Mercurial > repos > mikel-egana-aranguren > ncbo_services
comparison NCBO_services/ncbo_search.xml @ 14:54945f41b175
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| author | jose-minyarro |
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| date | Wed, 18 Jan 2012 03:57:27 -0500 |
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| 13:a745ae602157 | 14:54945f41b175 |
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| 1 <tool id="ncbo_search" name="Search for terms in bio-ontologies depending on the text provided" version="1.0.1"> | |
| 2 <description>Search for terms in bio-ontologies depending on the text provided</description> | |
| 3 <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_search_galaxy.jar $query $ontologyids $apikey > $output</command> | |
| 4 <inputs> | |
| 5 <param name="query" type="text" size="100" value="" label="Text to search for terms in the selected bio-ontologys"/> | |
| 6 <param name="ontologyids" type="select" multiple="true" label="Indicates the list of ontologies to search for during the search process"> | |
| 7 <option value="all" selected="true">ALL</option> | |
| 8 <option value="1394">Syndromic Surveillance Ontology</option> | |
| 9 <option value="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> | |
| 10 <option value="1158">Cell Behavior Ontology</option> | |
| 11 <option value="1033">NMR-instrument specific component of metabolomics investigations</option> | |
| 12 <option value="1351">Medical Subject Headings</option> | |
| 13 <option value="1146">Electrocardiography Ontology</option> | |
| 14 <option value="1041">Protein modification</option> | |
| 15 <option value="1058">SNP-Ontology</option> | |
| 16 <option value="1099">African Traditional Medicine</option> | |
| 17 <option value="1134">BioTop</option> | |
| 18 <option value="1247">GeoSpecies Ontology</option> | |
| 19 <option value="1024">Loggerhead nesting</option> | |
| 20 <option value="1257">MeGO</option> | |
| 21 <option value="1135">Pseudogene</option> | |
| 22 <option value="1126">Family Health History Ontology</option> | |
| 23 <option value="1108">Plant structure</option> | |
| 24 <option value="1114">Bilateria anatomy</option> | |
| 25 <option value="1100">Ontology for Genetic Interval</option> | |
| 26 <option value="1044">Sample processing and separation techniques</option> | |
| 27 <option value="1347">MedlinePlus Health Topics</option> | |
| 28 <option value="1152">Minimal anatomical terminology</option> | |
| 29 <option value="1063">Common Anatomy Reference Ontology</option> | |
| 30 <option value="1089">BIRNLex</option> | |
| 31 <option value="1116">Bleeding History Phenotype</option> | |
| 32 <option value="1104">Biomedical Resource Ontology</option> | |
| 33 <option value="1350">Logical Observation Identifier Names and Codes</option> | |
| 34 <option value="1082">Gene Regulation Ontology</option> | |
| 35 <option value="1047">Cereal plant development</option> | |
| 36 <option value="1349">Physician Data Query</option> | |
| 37 <option value="1190">Parasite Life Cycle</option> | |
| 38 <option value="1192">Proteomics Pipeline Infrastructure for CPTAC</option> | |
| 39 <option value="1352">National Drug File</option> | |
| 40 <option value="1059">Computer-based Patient Record Ontology</option> | |
| 41 <option value="1052">Protein Ontology</option> | |
| 42 <option value="1341">COSTART</option> | |
| 43 <option value="1344">International Classification of Primary Care</option> | |
| 44 <option value="1061">Suggested Ontology for Pharmacogenomics</option> | |
| 45 <option value="1353">SNOMED Clinical Terms</option> | |
| 46 <option value="1224">Symptom Ontology</option> | |
| 47 <option value="1013">eVOC (Expressed Sequence Annotation for Humans)</option> | |
| 48 <option value="1149">DermLex: The Dermatology Lexicon</option> | |
| 49 <option value="1311">Malaria Ontology</option> | |
| 50 <option value="1335">Parasite Experiment Ontology</option> | |
| 51 <option value="1370">Amphibian taxonomy</option> | |
| 52 <option value="1354">WHO Adverse Reaction Terminology</option> | |
| 53 <option value="1148">BioPortal Metadata</option> | |
| 54 <option value="1038">Plant growth and developmental stage</option> | |
| 55 <option value="1132">NCBI organismal classification</option> | |
| 56 <option value="1328">Ontology of homology and related concepts in biology</option> | |
| 57 <option value="1290">ABA Adult Mouse Brain</option> | |
| 58 <option value="1055">Galen</option> | |
| 59 <option value="1332">Basic Formal Ontology</option> | |
| 60 <option value="1183">Lipid Ontology</option> | |
| 61 <option value="1026">Multiple alignment</option> | |
| 62 <option value="1130">Cancer Research and Management ACGT Master Ontology</option> | |
| 63 <option value="1060">Epoch Clinical Trial Ontologies</option> | |
| 64 <option value="1369">PhysicalFields</option> | |
| 65 <option value="1086">Ontology for disease genetic investigation</option> | |
| 66 <option value="1122">Skin Physiology Ontology</option> | |
| 67 <option value="1142">Cardiac Electrophysiology Ontology</option> | |
| 68 <option value="1128">Comparative Data Analysis Ontology</option> | |
| 69 <option value="1088">MaHCO - An MHC Ontology</option> | |
| 70 <option value="1249">Smoking Behavior Risk Ontology</option> | |
| 71 <option value="1039">Proteomics data and process provenance</option> | |
| 72 <option value="1040">Protein-protein interaction</option> | |
| 73 <option value="1068">Subcellular Anatomy Ontology (SAO)</option> | |
| 74 <option value="1087">Ontology of Geographical Region</option> | |
| 75 <option value="1094">Pathogen transmission</option> | |
| 76 <option value="1131">MGED Ontology</option> | |
| 77 <option value="1106">Gene Regulation Ontology</option> | |
| 78 <option value="1054">Amino Acid</option> | |
| 79 <option value="1056">Basic Vertebrate Anatomy</option> | |
| 80 <option value="1083">NanoParticle Ontology</option> | |
| 81 <option value="1053">Foundational Model of Anatomy</option> | |
| 82 <option value="1092">Infectious disease</option> | |
| 83 <option value="1393">Information Artifact Ontology</option> | |
| 84 <option value="1395">MDSS Mo</option> | |
| 85 <option value="1397">Gazetteer</option> | |
| 86 <option value="1398">Ontology of Language Disorder in Autism</option> | |
| 87 <option value="1399">Pilot Ontology</option> | |
| 88 <option value="1406">linkingkin2pep</option> | |
| 89 <option value="1409">PKO_Re</option> | |
| 90 <option value="1410">Kinetic Simulation Algorithm Ontology</option> | |
| 91 <option value="1415">Common Terminology Criteria for Adverse Events</option> | |
| 92 <option value="1418">TOK_Ontology</option> | |
| 93 <option value="1419">Taxonomic rank vocabulary</option> | |
| 94 <option value="1422">MedDRA</option> | |
| 95 <option value="1424">National Drug Data File</option> | |
| 96 <option value="1425">ICD-10-PCS</option> | |
| 97 <option value="1426">Master Drug Data Base</option> | |
| 98 <option value="1429">ICPC-2 PLUS</option> | |
| 99 <option value="1430">AIR</option> | |
| 100 <option value="1438">Breast tissue cell lines</option> | |
| 101 <option value="1439">General Formal Ontology</option> | |
| 102 <option value="1440">General Formal Ontology: Biology</option> | |
| 103 <option value="1343">Health Level Seven</option> | |
| 104 <option value="1484">International Classification of External Causes of Injuries</option> | |
| 105 <option value="1487">Body System</option> | |
| 106 <option value="1490">Platynereis stage ontology</option> | |
| 107 <option value="1491">IMGT-ONTOLOGY</option> | |
| 108 <option value="1494">Tissue Microarray Ontology</option> | |
| 109 <option value="1497">PMA 2010</option> | |
| 110 <option value="1500">RNA ontology</option> | |
| 111 <option value="1501">Neomark Oral Cancer-Centred Ontology</option> | |
| 112 <option value="1504">Current Procedural Terminology</option> | |
| 113 <option value="1505">Ontology for MicroRNA Target Prediction</option> | |
| 114 <option value="1506">Gene Ontology Extension</option> | |
| 115 <option value="1507">Cell Cycle Ontology</option> | |
| 116 <option value="1509">ICPS Network</option> | |
| 117 <option value="1510">Metathesaurus CPT Hierarchical Terms</option> | |
| 118 <option value="1515">Interaction Network Ontology</option> | |
| 119 <option value="1516">ICD10</option> | |
| 120 <option value="1521">Neural Motor Recovery Ontology</option> | |
| 121 <option value="1522">BioPAX</option> | |
| 122 <option value="1523">OBOE SBC</option> | |
| 123 <option value="1524">OBOE</option> | |
| 124 <option value="1526">CRISP Thesaurus, 2006</option> | |
| 125 <option value="1527">VANDF</option> | |
| 126 <option value="1528">HUGO</option> | |
| 127 <option value="1529">HCPCS</option> | |
| 128 <option value="1530">Animal natural history and life history</option> | |
| 129 <option value="1534">apollo-akesios</option> | |
| 130 <option value="1537">Brucellosis Ontology</option> | |
| 131 <option value="1538">Role Ontology</option> | |
| 132 <option value="1539">Neural-Immune Gene Ontology</option> | |
| 133 <option value="1540">Ontology for Drug Discovery Investigations</option> | |
| 134 <option value="1541">Cell line ontology</option> | |
| 135 <option value="1545">Wheat trait </option> | |
| 136 <option value="1547">BRENDA tissue / enzyme source</option> | |
| 137 <option value="1552">Reproductive traits ontology</option> | |
| 138 <option value="1553">ICD10CM</option> | |
| 139 <option value="1560">Cognitive Paradigm Ontology</option> | |
| 140 <option value="1423">RxNORM</option> | |
| 141 <option value="1517">Human developmental anatomy, abstract version, v2</option> | |
| 142 <option value="1016">Drosophila development</option> | |
| 143 <option value="1062">PRotein Ontology (PRO)</option> | |
| 144 <option value="1000">Mouse adult gross anatomy</option> | |
| 145 <option value="1065">Tick gross anatomy</option> | |
| 146 <option value="1123">Ontology for Biomedical Investigations</option> | |
| 147 <option value="1078">Spatial Ontology</option> | |
| 148 <option value="1007">Chemical entities of biological interest</option> | |
| 149 <option value="1049">C. elegans development</option> | |
| 150 <option value="1070">Gene Ontology</option> | |
| 151 <option value="1136">Experimental Factor Ontology</option> | |
| 152 <option value="1141">Ontology of Physics for Biology</option> | |
| 153 <option value="1005">BRENDA tissue / enzyme source</option> | |
| 154 <option value="1321">Neural ElectroMagnetic Ontologies</option> | |
| 155 <option value="1043">Physico-chemical process</option> | |
| 156 <option value="1064">Fly taxonomy</option> | |
| 157 <option value="1076">Ontology of Clinical Research (OCRe)</option> | |
| 158 <option value="1110">Teleost Anatomy Ontology</option> | |
| 159 <option value="1362">Hymenoptera Anatomy Ontology</option> | |
| 160 <option value="1030">Mosquito gross anatomy</option> | |
| 161 <option value="1029">Molecule role (INOH Protein name/family name ontology)</option> | |
| 162 <option value="1144">Dendritic cell</option> | |
| 163 <option value="1125">Human Phenotype Ontology</option> | |
| 164 <option value="1023">Biological imaging methods</option> | |
| 165 <option value="1021">Human developmental anatomy, abstract version</option> | |
| 166 <option value="1046">Systems Biology</option> | |
| 167 <option value="1051">Zebrafish anatomy and development</option> | |
| 168 <option value="1037">Cereal plant trait</option> | |
| 169 <option value="1107">Phenotypic quality</option> | |
| 170 <option value="1081">Teleost taxonomy</option> | |
| 171 <option value="1048">C. elegans gross anatomy</option> | |
| 172 <option value="1050">Maize gross anatomy</option> | |
| 173 <option value="1036">Plant environmental conditions</option> | |
| 174 <option value="1109">Sequence types and features</option> | |
| 175 <option value="1022">Human developmental anatomy, timed version</option> | |
| 176 <option value="1095">Xenopus anatomy and development</option> | |
| 177 <option value="1027">Medaka fish anatomy and development</option> | |
| 178 <option value="1011">Event (INOH pathway ontology)</option> | |
| 179 <option value="1010">Mouse gross anatomy and development</option> | |
| 180 <option value="1015">Drosophila gross anatomy</option> | |
| 181 <option value="1090">Amphibian gross anatomy</option> | |
| 182 <option value="1019">Fungal gross anatomy</option> | |
| 183 <option value="1067">C. elegans phenotype</option> | |
| 184 <option value="1069">Environment Ontology</option> | |
| 185 <option value="1112">Units of measurement</option> | |
| 186 <option value="1091">Spider Ontology</option> | |
| 187 <option value="1017">FlyBase Controlled Vocabulary</option> | |
| 188 <option value="1348">Online Mendelian Inheritance in Man</option> | |
| 189 <option value="1172">Vaccine Ontology</option> | |
| 190 <option value="1222">Ascomycete phenotype ontology</option> | |
| 191 <option value="1105">Mass spectrometry</option> | |
| 192 <option value="1237">Situation-Based Access Control</option> | |
| 193 <option value="1008">Dictyostelium discoideum anatomy</option> | |
| 194 <option value="1150">Rat Strain Ontology</option> | |
| 195 <option value="1101">International Classification of Diseases</option> | |
| 196 <option value="1314">Cell Line Ontology</option> | |
| 197 <option value="1009">Human disease</option> | |
| 198 <option value="1084">NIFSTD</option> | |
| 199 <option value="1025">Mammalian phenotype</option> | |
| 200 <option value="1035">Pathway ontology</option> | |
| 201 <option value="1012">Evidence codes</option> | |
| 202 <option value="1115">Yeast phenotypes</option> | |
| 203 <option value="1001">Cereal plant gross anatomy</option> | |
| 204 <option value="1006">Cell type</option> | |
| 205 <option value="1077">Mosquito insecticide resistance</option> | |
| 206 <option value="1085">Ontology of Glucose Metabolism Disorder</option> | |
| 207 <option value="1057">RadLex</option> | |
| 208 <option value="1031">Mouse pathology</option> | |
| 209 <option value="1032">NCI Thesaurus</option> | |
| 210 <option value="1381">NIF Dysfunction</option> | |
| 211 <option value="1401">International Classification for Nursing Practice</option> | |
| 212 <option value="1402">NIF Cell</option> | |
| 213 <option value="1404">Uber anatomy ontology</option> | |
| 214 <option value="1407">Terminology for the Description of Dynamics</option> | |
| 215 <option value="1411">International Classification of Functioning, Disability and Health (ICF)</option> | |
| 216 <option value="1413">Software Ontology</option> | |
| 217 <option value="1414">Ontology for General Medical Science</option> | |
| 218 <option value="1444">Chemical Information Ontology</option> | |
| 219 <option value="1461">Translational Medicine Ontology</option> | |
| 220 <option value="1488">SysMO-JERM</option> | |
| 221 <option value="1489">Adverse Event Ontology</option> | |
| 222 <option value="1498">EDAM</option> | |
| 223 <option value="1532">SemanticScience Integrated Ontology</option> | |
| 224 <option value="1550">PHARE</option> | |
| 225 <option value="1555">Vertebrate Anatomy Ontology</option> | |
| 226 <option value="1565">Ontology of Medically Related Social Entities</option> | |
| 227 <option value="1567">Pharmacovigilance Ontology</option> | |
| 228 <option value="1568">Anatomical Entity Ontology</option> | |
| 229 <option value="1569">Host Pathogen Interactions Ontology</option> | |
| 230 <option value="1570">Traditional Medicine Constitution Value Set</option> | |
| 231 <option value="1571">Traditional Medicine Other Factors Value Set</option> | |
| 232 <option value="1572">Traditional Medicine Signs and Symptoms Value Set</option> | |
| 233 <option value="1573">Traditional Medicine Meridian Value Sets</option> | |
| 234 <option value="1574">vertebrate Homologous Organ Groups</option> | |
| 235 <option value="1575">ExO</option> | |
| 236 <option value="1576">FDA Medical Devices (2010)</option> | |
| 237 <option value="1578">HOM_ElixhauserScores</option> | |
| 238 <option value="1580">Adverse Event Reporting ontology</option> | |
| 239 <option value="1581">HEALTH_INDICATORS</option> | |
| 240 <option value="1582">COA</option> | |
| 241 <option value="1583">Clinical Measurement Ontology</option> | |
| 242 <option value="1584">Measurement Method Ontology</option> | |
| 243 <option value="1585">Experimental Conditions Ontology</option> | |
| 244 <option value="1587">Plant Ontology</option> | |
| 245 <option value="1588">Ontology of General Purpose Datatypes</option> | |
| 246 <option value="1596">MajDxCatgrs-DxRltdGrps</option> | |
| 247 <option value="1613">Bone Dysplasia Ontology</option> | |
| 248 <option value="1614">IxnO</option> | |
| 249 <option value="1615">Systems Chemical Biology/Chemogenomics </option> | |
| 250 <option value="1616">Phylogenetic Ontology</option> | |
| 251 <option value="1621">Neuro Behavior Ontology</option> | |
| 252 </param> | |
| 253 <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> | |
| 254 </inputs> | |
| 255 <outputs> | |
| 256 <data format="text" name="output" /> | |
| 257 </outputs> | |
| 258 <tests> | |
| 259 <test> | |
| 260 <param name="query"/> | |
| 261 <param name="ontologyids"/> | |
| 262 <param name="apikey"/> | |
| 263 </test> | |
| 264 </tests> | |
| 265 <help> | |
| 266 | |
| 267 **Usage** | |
| 268 Enter bioportal API key, a text, and the list of bioontolgies Ids to search for and the search interface retrieves the bioontology terms associated with the text provided. | |
| 269 Example of search text: Breast cancer | |
| 270 | |
| 271 **Contact** | |
| 272 | |
| 273 Please send any request or comment to jose.minyarro@um.es | |
| 274 | |
| 275 **More information** | |
| 276 | |
| 277 http://bioportal.bioontology.org | |
| 278 | |
| 279 </help> | |
| 280 | |
| 281 </tool> |