditional Medicine Signs and Symptoms Value Set</option> | |
| 488 <option value="k-1573">Traditional Medicine Meridian Value Sets</option> | |
| 489 <option value="k-1574">vertebrate Homologous Organ Groups</option> | |
| 490 <option value="k-1575">ExO</option> | |
| 491 <option value="k-1576">FDA Medical Devices (2010)</option> | |
| 492 <option value="k-1578">HOM_ElixhauserScores</option> | |
| 493 <option value="k-1580">Adverse Event Reporting ontology</option> | |
| 494 <option value="k-1581">HEALTH_INDICATORS</option> | |
| 495 <option value="k-1582">COA</option> | |
| 496 <option value="k-1583">Clinical Measurement Ontology</option> | |
| 497 <option value="k-1584">Measurement Method Ontology</option> | |
| 498 <option value="k-1585">Experimental Conditions Ontology</option> | |
| 499 <option value="k-1587">Plant Ontology</option> | |
| 500 <option value="k-1588">Ontology of General Purpose Datatypes</option> | |
| 501 <option value="k-1596">MajDxCatgrs-DxRltdGrps</option> | |
| 502 <option value="k-1613">Bone Dysplasia Ontology</option> | |
| 503 <option value="k-1614">IxnO</option> | |
| 504 <option value="k-1615">Systems Chemical Biology/Chemogenomics </option> | |
| 505 <option value="k-1616">Phylogenetic Ontology</option> | |
| 506 <option value="k-1621">Neuro Behavior Ontology</option> | |
| 507 </param> | |
| 508 <param name="semanticTypes" type="select" multiple="true" label="Indicates the list of semantic types to use in the annotation process"> | |
| 509 <option value="T-all" selected="true">ALL</option> | |
| 510 <option value="T000">UMLS concept</option> | |
| 511 <option value="T998">Jax Mouse/Human Gene dictionary concept</option> | |
| 512 <option value="T999">NCBO BioPortal concept</option> | |
| 513 <option value="T116">Amino Acid, Peptide, or Protein</option> | |
| 514 <option value="T121">Pharmacologic Substance</option> | |
| 515 <option value="T130">Indicator, Reagent, or Diagnostic Aid</option> | |
| 516 <option value="T119">Lipid</option> | |
| 517 <option value="T126">Enzyme</option> | |
| 518 <option value="T123">Biologically Active Substance</option> | |
| 519 <option value="T109">Organic Chemical</option> | |
| 520 <option value="T131">Hazardous or Poisonous Substance</option> | |
| 521 <option value="T110">Steroid</option> | |
| 522 <option value="T125">Hormone</option> | |
| 523 <option value="T114">Nucleic Acid, Nucleoside, or Nucleotide</option> | |
| 524 <option value="T111">Eicosanoid</option> | |
| 525 <option value="T118">Carbohydrate</option> | |
| 526 <option value="T124">Neuroreactive Substance or Biogenic Amine</option> | |
| 527 <option value="T127">Vitamin</option> | |
| 528 <option value="T195">Antibiotic</option> | |
| 529 <option value="T129">Immunologic Factor</option> | |
| 530 <option value="T024">Tissue</option> | |
| 531 <option value="T115">Organophosphorus Compound</option> | |
| 532 <option value="T073">Manufactured Object</option> | |
| 533 <option value="T081">Quantitative Concept</option> | |
| 534 <option value="T170">Intellectual Product</option> | |
| 535 <option value="T029">Body Location or Region</option> | |
| 536 <option value="T184">Sign or Symptom</option> | |
| 537 <option value="T033">Finding</option> | |
| 538 <option value="T037">Injury or Poisoning</option> | |
| 539 <option value="T191">Neoplastic Process</option> | |
| 540 <option value="T023">Body Part, Organ, or Organ Component</option> | |
| 541 <option value="T005">Virus</option> | |
| 542 <option value="T047">Disease or Syndrome</option> | |
| 543 <option value="T019">Congenital Abnormality</option> | |
| 544 <option value="T169">Functional Concept</option> | |
| 545 <option value="T190">Anatomical Abnormality</option> | |
| 546 <option value="T022">Body System</option> | |
| 547 <option value="T018">Embryonic Structure</option> | |
| 548 <option value="T101">Patient or Disabled Group</option> | |
| 549 <option value="T093">Health Care Related Organization</option> | |
| 550 <option value="T089">Regulation or Law</option> | |
| 551 <option value="T061">Therapeutic or Preventive Procedure</option> | |
| 552 <option value="T062">Research Activity</option> | |
| 553 <option value="T046">Pathologic Function</option> | |
| 554 <option value="T041">Mental Process</option> | |
| 555 <option value="T055">Individual Behavior</option> | |
| 556 <option value="T004">Fungus</option> | |
| 557 <option value="T060">Diagnostic Procedure</option> | |
| 558 <option value="T070">Natural Phenomenon or Process</option> | |
| 559 <option value="T197">Inorganic Chemical</option> | |
| 560 <option value="T057">Occupational Activity</option> | |
| 561 <option value="T083">Geographic Area</option> | |
| 562 <option value="T074">Medical Device</option> | |
| 563 <option value="T002">Plant</option> | |
| 564 <option value="T065">Educational Activity</option> | |
| 565 <option value="T092">Organization</option> | |
| 566 <option value="T009">Invertebrate</option> | |
| 567 <option value="T025">Cell</option> | |
| 568 <option value="T196">Element, Ion, or Isotope</option> | |
| 569 <option value="T067">Phenomenon or Process</option> | |
| 570 <option value="T080">Qualitative Concept</option> | |
| 571 <option value="T102">Group Attribute</option> | |
| 572 <option value="T098">Population Group</option> | |
| 573 <option value="T040">Organism Function</option> | |
| 574 <option value="T034">Laboratory or Test Result</option> | |
| 575 <option value="T201">Clinical Attribute</option> | |
| 576 <option value="T097">Professional or Occupational Group</option> | |
| 577 <option value="T064">Governmental or Regulatory Activity</option> | |
| 578 <option value="T054">Social Behavior</option> | |
| 579 <option value="T003">Alga</option> | |
| 580 <option value="T007">Bacterium</option> | |
| 581 <option value="T044">Molecular Function</option> | |
| 582 <option value="T053">Behavior</option> | |
| 583 <option value="T069">Environmental Effect of Humans</option> | |
| 584 <option value="T042">Organ or Tissue Function</option> | |
| 585 <option value="T103">Chemical</option> | |
| 586 <option value="T122">Biomedical or Dental Material</option> | |
| 587 <option value="T015">Mammal</option> | |
| 588 <option value="T020">Acquired Abnormality</option> | |
| 589 <option value="T030">Body Space or Junction</option> | |
| 590 <option value="T026">Cell Component</option> | |
| 591 <option value="T043">Cell Function</option> | |
| 592 <option value="T059">Laboratory Procedure</option> | |
| 593 <option value="T052">Activity</option> | |
| 594 <option value="T056">Daily or Recreational Activity</option> | |
| 595 <option value="T079">Temporal Concept</option> | |
| 596 <option value="T091">Biomedical Occupation or Discipline</option> | |
| 597 <option value="T192">Receptor</option> | |
| 598 <option value="T031">Body Substance</option> | |
| 599 <option value="T048">Mental or Behavioral Dysfunction</option> | |
| 600 <option value="T058">Health Care Activity</option> | |
| 601 <option value="T120">Chemical Viewed Functionally</option> | |
| 602 <option value="T100">Age Group</option> | |
| 603 <option value="T104">Chemical Viewed Structurally</option> | |
| 604 <option value="T171">Language</option> | |
| 605 <option value="T032">Organism Attribute</option> | |
| 606 <option value="T095">Self-help or Relief Organization</option> | |
| 607 <option value="T078">Idea or Concept</option> | |
| 608 <option value="T090">Occupation or Discipline</option> | |
| 609 <option value="T167">Substance</option> | |
| 610 <option value="T068">Human-caused Phenomenon or Process</option> | |
| 611 <option value="T168">Food</option> | |
| 612 <option value="T028">Gene or Genome</option> | |
| 613 <option value="T014">Reptile</option> | |
| 614 <option value="T050">Experimental Model of Disease</option> | |
| 615 <option value="T045">Genetic Function</option> | |
| 616 <option value="T011">Amphibian</option> | |
| 617 <option value="T013">Fish</option> | |
| 618 <option value="T094">Professional Society</option> | |
| 619 <option value="T087">Amino Acid Sequence</option> | |
| 620 <option value="T066">Machine Activity</option> | |
| 621 <option value="T185">Classification</option> | |
| 622 <option value="T006">Rickettsia or Chlamydia</option> | |
| 623 <option value="T049">Cell or Molecular Dysfunction</option> | |
| 624 <option value="T008">Animal</option> | |
| 625 <option value="T051">Event</option> | |
| 626 <option value="T038">Biologic Function</option> | |
| 627 <option value="T194">Archaeon</option> | |
| 628 <option value="T086">Nucleotide Sequence</option> | |
| 629 <option value="T039">Physiologic Function</option> | |
| 630 <option value="T012">Bird</option> | |
| 631 <option value="T063">Molecular Biology Research Technique</option> | |
| 632 <option value="T017">Anatomical Structure</option> | |
| 633 <option value="T082">Spatial Concept</option> | |
| 634 <option value="T088">Carbohydrate Sequence</option> | |
| 635 <option value="T099">Family Group</option> | |
| 636 <option value="T001">Organism</option> | |
| 637 <option value="T075">Research Device</option> | |
| 638 <option value="T096">Group</option> | |
| 639 <option value="T016">Human</option> | |
| 640 <option value="T072">Physical Object</option> | |
| 641 <option value="T071">Entity</option> | |
| 642 <option value="T200">Clinical Drug</option> | |
| 643 <option value="T085">Molecular Sequence</option> | |
| 644 <option value="T077">Conceptual Entity</option> | |
| 645 <option value="T010">Vertebrate</option> | |
| 646 <option value="T203">Drug Delivery Device</option> | |
| 647 <option value="T021">Fully Formed Anatomical Structure</option> | |
| 648 <option value="T204">Eukaryote</option> | |
| 649 </param> | |
| 650 <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"/> | |
| 651 <param name="mappingTypes" type="select" multiple="true" label="the list of mapping type to use during the mapping expansion step"> | |
| 652 <option value="m-all" selected="true">ALL</option> | |
| 653 <option value="m-null">None</option> | |
| 654 <option value="m-Automatic">Automatic</option> | |
| 655 <option value="m-Manual">Manual</option> | |
| 656 </param> | |
| 657 <param name="textToAnnotate" type="text" size="100" value="" label="Text to annotate"/> | |
| 658 <param name="format" type="select" label="File output format"> | |
| 659 <option value="xml" selected="true">XML</option> | |
| 660 <option value="text">Text</option> | |
| 661 <option value="tabDelimited">Tab Delimited</option> | |
| 662 </param> | |
| 663 <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> | |
| 664 </inputs> | |
| 665 <outputs> | |
| 666 <data format="text" name="output" /> | |
| 667 </outputs> | |
| 668 <tests> | |
| 669 <test> | |
| 670 <param name="longestOnly"/> | |
| 671 <param name="wholeWordOnly"/> | |
| 672 <param name="filterNumber"/> | |
| 673 <param name="stopWords"/> | |
| 674 <param name="withDefaultStopWords"/> | |
| 675 <param name="isTopWordsCaseSensitive"/> | |
| 676 <param name="mintermSize"/> | |
| 677 <param name="scored"/> | |
| 678 <param name="withSynonyms"/> | |
| 679 <param name="ontologiesToExpand"/> | |
| 680 <param name="ontologiesToKeepInResult"/> | |
| 681 <param name="semanticTypes"/> | |
| 682 <param name="levelMax"/> | |
| 683 <param name="mappingTypes"/> | |
| 684 <param name="textToAnnotate"/> | |
| 685 <param name="format"/> | |
| 686 <param name="apikey"/> | |
| 687 </test> | |
| 688 </tests> | |
| 689 <help> | |
| 690 | |
| 691 **Usage** | |
| 692 Enter bioportal API key, a text to annotate and specify the parameters, and the annotations will be retrieved. | |
| 693 | |
| 694 **Contact** | |
| 695 | |
| 696 Please send any request or comment to jose.minyarro@um.es | |
| 697 | |
| 698 **More information** | |
| 699 | |
| 700 http://bioportal.bioontology.org | |
| 701 | |
| 702 </help> | |
| 703 | |
| 704 </tool> |