10
+ − 1 <tool id="ncbo_recommender" name="Recommends a bio-ontology depending on annotations of a text" version="1.0.1">
+ − 2 <description>Provides a bio-ontology as a recommendation depending on the annotations from a biological text</description>
+ − 3 <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_recommender_galaxy.jar $text $format $ontologyId $apikey > $output </command>
+ − 4 <inputs>
+ − 5 <param name="text" type="text" size="100" value="" label="Text to provide a recommendation of the most suitable bio-ontology"/>
+ − 6 <param name="format" type="select" label="File output format">
+ − 7 <option value="xml" selected="true">XML</option>
+ − 8 <option value="text">Text</option>
+ − 9 <option value="simpleText">Simple Text</option>
+ − 10 </param>
+ − 11 <param name="ontologyId" type="select" multiple="true" label="Indicates the list of ontologies to search for the recommendation process">
+ − 12 <option value="all" selected="true">ALL</option>
+ − 13 <option value="1394">Syndromic Surveillance Ontology</option>
+ − 14 <option value="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
+ − 15 <option value="1158">Cell Behavior Ontology</option>
+ − 16 <option value="1033">NMR-instrument specific component of metabolomics investigations</option>
+ − 17 <option value="1351">Medical Subject Headings</option>
+ − 18 <option value="1146">Electrocardiography Ontology</option>
+ − 19 <option value="1041">Protein modification</option>
+ − 20 <option value="1058">SNP-Ontology</option>
+ − 21 <option value="1099">African Traditional Medicine</option>
+ − 22 <option value="1134">BioTop</option>
+ − 23 <option value="1247">GeoSpecies Ontology</option>
+ − 24 <option value="1024">Loggerhead nesting</option>
+ − 25 <option value="1257">MeGO</option>
+ − 26 <option value="1135">Pseudogene</option>
+ − 27 <option value="1126">Family Health History Ontology</option>
+ − 28 <option value="1108">Plant structure</option>
+ − 29 <option value="1114">Bilateria anatomy</option>
+ − 30 <option value="1100">Ontology for Genetic Interval</option>
+ − 31 <option value="1044">Sample processing and separation techniques</option>
+ − 32 <option value="1347">MedlinePlus Health Topics</option>
+ − 33 <option value="1152">Minimal anatomical terminology</option>
+ − 34 <option value="1063">Common Anatomy Reference Ontology</option>
+ − 35 <option value="1089">BIRNLex</option>
+ − 36 <option value="1116">Bleeding History Phenotype</option>
+ − 37 <option value="1104">Biomedical Resource Ontology</option>
+ − 38 <option value="1350">Logical Observation Identifier Names and Codes</option>
+ − 39 <option value="1082">Gene Regulation Ontology</option>
+ − 40 <option value="1047">Cereal plant development</option>
+ − 41 <option value="1349">Physician Data Query</option>
+ − 42 <option value="1190">Parasite Life Cycle</option>
+ − 43 <option value="1192">Proteomics Pipeline Infrastructure for CPTAC</option>
+ − 44 <option value="1352">National Drug File</option>
+ − 45 <option value="1059">Computer-based Patient Record Ontology</option>
+ − 46 <option value="1052">Protein Ontology</option>
+ − 47 <option value="1341">COSTART</option>
+ − 48 <option value="1344">International Classification of Primary Care</option>
+ − 49 <option value="1061">Suggested Ontology for Pharmacogenomics</option>
+ − 50 <option value="1353">SNOMED Clinical Terms</option>
+ − 51 <option value="1224">Symptom Ontology</option>
+ − 52 <option value="1013">eVOC (Expressed Sequence Annotation for Humans)</option>
+ − 53 <option value="1149">DermLex: The Dermatology Lexicon</option>
+ − 54 <option value="1311">Malaria Ontology</option>
+ − 55 <option value="1335">Parasite Experiment Ontology</option>
+ − 56 <option value="1370">Amphibian taxonomy</option>
+ − 57 <option value="1354">WHO Adverse Reaction Terminology</option>
+ − 58 <option value="1148">BioPortal Metadata</option>
+ − 59 <option value="1038">Plant growth and developmental stage</option>
+ − 60 <option value="1132">NCBI organismal classification</option>
+ − 61 <option value="1328">Ontology of homology and related concepts in biology</option>
+ − 62 <option value="1290">ABA Adult Mouse Brain</option>
+ − 63 <option value="1055">Galen</option>
+ − 64 <option value="1332">Basic Formal Ontology</option>
+ − 65 <option value="1183">Lipid Ontology</option>
+ − 66 <option value="1026">Multiple alignment</option>
+ − 67 <option value="1130">Cancer Research and Management ACGT Master Ontology</option>
+ − 68 <option value="1060">Epoch Clinical Trial Ontologies</option>
+ − 69 <option value="1369">PhysicalFields</option>
+ − 70 <option value="1086">Ontology for disease genetic investigation</option>
+ − 71 <option value="1122">Skin Physiology Ontology</option>
+ − 72 <option value="1142">Cardiac Electrophysiology Ontology</option>
+ − 73 <option value="1128">Comparative Data Analysis Ontology</option>
+ − 74 <option value="1088">MaHCO - An MHC Ontology</option>
+ − 75 <option value="1249">Smoking Behavior Risk Ontology</option>
+ − 76 <option value="1039">Proteomics data and process provenance</option>
+ − 77 <option value="1040">Protein-protein interaction</option>
+ − 78 <option value="1068">Subcellular Anatomy Ontology (SAO)</option>
+ − 79 <option value="1087">Ontology of Geographical Region</option>
+ − 80 <option value="1094">Pathogen transmission</option>
+ − 81 <option value="1131">MGED Ontology</option>
+ − 82 <option value="1106">Gene Regulation Ontology</option>
+ − 83 <option value="1054">Amino Acid</option>
+ − 84 <option value="1056">Basic Vertebrate Anatomy</option>
+ − 85 <option value="1083">NanoParticle Ontology</option>
+ − 86 <option value="1053">Foundational Model of Anatomy</option>
+ − 87 <option value="1092">Infectious disease</option>
+ − 88 <option value="1393">Information Artifact Ontology</option>
+ − 89 <option value="1395">MDSS Mo</option>
+ − 90 <option value="1397">Gazetteer</option>
+ − 91 <option value="1398">Ontology of Language Disorder in Autism</option>
+ − 92 <option value="1399">Pilot Ontology</option>
+ − 93 <option value="1406">linkingkin2pep</option>
+ − 94 <option value="1409">PKO_Re</option>
+ − 95 <option value="1410">Kinetic Simulation Algorithm Ontology</option>
+ − 96 <option value="1415">Common Terminology Criteria for Adverse Events</option>
+ − 97 <option value="1418">TOK_Ontology</option>
+ − 98 <option value="1419">Taxonomic rank vocabulary</option>
+ − 99 <option value="1422">MedDRA</option>
+ − 100 <option value="1424">National Drug Data File</option>
+ − 101 <option value="1425">ICD-10-PCS</option>
+ − 102 <option value="1426">Master Drug Data Base</option>
+ − 103 <option value="1429">ICPC-2 PLUS</option>
+ − 104 <option value="1430">AIR</option>
+ − 105 <option value="1438">Breast tissue cell lines</option>
+ − 106 <option value="1439">General Formal Ontology</option>
+ − 107 <option value="1440">General Formal Ontology: Biology</option>
+ − 108 <option value="1343">Health Level Seven</option>
+ − 109 <option value="1484">International Classification of External Causes of Injuries</option>
+ − 110 <option value="1487">Body System</option>
+ − 111 <option value="1490">Platynereis stage ontology</option>
+ − 112 <option value="1491">IMGT-ONTOLOGY</option>
+ − 113 <option value="1494">Tissue Microarray Ontology</option>
+ − 114 <option value="1497">PMA 2010</option>
+ − 115 <option value="1500">RNA ontology</option>
+ − 116 <option value="1501">Neomark Oral Cancer-Centred Ontology</option>
+ − 117 <option value="1504">Current Procedural Terminology</option>
+ − 118 <option value="1505">Ontology for MicroRNA Target Prediction</option>
+ − 119 <option value="1506">Gene Ontology Extension</option>
+ − 120 <option value="1507">Cell Cycle Ontology</option>
+ − 121 <option value="1509">ICPS Network</option>
+ − 122 <option value="1510">Metathesaurus CPT Hierarchical Terms</option>
+ − 123 <option value="1515">Interaction Network Ontology</option>
+ − 124 <option value="1516">ICD10</option>
+ − 125 <option value="1521">Neural Motor Recovery Ontology</option>
+ − 126 <option value="1522">BioPAX</option>
+ − 127 <option value="1523">OBOE SBC</option>
+ − 128 <option value="1524">OBOE</option>
+ − 129 <option value="1526">CRISP Thesaurus, 2006</option>
+ − 130 <option value="1527">VANDF</option>
+ − 131 <option value="1528">HUGO</option>
+ − 132 <option value="1529">HCPCS</option>
+ − 133 <option value="1530">Animal natural history and life history</option>
+ − 134 <option value="1534">apollo-akesios</option>
+ − 135 <option value="1537">Brucellosis Ontology</option>
+ − 136 <option value="1538">Role Ontology</option>
+ − 137 <option value="1539">Neural-Immune Gene Ontology</option>
+ − 138 <option value="1540">Ontology for Drug Discovery Investigations</option>
+ − 139 <option value="1541">Cell line ontology</option>
+ − 140 <option value="1545">Wheat trait </option>
+ − 141 <option value="1547">BRENDA tissue / enzyme source</option>
+ − 142 <option value="1552">Reproductive traits ontology</option>
+ − 143 <option value="1553">ICD10CM</option>
+ − 144 <option value="1560">Cognitive Paradigm Ontology</option>
+ − 145 <option value="1423">RxNORM</option>
+ − 146 <option value="1517">Human developmental anatomy, abstract version, v2</option>
+ − 147 <option value="1016">Drosophila development</option>
+ − 148 <option value="1062">PRotein Ontology (PRO)</option>
+ − 149 <option value="1000">Mouse adult gross anatomy</option>
+ − 150 <option value="1065">Tick gross anatomy</option>
+ − 151 <option value="1123">Ontology for Biomedical Investigations</option>
+ − 152 <option value="1078">Spatial Ontology</option>
+ − 153 <option value="1007">Chemical entities of biological interest</option>
+ − 154 <option value="1049">C. elegans development</option>
+ − 155 <option value="1070">Gene Ontology</option>
+ − 156 <option value="1136">Experimental Factor Ontology</option>
+ − 157 <option value="1141">Ontology of Physics for Biology</option>
+ − 158 <option value="1005">BRENDA tissue / enzyme source</option>
+ − 159 <option value="1321">Neural ElectroMagnetic Ontologies</option>
+ − 160 <option value="1043">Physico-chemical process</option>
+ − 161 <option value="1064">Fly taxonomy</option>
+ − 162 <option value="1076">Ontology of Clinical Research (OCRe)</option>
+ − 163 <option value="1110">Teleost Anatomy Ontology</option>
+ − 164 <option value="1362">Hymenoptera Anatomy Ontology</option>
+ − 165 <option value="1030">Mosquito gross anatomy</option>
+ − 166 <option value="1029">Molecule role (INOH Protein name/family name ontology)</option>
+ − 167 <option value="1144">Dendritic cell</option>
+ − 168 <option value="1125">Human Phenotype Ontology</option>
+ − 169 <option value="1023">Biological imaging methods</option>
+ − 170 <option value="1021">Human developmental anatomy, abstract version</option>
+ − 171 <option value="1046">Systems Biology</option>
+ − 172 <option value="1051">Zebrafish anatomy and development</option>
+ − 173 <option value="1037">Cereal plant trait</option>
+ − 174 <option value="1107">Phenotypic quality</option>
+ − 175 <option value="1081">Teleost taxonomy</option>
+ − 176 <option value="1048">C. elegans gross anatomy</option>
+ − 177 <option value="1050">Maize gross anatomy</option>
+ − 178 <option value="1036">Plant environmental conditions</option>
+ − 179 <option value="1109">Sequence types and features</option>
+ − 180 <option value="1022">Human developmental anatomy, timed version</option>
+ − 181 <option value="1095">Xenopus anatomy and development</option>
+ − 182 <option value="1027">Medaka fish anatomy and development</option>
+ − 183 <option value="1011">Event (INOH pathway ontology)</option>
+ − 184 <option value="1010">Mouse gross anatomy and development</option>
+ − 185 <option value="1015">Drosophila gross anatomy</option>
+ − 186 <option value="1090">Amphibian gross anatomy</option>
+ − 187 <option value="1019">Fungal gross anatomy</option>
+ − 188 <option value="1067">C. elegans phenotype</option>
+ − 189 <option value="1069">Environment Ontology</option>
+ − 190 <option value="1112">Units of measurement</option>
+ − 191 <option value="1091">Spider Ontology</option>
+ − 192 <option value="1017">FlyBase Controlled Vocabulary</option>
+ − 193 <option value="1348">Online Mendelian Inheritance in Man</option>
+ − 194 <option value="1172">Vaccine Ontology</option>
+ − 195 <option value="1222">Ascomycete phenotype ontology</option>
+ − 196 <option value="1105">Mass spectrometry</option>
+ − 197 <option value="1237">Situation-Based Access Control</option>
+ − 198 <option value="1008">Dictyostelium discoideum anatomy</option>
+ − 199 <option value="1150">Rat Strain Ontology</option>
+ − 200 <option value="1101">International Classification of Diseases</option>
+ − 201 <option value="1314">Cell Line Ontology</option>
+ − 202 <option value="1009">Human disease</option>
+ − 203 <option value="1084">NIFSTD</option>
+ − 204 <option value="1025">Mammalian phenotype</option>
+ − 205 <option value="1035">Pathway ontology</option>
+ − 206 <option value="1012">Evidence codes</option>
+ − 207 <option value="1115">Yeast phenotypes</option>
+ − 208 <option value="1001">Cereal plant gross anatomy</option>
+ − 209 <option value="1006">Cell type</option>
+ − 210 <option value="1077">Mosquito insecticide resistance</option>
+ − 211 <option value="1085">Ontology of Glucose Metabolism Disorder</option>
+ − 212 <option value="1057">RadLex</option>
+ − 213 <option value="1031">Mouse pathology</option>
+ − 214 <option value="1032">NCI Thesaurus</option>
+ − 215 <option value="1381">NIF Dysfunction</option>
+ − 216 <option value="1401">International Classification for Nursing Practice</option>
+ − 217 <option value="1402">NIF Cell</option>
+ − 218 <option value="1404">Uber anatomy ontology</option>
+ − 219 <option value="1407">Terminology for the Description of Dynamics</option>
+ − 220 <option value="1411">International Classification of Functioning, Disability and Health (ICF)</option>
+ − 221 <option value="1413">Software Ontology</option>
+ − 222 <option value="1414">Ontology for General Medical Science</option>
+ − 223 <option value="1444">Chemical Information Ontology</option>
+ − 224 <option value="1461">Translational Medicine Ontology</option>
+ − 225 <option value="1488">SysMO-JERM</option>
+ − 226 <option value="1489">Adverse Event Ontology</option>
+ − 227 <option value="1498">EDAM</option>
+ − 228 <option value="1532">SemanticScience Integrated Ontology</option>
+ − 229 <option value="1550">PHARE</option>
+ − 230 <option value="1555">Vertebrate Anatomy Ontology</option>
+ − 231 <option value="1565">Ontology of Medically Related Social Entities</option>
+ − 232 <option value="1567">Pharmacovigilance Ontology</option>
+ − 233 <option value="1568">Anatomical Entity Ontology</option>
+ − 234 <option value="1569">Host Pathogen Interactions Ontology</option>
+ − 235 <option value="1570">Traditional Medicine Constitution Value Set</option>
+ − 236 <option value="1571">Traditional Medicine Other Factors Value Set</option>
+ − 237 <option value="1572">Traditional Medicine Signs and Symptoms Value Set</option>
+ − 238 <option value="1573">Traditional Medicine Meridian Value Sets</option>
+ − 239 <option value="1574">vertebrate Homologous Organ Groups</option>
+ − 240 <option value="1575">ExO</option>
+ − 241 <option value="1576">FDA Medical Devices (2010)</option>
+ − 242 <option value="1578">HOM_ElixhauserScores</option>
+ − 243 <option value="1580">Adverse Event Reporting ontology</option>
+ − 244 <option value="1581">HEALTH_INDICATORS</option>
+ − 245 <option value="1582">COA</option>
+ − 246 <option value="1583">Clinical Measurement Ontology</option>
+ − 247 <option value="1584">Measurement Method Ontology</option>
+ − 248 <option value="1585">Experimental Conditions Ontology</option>
+ − 249 <option value="1587">Plant Ontology</option>
+ − 250 <option value="1588">Ontology of General Purpose Datatypes</option>
+ − 251 <option value="1596">MajDxCatgrs-DxRltdGrps</option>
+ − 252 <option value="1613">Bone Dysplasia Ontology</option>
+ − 253 <option value="1614">IxnO</option>
+ − 254 <option value="1615">Systems Chemical Biology/Chemogenomics </option>
+ − 255 <option value="1616">Phylogenetic Ontology</option>
+ − 256 <option value="1621">Neuro Behavior Ontology</option>
+ − 257 </param>
+ − 258 <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/>
+ − 259 </inputs>
+ − 260 <outputs>
+ − 261 <data format="text" name="output" />
+ − 262 </outputs>
+ − 263 <tests>
+ − 264 <test>
+ − 265 <param name="text"/>
+ − 266 <param name="format"/>
+ − 267 <param name="ontologyId"/>
+ − 268 <param name="apikey"/>
+ − 269 </test>
+ − 270 </tests>
+ − 271 <help>
+ − 272
+ − 273 **Usage**
+ − 274 Enter bioportal API key, a text, the output format and a list of bioontolgies Ids and the recommender retrieves the bioontology with the best annotations.
+ − 275
+ − 276 **Contact**
+ − 277
+ − 278 Please send any request or comment to jose.minyarro@um.es
+ − 279
+ − 280 **More information**
+ − 281
+ − 282 http://bioportal.bioontology.org
+ − 283
+ − 284 </help>
+ − 285
+ − 286 </tool>
