Mercurial > repos > mikel-egana-aranguren > ncbo_services
comparison get_ontology.xml @ 27:e2b16720ef25 draft
Directories re-arranged for easier installation via mercurial
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Mon, 08 Oct 2012 14:25:04 +0200 |
parents | NCBO_services/get_ontology.xml@354aa87772e0 |
children |
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26:354aa87772e0 | 27:e2b16720ef25 |
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1 <tool id="get_ontology" name="Get ontology by id" version="1.0.3"> | |
2 <description>Retrieves an ontology from bioportal using its id</description> | |
3 <!-- <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_galaxy.jar $api_key $ontology_id > $output </command> --> | |
4 <command> | |
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 | |
6 #else #java -jar ${__tool_data_path__}/shared/jars/get_ontology.jar $api_key $id_opts.ontology_id > $output | |
7 #end if | |
8 </command> | |
9 | |
10 <inputs> | |
11 <param name="api_key" type="text" size="100" label="BioPortal API key" /> | |
12 | |
13 <!-- <param name="ontology_id" type="text" size="100" label="Provide ontology id ... " /> --> | |
14 | |
15 <conditional name="id_opts"> | |
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"> | |
17 <option value="id_by_hand">Provide id by hand</option> | |
18 <option value="choose_from_list">Choose ontology from list</option> | |
19 </param>--> | |
20 | |
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"/> | |
22 | |
23 <when value="id_by_hand"> | |
24 <param name="ontology_id" type="text" size="100" label="Provide ontology id" /> | |
25 </when> | |
26 | |
27 <when value="choose_from_list"> | |
28 <!-- Automatically generated with http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey --> | |
29 <param name="ontology_id" type="select" multiple="false" label="Choose ontology from this list"> | |
30 <option value="1158">Cell Behavior Ontology</option> | |
31 <option value="1016">Drosophila development</option> | |
32 <option value="1033">NMR-instrument specific component of metabolomics investigations</option> | |
33 <option value="1351">Medical Subject Headings</option> | |
34 <option value="1146">Electrocardiography Ontology</option> | |
35 <option value="1041">Protein modification</option> | |
36 <option value="1062">PRotein Ontology (PRO)</option> | |
37 <option value="1000">Mouse adult gross anatomy</option> | |
38 <option value="1065">Tick gross anatomy</option> | |
39 <option value="1123">Ontology for Biomedical Investigations</option> | |
40 <option value="1058">SNP-Ontology</option> | |
41 <option value="1099">African Traditional Medicine</option> | |
42 <option value="1134">BioTop</option> | |
43 <option value="1078">Spatial Ontology</option> | |
44 <option value="1247">GeoSpecies Ontology</option> | |
45 <option value="1007">Chemical entities of biological interest</option> | |
46 <option value="1024">Loggerhead nesting</option> | |
47 <option value="1257">MeGO</option> | |
48 <option value="1135">Pseudogene</option> | |
49 <option value="1049">C. elegans development</option> | |
50 <option value="1070">Gene Ontology</option> | |
51 <option value="1126">Family Health History Ontology</option> | |
52 <option value="1108">Plant Anatomy</option> | |
53 <option value="1114">Bilateria anatomy</option> | |
54 <option value="1100">Ontology for Genetic Interval</option> | |
55 <option value="1136">Experimental Factor Ontology</option> | |
56 <option value="1141">Ontology of Physics for Biology</option> | |
57 <option value="1044">Sample processing and separation techniques</option> | |
58 <option value="1347">MedlinePlus Health Topics</option> | |
59 <option value="1005">BRENDA tissue / enzyme source</option> | |
60 <option value="1152">Minimal anatomical terminology</option> | |
61 <option value="1063">Common Anatomy Reference Ontology</option> | |
62 <option value="1321">Neural ElectroMagnetic Ontologies</option> | |
63 <option value="1043">Physico-chemical process</option> | |
64 <option value="1064">Fly taxonomy</option> | |
65 <option value="1089">BIRNLex</option> | |
66 <option value="1076">Ontology of Clinical Research (OCRe)</option> | |
67 <option value="1110">Teleost Anatomy Ontology</option> | |
68 <option value="1362">Hymenoptera Anatomy Ontology</option> | |
69 <option value="1030">Mosquito gross anatomy</option> | |
70 <option value="1029">Molecule role (INOH Protein name/family name ontology)</option> | |
71 <option value="1116">Bleeding History Phenotype</option> | |
72 <option value="1104">Biomedical Resource Ontology</option> | |
73 <option value="1144">Dendritic cell</option> | |
74 <option value="1125">Human Phenotype Ontology</option> | |
75 <option value="1023">Biological imaging methods</option> | |
76 <option value="1021">Human developmental anatomy, abstract version</option> | |
77 <option value="1046">Systems Biology</option> | |
78 <option value="1051">Zebrafish anatomy and development</option> | |
79 <option value="1037">Plant Trait Ontology</option> | |
80 <option value="1350">Logical Observation Identifier Names and Codes</option> | |
81 <option value="1082">Gene Regulation Ontology</option> | |
82 <option value="1107">Phenotypic quality</option> | |
83 <option value="1081">Teleost taxonomy</option> | |
84 <option value="1048">C. elegans gross anatomy</option> | |
85 <option value="1050">Maize gross anatomy</option> | |
86 <option value="1047">Cereal Plant Development</option> | |
87 <option value="1349">Physician Data Query</option> | |
88 <option value="1190">Ontology for Parasite LifeCycle</option> | |
89 <option value="1036">Plant environmental conditions</option> | |
90 <option value="1109">Sequence types and features</option> | |
91 <option value="1192">Proteomics Pipeline Infrastructure for CPTAC</option> | |
92 <option value="1352">National Drug File</option> | |
93 <option value="1059">Computer-based Patient Record Ontology</option> | |
94 <option value="1052">Protein Ontology</option> | |
95 <option value="1341">COSTART</option> | |
96 <option value="1304">Breast Cancer Grading Ontology</option> | |
97 <option value="1344">International Classification of Primary Care</option> | |
98 <option value="1061">Suggested Ontology for Pharmacogenomics</option> | |
99 <option value="1353">SNOMED Clinical Terms</option> | |
100 <option value="1022">Human developmental anatomy, timed version</option> | |
101 <option value="1014">Physico-chemical methods and properties</option> | |
102 <option value="1224">Symptom Ontology</option> | |
103 <option value="1095">Xenopus anatomy and development</option> | |
104 <option value="1042">OBO relationship types</option> | |
105 <option value="1013">eVOC (Expressed Sequence Annotation for Humans)</option> | |
106 <option value="1149">DermLex: The Dermatology Lexicon</option> | |
107 <option value="1311">Malaria Ontology</option> | |
108 <option value="1335">Parasite Experiment Ontology</option> | |
109 <option value="1370">Amphibian taxonomy</option> | |
110 <option value="1027">Medaka fish anatomy and development</option> | |
111 <option value="1354">WHO Adverse Reaction Terminology</option> | |
112 <option value="1011">Event (INOH pathway ontology)</option> | |
113 <option value="1010">Mouse gross anatomy and development</option> | |
114 <option value="1015">Drosophila gross anatomy</option> | |
115 <option value="1090">Amphibian gross anatomy</option> | |
116 <option value="1020">Habronattus courtship</option> | |
117 <option value="1148">BioPortal Metadata</option> | |
118 <option value="1038">Plant Growth and Development Stage</option> | |
119 <option value="1132">NCBI organismal classification</option> | |
120 <option value="1328">Ontology of homology and related concepts in biology</option> | |
121 <option value="1019">Fungal gross anatomy</option> | |
122 <option value="1290">ABA Adult Mouse Brain</option> | |
123 <option value="1067">C. elegans phenotype</option> | |
124 <option value="1069">Environment Ontology</option> | |
125 <option value="1055">Galen</option> | |
126 <option value="1332">Basic Formal Ontology</option> | |
127 <option value="1183">Lipid Ontology</option> | |
128 <option value="1026">Multiple alignment</option> | |
129 <option value="1130">Cancer Research and Management ACGT Master Ontology</option> | |
130 <option value="1060">Epoch Clinical Trial Ontologies</option> | |
131 <option value="1112">Units of measurement</option> | |
132 <option value="1369">PhysicalFields</option> | |
133 <option value="1086">Ontology for disease genetic investigation</option> | |
134 <option value="1091">Spider Ontology</option> | |
135 <option value="1017">FlyBase Controlled Vocabulary</option> | |
136 <option value="1348">Online Mendelian Inheritance in Man</option> | |
137 <option value="1122">Skin Physiology Ontology</option> | |
138 <option value="1142">Cardiac Electrophysiology Ontology</option> | |
139 <option value="1128">Comparative Data Analysis Ontology</option> | |
140 <option value="1172">Vaccine Ontology</option> | |
141 <option value="1088">MaHCO - An MHC Ontology</option> | |
142 <option value="1245">Cell line ontology</option> | |
143 <option value="1222">Ascomycete phenotype ontology</option> | |
144 <option value="1249">Smoking Behavior Risk Ontology</option> | |
145 <option value="1039">Proteomics data and process provenance</option> | |
146 <option value="1105">Mass spectrometry</option> | |
147 <option value="1040">Protein-protein interaction</option> | |
148 <option value="1237">Situation-Based Access Control</option> | |
149 <option value="1008">Dictyostelium discoideum anatomy</option> | |
150 <option value="1068">Subcellular Anatomy Ontology (SAO)</option> | |
151 <option value="1087">Ontology of Geographical Region</option> | |
152 <option value="1150">Rat Strain Ontology</option> | |
153 <option value="1101">International Classification of Diseases</option> | |
154 <option value="1314">Cell Line Ontology</option> | |
155 <option value="1009">Human disease ontology</option> | |
156 <option value="1094">Pathogen transmission</option> | |
157 <option value="1084">NIFSTD</option> | |
158 <option value="1025">Mammalian phenotype</option> | |
159 <option value="1131">MGED Ontology</option> | |
160 <option value="1035">Pathway ontology</option> | |
161 <option value="1106">Gene Regulation Ontology</option> | |
162 <option value="1054">Amino Acid</option> | |
163 <option value="1056">Basic Vertebrate Anatomy</option> | |
164 <option value="1012">Evidence codes</option> | |
165 <option value="1115">Yeast phenotypes</option> | |
166 <option value="1001">Cereal plant gross anatomy</option> | |
167 <option value="1006">Cell type</option> | |
168 <option value="1077">Mosquito insecticide resistance</option> | |
169 <option value="1085">Ontology of Glucose Metabolism Disorder</option> | |
170 <option value="1057">RadLex</option> | |
171 <option value="1083">NanoParticle Ontology</option> | |
172 <option value="1053">Foundational Model of Anatomy</option> | |
173 <option value="1031">Mouse pathology</option> | |
174 <option value="1092">Infectious Disease Ontology</option> | |
175 <option value="1032">NCI Thesaurus</option> | |
176 <option value="1381">NIF Dysfunction</option> | |
177 <option value="1393">Information Artifact Ontology</option> | |
178 <option value="1394">Syndromic Surveillance Ontology</option> | |
179 <option value="1395">MDSS Mo</option> | |
180 <option value="1397">Gazetteer</option> | |
181 <option value="1398">Ontology of Language Disorder in Autism</option> | |
182 <option value="1399">Pilot Ontology</option> | |
183 <option value="1401">International Classification for Nursing Practice</option> | |
184 <option value="1402">NIF Cell</option> | |
185 <option value="1404">Uber anatomy ontology</option> | |
186 <option value="1406">linkingkin2pep</option> | |
187 <option value="1407">Terminology for the Description of Dynamics</option> | |
188 <option value="1409">PKO_Re</option> | |
189 <option value="1410">Kinetic Simulation Algorithm Ontology</option> | |
190 <option value="1411">International Classification of Functioning, Disability and Health (ICF)</option> | |
191 <option value="1413">Software Ontology</option> | |
192 <option value="1414">Ontology for General Medical Science</option> | |
193 <option value="1415">Common Terminology Criteria for Adverse Events</option> | |
194 <option value="1417">Influenza Ontology</option> | |
195 <option value="1418">TOK_Ontology</option> | |
196 <option value="1419">Taxonomic rank vocabulary</option> | |
197 <option value="1422">MedDRA</option> | |
198 <option value="1423">RxNORM</option> | |
199 <option value="1424">National Drug Data File</option> | |
200 <option value="1425">ICD-10-PCS</option> | |
201 <option value="1426">Master Drug Data Base</option> | |
202 <option value="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> | |
203 <option value="1428">Nursing Interventions Classification (NIC)</option> | |
204 <option value="1429">ICPC-2 PLUS</option> | |
205 <option value="1430">AI/RHEUM</option> | |
206 <option value="1438">Breast tissue cell lines</option> | |
207 <option value="1439">General Formal Ontology</option> | |
208 <option value="1440">General Formal Ontology: Biology</option> | |
209 <option value="1444">Chemical Information Ontology</option> | |
210 <option value="1343">Health Level Seven</option> | |
211 <option value="1461">Translational Medicine Ontology</option> | |
212 <option value="1484">International Classification of External Causes of Injuries</option> | |
213 <option value="1487">Body System</option> | |
214 <option value="1488">SysMO-JERM</option> | |
215 <option value="1489">Ontology of Adverse Events (OAE)</option> | |
216 <option value="1490">Platynereis stage ontology</option> | |
217 <option value="1491">IMGT-ONTOLOGY</option> | |
218 <option value="1494">Tissue Microarray Ontology</option> | |
219 <option value="1497">PMA 2010</option> | |
220 <option value="1498">Bioinformatics operations, types of data, data formats and topics</option> | |
221 <option value="1499">NCI Metathesaurus</option> | |
222 <option value="1500">RNA ontology</option> | |
223 <option value="1501">Neomark Oral Cancer-Centred Ontology</option> | |
224 <option value="1504">Current Procedural Terminology</option> | |
225 <option value="1505">Ontology for MicroRNA Target Prediction</option> | |
226 <option value="1506">Gene Ontology Extension</option> | |
227 <option value="1507">Cell Cycle Ontology</option> | |
228 <option value="1509">ICPS Network</option> | |
229 <option value="1510">Metathesaurus CPT Hierarchical Terms</option> | |
230 <option value="1515">Interaction Network Ontology</option> | |
231 <option value="1516">ICD10</option> | |
232 <option value="1517">Human developmental anatomy, abstract version, v2</option> | |
233 <option value="1520">Leukocyte Surface Markers</option> | |
234 <option value="1521">Neural Motor Recovery Ontology</option> | |
235 <option value="1522">BioPAX</option> | |
236 <option value="1523">OBOE SBC</option> | |
237 <option value="1524">OBOE</option> | |
238 <option value="1526">CRISP Thesaurus, 2006</option> | |
239 <option value="1527">VANDF</option> | |
240 <option value="1528">HUGO</option> | |
241 <option value="1529">HCPCS</option> | |
242 <option value="1530">Animal natural history and life history</option> | |
243 <option value="1532">SemanticScience Integrated Ontology</option> | |
244 <option value="1533">BioAssay Ontology</option> | |
245 <option value="1534">apollo-akesios</option> | |
246 <option value="1535">Terminology of Anatomy of Human Histology</option> | |
247 <option value="1536">Terminology of Anatomy of Human Embryology</option> | |
248 <option value="1537">Brucellosis Ontology</option> | |
249 <option value="1538">Role Ontology</option> | |
250 <option value="1539">Neural-Immune Gene Ontology</option> | |
251 <option value="1540">Ontology for Drug Discovery Investigations</option> | |
252 <option value="1541">Cell line ontology</option> | |
253 <option value="1544">Crop Ontology</option> | |
254 <option value="1545">Wheat trait </option> | |
255 <option value="1550">PHARE</option> | |
256 <option value="1552">Reproductive trait and phenotype ontology</option> | |
257 <option value="1553">ICD10CM</option> | |
258 <option value="1555">Vertebrate Anatomy Ontology</option> | |
259 <option value="1560">Cognitive Paradigm Ontology</option> | |
260 <option value="1565">Ontology of Medically Related Social Entities</option> | |
261 <option value="1567">Pharmacovigilance Ontology</option> | |
262 <option value="1568">Anatomical Entity Ontology</option> | |
263 <option value="1569">Host Pathogen Interactions Ontology</option> | |
264 <option value="1570">Traditional Medicine Constitution Value Set</option> | |
265 <option value="1571">Traditional Medicine Other Factors Value Set</option> | |
266 <option value="1572">Traditional Medicine Signs and Symptoms Value Set</option> | |
267 <option value="1573">Traditional Medicine Meridian Value Sets</option> | |
268 <option value="1574">vertebrate Homologous Organ Groups</option> | |
269 <option value="1575">ExO</option> | |
270 <option value="1576">FDA Medical Devices (2010)</option> | |
271 <option value="1578">HOM_ElixhauserScores</option> | |
272 <option value="1580">Adverse Event Reporting ontology</option> | |
273 <option value="1581">HEALTH_INDICATORS</option> | |
274 <option value="1582">CAO</option> | |
275 <option value="1583">Clinical Measurement Ontology</option> | |
276 <option value="1584">Measurement Method Ontology</option> | |
277 <option value="1585">Experimental Conditions Ontology</option> | |
278 <option value="1586">Orphanet Ontology of Rare Diseases</option> | |
279 <option value="1587">Plant Ontology</option> | |
280 <option value="1588">Ontology of General Purpose Datatypes</option> | |
281 <option value="1596">HOM_MDCs-DRGS</option> | |
282 <option value="1613">Bone Dysplasia Ontology</option> | |
283 <option value="1614">IxnO</option> | |
284 <option value="1615">Systems Chemical Biology/Chemogenomics </option> | |
285 <option value="1616">Phylogenetic Ontology</option> | |
286 <option value="1621">Neuro Behavior Ontology</option> | |
287 <option value="1625">HOM-ICD9CM_PROCEDURES</option> | |
288 <option value="1626">Enzyme Mechanism Ontology</option> | |
289 <option value="1627">HOMERUN Ontology</option> | |
290 <option value="1629">HOM-UCARE</option> | |
291 <option value="1630">HOM-EPIC</option> | |
292 <option value="1631">HOM-HARVARD</option> | |
293 <option value="1632">Web-Service Interaction Ontology</option> | |
294 <option value="1633">Cognitive Atlas</option> | |
295 <option value="1638">Ontology of Data Mining</option> | |
296 <option value="1639">Epilepsy</option> | |
297 <option value="1640">Pediatric Terminology</option> | |
298 <option value="1641">HOM-ICD9CM-ECODES</option> | |
299 <option value="1642">HOM-DXPROCS_MDCDRG</option> | |
300 <option value="1643">HOM-ICD9_PROCS_OSHPD</option> | |
301 <option value="1645">HOM-MDCDRG_OSHPD</option> | |
302 <option value="1647">HOM-ICD9_DXandVCODES_OSHPD</option> | |
303 <option value="1648">HOM-DATASOURCE_OSHPD</option> | |
304 <option value="1649">HOM-OSHPD</option> | |
305 <option value="1650">Units Ontology</option> | |
306 <option value="1651">Sleep Domain Ontology</option> | |
307 <option value="1652">HOM-OSHPD_UseCase</option> | |
308 <option value="1653">HOM-PROCS2_OSHPD</option> | |
309 <option value="1654">HOM-DXVCODES2_OSHPD</option> | |
310 <option value="1655">PharmGKB-in-OWL</option> | |
311 <option value="1656">PhenomeBLAST ontology</option> | |
312 <option value="1657">Quadrupedal Gait</option> | |
313 <option value="1658">Hewan Invertebrata</option> | |
314 <option value="1659">Vertebrate Trait Ontology</option> | |
315 <option value="1660">HOM-DATASOURCE_EPIC</option> | |
316 <option value="1661">HOM-Transplant Ontology</option> | |
317 <option value="1665">Student Health Record</option> | |
318 <option value="1666">Emotion Ontology</option> | |
319 <option value="1667">HOM-DATASOURCE_OSHPDSC</option> | |
320 <option value="1668">HOM-OSHPD-SC</option> | |
321 <option value="1670">ICD_Oncology-3</option> | |
322 <option value="1671">Quantitative Imaging Biomarker Ontology</option> | |
323 <option value="1672">DIKB-Evidence-Ontology</option> | |
324 <option value="1675">CEEROntology</option> | |
325 <option value="1676">Randomized Controlled Trials (RCT) Ontology</option> | |
326 <option value="1679">JADNI test ontology2</option> | |
327 <option value="1680">BioActivity Ontology3</option> | |
328 <option value="1681">JADNI test ontology</option> | |
329 <option value="1682">Human disease in Bioactivity</option> | |
330 <option value="1683">BioActivity Ontology</option> | |
331 <option value="1684">BioActivity Ontology2</option> | |
332 <option value="1686">Neomark Oral Cancer Ontology</option> | |
333 <option value="1688">UniprotCoreBH</option> | |
334 <option value="1689">Fission Yeast Phenotype Ontology</option> | |
335 <option value="1691">yipd_test</option> | |
336 <option value="1692">test-purl</option> | |
337 <option value="1693">ICD9-ICD10-PCS (partial)</option> | |
338 <option value="1694">HOM-CPT</option> | |
339 <option value="1696">Synapse Ontology</option> | |
340 <option value="1697">HOM-ORTHO</option> | |
341 <option value="1698">HOM-DATASRC-ORTHO</option> | |
342 <option value="1699">VIVO</option> | |
343 <option value="1700">Test Pradip PURL</option> | |
344 <option value="1701">HOM-ORTHOSURGERY</option> | |
345 <option value="1702">Eurofut</option> | |
346 </param> | |
347 </when> | |
348 </conditional> | |
349 </inputs> | |
350 <outputs> | |
351 <data format="text" name="output" /> | |
352 </outputs> | |
353 <tests> | |
354 <test> | |
355 <param name="api_key"/> | |
356 <param name="id_opts.ontology_id"/> | |
357 </test> | |
358 </tests> | |
359 <help> | |
360 | |
361 **What it does** | |
362 | |
363 It retrieves an ontology from BioPortal. | |
364 | |
365 **Parameters** | |
366 | |
367 * Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. | |
368 * Ontology ID: provide it by hand (e.g. 1522 for BioPAX), or select from list. | |
369 | |
370 **Contact** | |
371 | |
372 Please send any request or comment to mikel.egana.aranguren@gmail.com. | |
373 | |
374 **More information** | |
375 | |
376 http://bioportal.bioontology.org | |
377 | |
378 http://www.bioontology.org/wiki/index.php/BioPortal_REST_services | |
379 | |
380 | |
381 | |
382 </help> | |
383 | |
384 </tool> |