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comparison ncbo_recommender.xml @ 27:e2b16720ef25 draft

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Directories re-arranged for easier installation via mercurial
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 14:25:04 +0200
parents NCBO_services/ncbo_recommender.xml@66c0e85d6485
children
comparison
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26:354aa87772e0 27:e2b16720ef25
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>