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1 <tool id="get_ontology" name="Get ontology by id" version="1.0.3">
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2 <description>Retrieves an ontology from bioportal using its id</description>
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3 <!-- <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_galaxy.jar $api_key $ontology_id > $output </command> -->
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4 <command>
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5 #if $id_opts.id_opts_menu=="id_by_hand" #java -jar ${__tool_data_path__}/shared/jars/get_ontology.jar $api_key $id_opts.ontology_id > $output
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6 #else #java -jar ${__tool_data_path__}/shared/jars/get_ontology.jar $api_key $id_opts.ontology_id > $output
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7 #end if
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8 </command>
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9
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10 <inputs>
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11 <param name="api_key" type="text" size="100" label="BioPortal API key" />
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12
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13 <!-- <param name="ontology_id" type="text" size="100" label="Provide ontology id ... " /> -->
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14
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15 <conditional name="id_opts">
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16 <!--<param name="id_opts_menu" type="select" value="none" multiple="false" label="Choose: provide id by hand (e.g. 1522 for BioPAX) or choose ontology from list">
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17 <option value="id_by_hand">Provide id by hand</option>
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18 <option value="choose_from_list">Choose ontology from list</option>
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19 </param>-->
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20
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21 <param name="id_opts_menu" type="boolean" value="False" truevalue="id_by_hand" falsevalue="choose_from_list" label="Tick the box if you want to enter the ontology ID by hand (e.g. 1522 for BioPAX). Otherwise use the dropdown menu bellow"/>
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22
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23 <when value="id_by_hand">
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24 <param name="ontology_id" type="text" size="100" label="Provide ontology id" />
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25 </when>
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26
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27 <when value="choose_from_list">
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28 <!-- Automatically generated with http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey -->
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29 <param name="ontology_id" type="select" multiple="false" label="Choose ontology from this list">
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30 <option value="1158">Cell Behavior Ontology</option>
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31 <option value="1016">Drosophila development</option>
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32 <option value="1033">NMR-instrument specific component of metabolomics investigations</option>
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33 <option value="1351">Medical Subject Headings</option>
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34 <option value="1146">Electrocardiography Ontology</option>
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35 <option value="1041">Protein modification</option>
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36 <option value="1062">PRotein Ontology (PRO)</option>
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37 <option value="1000">Mouse adult gross anatomy</option>
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38 <option value="1065">Tick gross anatomy</option>
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39 <option value="1123">Ontology for Biomedical Investigations</option>
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40 <option value="1058">SNP-Ontology</option>
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41 <option value="1099">African Traditional Medicine</option>
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42 <option value="1134">BioTop</option>
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43 <option value="1078">Spatial Ontology</option>
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44 <option value="1247">GeoSpecies Ontology</option>
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45 <option value="1007">Chemical entities of biological interest</option>
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46 <option value="1024">Loggerhead nesting</option>
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47 <option value="1257">MeGO</option>
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48 <option value="1135">Pseudogene</option>
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49 <option value="1049">C. elegans development</option>
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50 <option value="1070">Gene Ontology</option>
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51 <option value="1126">Family Health History Ontology</option>
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52 <option value="1108">Plant Anatomy</option>
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53 <option value="1114">Bilateria anatomy</option>
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54 <option value="1100">Ontology for Genetic Interval</option>
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55 <option value="1136">Experimental Factor Ontology</option>
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56 <option value="1141">Ontology of Physics for Biology</option>
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57 <option value="1044">Sample processing and separation techniques</option>
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58 <option value="1347">MedlinePlus Health Topics</option>
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59 <option value="1005">BRENDA tissue / enzyme source</option>
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60 <option value="1152">Minimal anatomical terminology</option>
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61 <option value="1063">Common Anatomy Reference Ontology</option>
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62 <option value="1321">Neural ElectroMagnetic Ontologies</option>
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63 <option value="1043">Physico-chemical process</option>
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64 <option value="1064">Fly taxonomy</option>
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65 <option value="1089">BIRNLex</option>
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66 <option value="1076">Ontology of Clinical Research (OCRe)</option>
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67 <option value="1110">Teleost Anatomy Ontology</option>
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68 <option value="1362">Hymenoptera Anatomy Ontology</option>
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69 <option value="1030">Mosquito gross anatomy</option>
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70 <option value="1029">Molecule role (INOH Protein name/family name ontology)</option>
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71 <option value="1116">Bleeding History Phenotype</option>
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72 <option value="1104">Biomedical Resource Ontology</option>
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73 <option value="1144">Dendritic cell</option>
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74 <option value="1125">Human Phenotype Ontology</option>
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75 <option value="1023">Biological imaging methods</option>
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76 <option value="1021">Human developmental anatomy, abstract version</option>
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77 <option value="1046">Systems Biology</option>
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78 <option value="1051">Zebrafish anatomy and development</option>
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79 <option value="1037">Plant Trait Ontology</option>
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80 <option value="1350">Logical Observation Identifier Names and Codes</option>
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81 <option value="1082">Gene Regulation Ontology</option>
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82 <option value="1107">Phenotypic quality</option>
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83 <option value="1081">Teleost taxonomy</option>
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84 <option value="1048">C. elegans gross anatomy</option>
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85 <option value="1050">Maize gross anatomy</option>
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86 <option value="1047">Cereal Plant Development</option>
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87 <option value="1349">Physician Data Query</option>
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88 <option value="1190">Ontology for Parasite LifeCycle</option>
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89 <option value="1036">Plant environmental conditions</option>
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90 <option value="1109">Sequence types and features</option>
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91 <option value="1192">Proteomics Pipeline Infrastructure for CPTAC</option>
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92 <option value="1352">National Drug File</option>
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93 <option value="1059">Computer-based Patient Record Ontology</option>
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94 <option value="1052">Protein Ontology</option>
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95 <option value="1341">COSTART</option>
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96 <option value="1304">Breast Cancer Grading Ontology</option>
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97 <option value="1344">International Classification of Primary Care</option>
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98 <option value="1061">Suggested Ontology for Pharmacogenomics</option>
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99 <option value="1353">SNOMED Clinical Terms</option>
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100 <option value="1022">Human developmental anatomy, timed version</option>
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101 <option value="1014">Physico-chemical methods and properties</option>
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102 <option value="1224">Symptom Ontology</option>
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103 <option value="1095">Xenopus anatomy and development</option>
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104 <option value="1042">OBO relationship types</option>
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105 <option value="1013">eVOC (Expressed Sequence Annotation for Humans)</option>
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106 <option value="1149">DermLex: The Dermatology Lexicon</option>
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107 <option value="1311">Malaria Ontology</option>
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108 <option value="1335">Parasite Experiment Ontology</option>
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109 <option value="1370">Amphibian taxonomy</option>
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110 <option value="1027">Medaka fish anatomy and development</option>
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111 <option value="1354">WHO Adverse Reaction Terminology</option>
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112 <option value="1011">Event (INOH pathway ontology)</option>
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113 <option value="1010">Mouse gross anatomy and development</option>
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114 <option value="1015">Drosophila gross anatomy</option>
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115 <option value="1090">Amphibian gross anatomy</option>
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116 <option value="1020">Habronattus courtship</option>
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117 <option value="1148">BioPortal Metadata</option>
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118 <option value="1038">Plant Growth and Development Stage</option>
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119 <option value="1132">NCBI organismal classification</option>
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120 <option value="1328">Ontology of homology and related concepts in biology</option>
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121 <option value="1019">Fungal gross anatomy</option>
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122 <option value="1290">ABA Adult Mouse Brain</option>
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123 <option value="1067">C. elegans phenotype</option>
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124 <option value="1069">Environment Ontology</option>
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125 <option value="1055">Galen</option>
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126 <option value="1332">Basic Formal Ontology</option>
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127 <option value="1183">Lipid Ontology</option>
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128 <option value="1026">Multiple alignment</option>
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129 <option value="1130">Cancer Research and Management ACGT Master Ontology</option>
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130 <option value="1060">Epoch Clinical Trial Ontologies</option>
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131 <option value="1112">Units of measurement</option>
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132 <option value="1369">PhysicalFields</option>
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133 <option value="1086">Ontology for disease genetic investigation</option>
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134 <option value="1091">Spider Ontology</option>
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135 <option value="1017">FlyBase Controlled Vocabulary</option>
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136 <option value="1348">Online Mendelian Inheritance in Man</option>
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137 <option value="1122">Skin Physiology Ontology</option>
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138 <option value="1142">Cardiac Electrophysiology Ontology</option>
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139 <option value="1128">Comparative Data Analysis Ontology</option>
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140 <option value="1172">Vaccine Ontology</option>
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141 <option value="1088">MaHCO - An MHC Ontology</option>
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142 <option value="1245">Cell line ontology</option>
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143 <option value="1222">Ascomycete phenotype ontology</option>
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144 <option value="1249">Smoking Behavior Risk Ontology</option>
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145 <option value="1039">Proteomics data and process provenance</option>
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146 <option value="1105">Mass spectrometry</option>
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147 <option value="1040">Protein-protein interaction</option>
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148 <option value="1237">Situation-Based Access Control</option>
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149 <option value="1008">Dictyostelium discoideum anatomy</option>
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150 <option value="1068">Subcellular Anatomy Ontology (SAO)</option>
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151 <option value="1087">Ontology of Geographical Region</option>
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152 <option value="1150">Rat Strain Ontology</option>
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153 <option value="1101">International Classification of Diseases</option>
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154 <option value="1314">Cell Line Ontology</option>
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155 <option value="1009">Human disease ontology</option>
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156 <option value="1094">Pathogen transmission</option>
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157 <option value="1084">NIFSTD</option>
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158 <option value="1025">Mammalian phenotype</option>
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159 <option value="1131">MGED Ontology</option>
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160 <option value="1035">Pathway ontology</option>
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161 <option value="1106">Gene Regulation Ontology</option>
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162 <option value="1054">Amino Acid</option>
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163 <option value="1056">Basic Vertebrate Anatomy</option>
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164 <option value="1012">Evidence codes</option>
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165 <option value="1115">Yeast phenotypes</option>
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166 <option value="1001">Cereal plant gross anatomy</option>
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167 <option value="1006">Cell type</option>
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168 <option value="1077">Mosquito insecticide resistance</option>
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169 <option value="1085">Ontology of Glucose Metabolism Disorder</option>
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170 <option value="1057">RadLex</option>
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171 <option value="1083">NanoParticle Ontology</option>
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172 <option value="1053">Foundational Model of Anatomy</option>
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173 <option value="1031">Mouse pathology</option>
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174 <option value="1092">Infectious Disease Ontology</option>
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175 <option value="1032">NCI Thesaurus</option>
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176 <option value="1381">NIF Dysfunction</option>
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177 <option value="1393">Information Artifact Ontology</option>
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178 <option value="1394">Syndromic Surveillance Ontology</option>
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179 <option value="1395">MDSS Mo</option>
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180 <option value="1397">Gazetteer</option>
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181 <option value="1398">Ontology of Language Disorder in Autism</option>
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182 <option value="1399">Pilot Ontology</option>
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183 <option value="1401">International Classification for Nursing Practice</option>
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184 <option value="1402">NIF Cell</option>
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185 <option value="1404">Uber anatomy ontology</option>
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186 <option value="1406">linkingkin2pep</option>
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187 <option value="1407">Terminology for the Description of Dynamics</option>
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188 <option value="1409">PKO_Re</option>
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189 <option value="1410">Kinetic Simulation Algorithm Ontology</option>
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190 <option value="1411">International Classification of Functioning, Disability and Health (ICF)</option>
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191 <option value="1413">Software Ontology</option>
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192 <option value="1414">Ontology for General Medical Science</option>
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193 <option value="1415">Common Terminology Criteria for Adverse Events</option>
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194 <option value="1417">Influenza Ontology</option>
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195 <option value="1418">TOK_Ontology</option>
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196 <option value="1419">Taxonomic rank vocabulary</option>
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197 <option value="1422">MedDRA</option>
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198 <option value="1423">RxNORM</option>
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199 <option value="1424">National Drug Data File</option>
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200 <option value="1425">ICD-10-PCS</option>
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201 <option value="1426">Master Drug Data Base</option>
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202 <option value="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
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203 <option value="1428">Nursing Interventions Classification (NIC)</option>
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204 <option value="1429">ICPC-2 PLUS</option>
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205 <option value="1430">AI/RHEUM</option>
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206 <option value="1438">Breast tissue cell lines</option>
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207 <option value="1439">General Formal Ontology</option>
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208 <option value="1440">General Formal Ontology: Biology</option>
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209 <option value="1444">Chemical Information Ontology</option>
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210 <option value="1343">Health Level Seven</option>
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211 <option value="1461">Translational Medicine Ontology</option>
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212 <option value="1484">International Classification of External Causes of Injuries</option>
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213 <option value="1487">Body System</option>
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214 <option value="1488">SysMO-JERM</option>
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215 <option value="1489">Ontology of Adverse Events (OAE)</option>
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216 <option value="1490">Platynereis stage ontology</option>
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217 <option value="1491">IMGT-ONTOLOGY</option>
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218 <option value="1494">Tissue Microarray Ontology</option>
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219 <option value="1497">PMA 2010</option>
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220 <option value="1498">Bioinformatics operations, types of data, data formats and topics</option>
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221 <option value="1499">NCI Metathesaurus</option>
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222 <option value="1500">RNA ontology</option>
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223 <option value="1501">Neomark Oral Cancer-Centred Ontology</option>
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224 <option value="1504">Current Procedural Terminology</option>
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225 <option value="1505">Ontology for MicroRNA Target Prediction</option>
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226 <option value="1506">Gene Ontology Extension</option>
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227 <option value="1507">Cell Cycle Ontology</option>
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228 <option value="1509">ICPS Network</option>
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229 <option value="1510">Metathesaurus CPT Hierarchical Terms</option>
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230 <option value="1515">Interaction Network Ontology</option>
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231 <option value="1516">ICD10</option>
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232 <option value="1517">Human developmental anatomy, abstract version, v2</option>
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233 <option value="1520">Leukocyte Surface Markers</option>
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234 <option value="1521">Neural Motor Recovery Ontology</option>
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235 <option value="1522">BioPAX</option>
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236 <option value="1523">OBOE SBC</option>
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237 <option value="1524">OBOE</option>
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238 <option value="1526">CRISP Thesaurus, 2006</option>
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239 <option value="1527">VANDF</option>
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240 <option value="1528">HUGO</option>
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241 <option value="1529">HCPCS</option>
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242 <option value="1530">Animal natural history and life history</option>
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243 <option value="1532">SemanticScience Integrated Ontology</option>
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244 <option value="1533">BioAssay Ontology</option>
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245 <option value="1534">apollo-akesios</option>
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246 <option value="1535">Terminology of Anatomy of Human Histology</option>
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247 <option value="1536">Terminology of Anatomy of Human Embryology</option>
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248 <option value="1537">Brucellosis Ontology</option>
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249 <option value="1538">Role Ontology</option>
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250 <option value="1539">Neural-Immune Gene Ontology</option>
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251 <option value="1540">Ontology for Drug Discovery Investigations</option>
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252 <option value="1541">Cell line ontology</option>
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253 <option value="1544">Crop Ontology</option>
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254 <option value="1545">Wheat trait </option>
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255 <option value="1550">PHARE</option>
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256 <option value="1552">Reproductive trait and phenotype ontology</option>
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257 <option value="1553">ICD10CM</option>
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258 <option value="1555">Vertebrate Anatomy Ontology</option>
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259 <option value="1560">Cognitive Paradigm Ontology</option>
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260 <option value="1565">Ontology of Medically Related Social Entities</option>
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261 <option value="1567">Pharmacovigilance Ontology</option>
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262 <option value="1568">Anatomical Entity Ontology</option>
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263 <option value="1569">Host Pathogen Interactions Ontology</option>
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264 <option value="1570">Traditional Medicine Constitution Value Set</option>
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265 <option value="1571">Traditional Medicine Other Factors Value Set</option>
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266 <option value="1572">Traditional Medicine Signs and Symptoms Value Set</option>
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267 <option value="1573">Traditional Medicine Meridian Value Sets</option>
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268 <option value="1574">vertebrate Homologous Organ Groups</option>
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269 <option value="1575">ExO</option>
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270 <option value="1576">FDA Medical Devices (2010)</option>
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271 <option value="1578">HOM_ElixhauserScores</option>
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272 <option value="1580">Adverse Event Reporting ontology</option>
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273 <option value="1581">HEALTH_INDICATORS</option>
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274 <option value="1582">CAO</option>
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275 <option value="1583">Clinical Measurement Ontology</option>
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276 <option value="1584">Measurement Method Ontology</option>
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277 <option value="1585">Experimental Conditions Ontology</option>
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278 <option value="1586">Orphanet Ontology of Rare Diseases</option>
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279 <option value="1587">Plant Ontology</option>
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280 <option value="1588">Ontology of General Purpose Datatypes</option>
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281 <option value="1596">HOM_MDCs-DRGS</option>
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282 <option value="1613">Bone Dysplasia Ontology</option>
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283 <option value="1614">IxnO</option>
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284 <option value="1615">Systems Chemical Biology/Chemogenomics </option>
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285 <option value="1616">Phylogenetic Ontology</option>
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286 <option value="1621">Neuro Behavior Ontology</option>
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287 <option value="1625">HOM-ICD9CM_PROCEDURES</option>
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288 <option value="1626">Enzyme Mechanism Ontology</option>
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289 <option value="1627">HOMERUN Ontology</option>
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290 <option value="1629">HOM-UCARE</option>
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291 <option value="1630">HOM-EPIC</option>
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292 <option value="1631">HOM-HARVARD</option>
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293 <option value="1632">Web-Service Interaction Ontology</option>
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294 <option value="1633">Cognitive Atlas</option>
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295 <option value="1638">Ontology of Data Mining</option>
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296 <option value="1639">Epilepsy</option>
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297 <option value="1640">Pediatric Terminology</option>
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298 <option value="1641">HOM-ICD9CM-ECODES</option>
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299 <option value="1642">HOM-DXPROCS_MDCDRG</option>
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300 <option value="1643">HOM-ICD9_PROCS_OSHPD</option>
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301 <option value="1645">HOM-MDCDRG_OSHPD</option>
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302 <option value="1647">HOM-ICD9_DXandVCODES_OSHPD</option>
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303 <option value="1648">HOM-DATASOURCE_OSHPD</option>
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304 <option value="1649">HOM-OSHPD</option>
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305 <option value="1650">Units Ontology</option>
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306 <option value="1651">Sleep Domain Ontology</option>
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307 <option value="1652">HOM-OSHPD_UseCase</option>
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308 <option value="1653">HOM-PROCS2_OSHPD</option>
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309 <option value="1654">HOM-DXVCODES2_OSHPD</option>
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310 <option value="1655">PharmGKB-in-OWL</option>
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311 <option value="1656">PhenomeBLAST ontology</option>
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312 <option value="1657">Quadrupedal Gait</option>
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313 <option value="1658">Hewan Invertebrata</option>
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314 <option value="1659">Vertebrate Trait Ontology</option>
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315 <option value="1660">HOM-DATASOURCE_EPIC</option>
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316 <option value="1661">HOM-Transplant Ontology</option>
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317 <option value="1665">Student Health Record</option>
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318 <option value="1666">Emotion Ontology</option>
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319 <option value="1667">HOM-DATASOURCE_OSHPDSC</option>
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320 <option value="1668">HOM-OSHPD-SC</option>
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321 <option value="1670">ICD_Oncology-3</option>
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322 <option value="1671">Quantitative Imaging Biomarker Ontology</option>
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323 <option value="1672">DIKB-Evidence-Ontology</option>
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324 <option value="1675">CEEROntology</option>
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325 <option value="1676">Randomized Controlled Trials (RCT) Ontology</option>
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326 <option value="1679">JADNI test ontology2</option>
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327 <option value="1680">BioActivity Ontology3</option>
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328 <option value="1681">JADNI test ontology</option>
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329 <option value="1682">Human disease in Bioactivity</option>
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330 <option value="1683">BioActivity Ontology</option>
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331 <option value="1684">BioActivity Ontology2</option>
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332 <option value="1686">Neomark Oral Cancer Ontology</option>
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333 <option value="1688">UniprotCoreBH</option>
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334 <option value="1689">Fission Yeast Phenotype Ontology</option>
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335 <option value="1691">yipd_test</option>
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336 <option value="1692">test-purl</option>
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337 <option value="1693">ICD9-ICD10-PCS (partial)</option>
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338 <option value="1694">HOM-CPT</option>
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339 <option value="1696">Synapse Ontology</option>
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340 <option value="1697">HOM-ORTHO</option>
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341 <option value="1698">HOM-DATASRC-ORTHO</option>
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342 <option value="1699">VIVO</option>
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343 <option value="1700">Test Pradip PURL</option>
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344 <option value="1701">HOM-ORTHOSURGERY</option>
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345 <option value="1702">Eurofut</option>
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346 </param>
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347 </when>
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348 </conditional>
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349 </inputs>
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350 <outputs>
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351 <data format="text" name="output" />
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352 </outputs>
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353 <tests>
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354 <test>
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355 <param name="api_key"/>
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356 <param name="id_opts.ontology_id"/>
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357 </test>
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358 </tests>
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359 <help>
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360
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361 **What it does**
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362
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363 It retrieves an ontology from BioPortal.
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364
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365 **Parameters**
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366
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367 * Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org.
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368 * Ontology ID: provide it by hand (e.g. 1522 for BioPAX), or select from list.
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369
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370 **Contact**
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371
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372 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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373
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374 **More information**
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375
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376 http://bioportal.bioontology.org
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377
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378 http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
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379
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380
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381
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382 </help>
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383
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384 </tool>
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