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>
date Mon, 08 Oct 2012 14:25:04 +0200
parents NCBO_services/get_ontology.xml@354aa87772e0
children
comparison
equal deleted inserted replaced
26:354aa87772e0 27:e2b16720ef25
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>