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