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comparison ncbo_annotator.xml @ 4:1aa0a6639913

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author jose-minyarro
date Wed, 18 Jan 2012 03:44:58 -0500
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1 <tool id="ncbo_annotator" name="Annotates a text with bio-ontology terms" version="1.0.1">
2 <description>Annotates biological texts with the terms of the bio-ontologies from BioPortal</description>
3 <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_annotator_galaxy.jar $longestOnly $wholeWordOnly $filterNumber $stopWords $withDefaultStopWords $isTopWordsCaseSensitive $mintermSize $scored $withSynonyms $ontologiesToExpand $ontologiesToKeepInResult $semanticTypes $levelMax $mappingTypes $textToAnnotate $format $apikey > $output </command>
4 <inputs>
5 <param name="longestOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only the longest word"/>
6 <param name="wholeWordOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only whole words"/>
7 <param name="filterNumber" type="boolean" value="true" label="Tick the box if the Annotator should filter numbers before annotating the text"/>
8 <param name="stopWords" type="text" value="" size="100" label="List the words that the Annotator should omit from the text"/>
9 <param name="withDefaultStopWords" type="boolean" value="true" label="Tick the box if the Annotator should use the default list of stop words"/>
10 <param name="isTopWordsCaseSensitive" type="boolean" value="false" label="Tick the box whether the stop words are case sensitive or not"/>
11 <param name="mintermSize" type="integer" value="3" min="0" max="100" label="Indicates the minimum length for the terms to annotate"/>
12 <param name="scored" type="boolean" value="true" label="Tick the box whether the Annotator should assign a numeric accuracy to each annotation or not"/>
13 <param name="withSynonyms" type="boolean" value="true" label="Tick the box if the Annotator should use synonyms in the direct annotation"/>
14 <param name="ontologiesToExpand" type="select" multiple="true" label="Indicates the list of ontologies to use with the mapping semantic expansion component">
15 <option value="e-all" selected="true">ALL</option>
16 <option value="e-1394">Syndromic Surveillance Ontology</option>
17 <option value="e-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
18 <option value="e-1158">Cell Behavior Ontology</option>
19 <option value="e-1033">NMR-instrument specific component of metabolomics investigations</option>
20 <option value="e-1351">Medical Subject Headings</option>
21 <option value="e-1146">Electrocardiography Ontology</option>
22 <option value="e-1041">Protein modification</option>
23 <option value="e-1058">SNP-Ontology</option>
24 <option value="e-1099">African Traditional Medicine</option>
25 <option value="e-1134">BioTop</option>
26 <option value="e-1247">GeoSpecies Ontology</option>
27 <option value="e-1024">Loggerhead nesting</option>
28 <option value="e-1257">MeGO</option>
29 <option value="e-1135">Pseudogene</option>
30 <option value="e-1126">Family Health History Ontology</option>
31 <option value="e-1108">Plant structure</option>
32 <option value="e-1114">Bilateria anatomy</option>
33 <option value="e-1100">Ontology for Genetic Interval</option>
34 <option value="e-1044">Sample processing and separation techniques</option>
35 <option value="e-1347">MedlinePlus Health Topics</option>
36 <option value="e-1152">Minimal anatomical terminology</option>
37 <option value="e-1063">Common Anatomy Reference Ontology</option>
38 <option value="e-1089">BIRNLex</option>
39 <option value="e-1116">Bleeding History Phenotype</option>
40 <option value="e-1104">Biomedical Resource Ontology</option>
41 <option value="e-1350">Logical Observation Identifier Names and Codes</option>
42 <option value="e-1082">Gene Regulation Ontology</option>
43 <option value="e-1047">Cereal plant development</option>
44 <option value="e-1349">Physician Data Query</option>
45 <option value="e-1190">Parasite Life Cycle</option>
46 <option value="e-1192">Proteomics Pipeline Infrastructure for CPTAC</option>
47 <option value="e-1352">National Drug File</option>
48 <option value="e-1059">Computer-based Patient Record Ontology</option>
49 <option value="e-1052">Protein Ontology</option>
50 <option value="e-1341">COSTART</option>
51 <option value="e-1344">International Classification of Primary Care</option>
52 <option value="e-1061">Suggested Ontology for Pharmacogenomics</option>
53 <option value="e-1353">SNOMED Clinical Terms</option>
54 <option value="e-1224">Symptom Ontology</option>
55 <option value="e-1013">eVOC (Expressed Sequence Annotation for Humans)</option>
56 <option value="e-1149">DermLex: The Dermatology Lexicon</option>
57 <option value="e-1311">Malaria Ontology</option>
58 <option value="e-1335">Parasite Experiment Ontology</option>
59 <option value="e-1370">Amphibian taxonomy</option>
60 <option value="e-1354">WHO Adverse Reaction Terminology</option>
61 <option value="e-1148">BioPortal Metadata</option>
62 <option value="e-1038">Plant growth and developmental stage</option>
63 <option value="e-1132">NCBI organismal classification</option>
64 <option value="e-1328">Ontology of homology and related concepts in biology</option>
65 <option value="e-1290">ABA Adult Mouse Brain</option>
66 <option value="e-1055">Galen</option>
67 <option value="e-1332">Basic Formal Ontology</option>
68 <option value="e-1183">Lipid Ontology</option>
69 <option value="e-1026">Multiple alignment</option>
70 <option value="e-1130">Cancer Research and Management ACGT Master Ontology</option>
71 <option value="e-1060">Epoch Clinical Trial Ontologies</option>
72 <option value="e-1369">PhysicalFields</option>
73 <option value="e-1086">Ontology for disease genetic investigation</option>
74 <option value="e-1122">Skin Physiology Ontology</option>
75 <option value="e-1142">Cardiac Electrophysiology Ontology</option>
76 <option value="e-1128">Comparative Data Analysis Ontology</option>
77 <option value="e-1088">MaHCO - An MHC Ontology</option>
78 <option value="e-1249">Smoking Behavior Risk Ontology</option>
79 <option value="e-1039">Proteomics data and process provenance</option>
80 <option value="e-1040">Protein-protein interaction</option>
81 <option value="e-1068">Subcellular Anatomy Ontology (SAO)</option>
82 <option value="e-1087">Ontology of Geographical Region</option>
83 <option value="e-1094">Pathogen transmission</option>
84 <option value="e-1131">MGED Ontology</option>
85 <option value="e-1106">Gene Regulation Ontology</option>
86 <option value="e-1054">Amino Acid</option>
87 <option value="e-1056">Basic Vertebrate Anatomy</option>
88 <option value="e-1083">NanoParticle Ontology</option>
89 <option value="e-1053">Foundational Model of Anatomy</option>
90 <option value="e-1092">Infectious disease</option>
91 <option value="e-1393">Information Artifact Ontology</option>
92 <option value="e-1395">MDSS Mo</option>
93 <option value="e-1397">Gazetteer</option>
94 <option value="e-1398">Ontology of Language Disorder in Autism</option>
95 <option value="e-1399">Pilot Ontology</option>
96 <option value="e-1406">linkingkin2pep</option>
97 <option value="e-1409">PKO_Re</option>
98 <option value="e-1410">Kinetic Simulation Algorithm Ontology</option>
99 <option value="e-1415">Common Terminology Criteria for Adverse Events</option>
100 <option value="e-1418">TOK_Ontology</option>
101 <option value="e-1419">Taxonomic rank vocabulary</option>
102 <option value="e-1422">MedDRA</option>
103 <option value="e-1424">National Drug Data File</option>
104 <option value="e-1425">ICD-10-PCS</option>
105 <option value="e-1426">Master Drug Data Base</option>
106 <option value="e-1429">ICPC-2 PLUS</option>
107 <option value="e-1430">AIR</option>
108 <option value="e-1438">Breast tissue cell lines</option>
109 <option value="e-1439">General Formal Ontology</option>
110 <option value="e-1440">General Formal Ontology: Biology</option>
111 <option value="e-1343">Health Level Seven</option>
112 <option value="e-1484">International Classification of External Causes of Injuries</option>
113 <option value="e-1487">Body System</option>
114 <option value="e-1490">Platynereis stage ontology</option>
115 <option value="e-1491">IMGT-ONTOLOGY</option>
116 <option value="e-1494">Tissue Microarray Ontology</option>
117 <option value="e-1497">PMA 2010</option>
118 <option value="e-1500">RNA ontology</option>
119 <option value="e-1501">Neomark Oral Cancer-Centred Ontology</option>
120 <option value="e-1504">Current Procedural Terminology</option>
121 <option value="e-1505">Ontology for MicroRNA Target Prediction</option>
122 <option value="e-1506">Gene Ontology Extension</option>
123 <option value="e-1507">Cell Cycle Ontology</option>
124 <option value="e-1509">ICPS Network</option>
125 <option value="e-1510">Metathesaurus CPT Hierarchical Terms</option>
126 <option value="e-1515">Interaction Network Ontology</option>
127 <option value="e-1516">ICD10</option>
128 <option value="e-1521">Neural Motor Recovery Ontology</option>
129 <option value="e-1522">BioPAX</option>
130 <option value="e-1523">OBOE SBC</option>
131 <option value="e-1524">OBOE</option>
132 <option value="e-1526">CRISP Thesaurus, 2006</option>
133 <option value="e-1527">VANDF</option>
134 <option value="e-1528">HUGO</option>
135 <option value="e-1529">HCPCS</option>
136 <option value="e-1530">Animal natural history and life history</option>
137 <option value="e-1534">apollo-akesios</option>
138 <option value="e-1537">Brucellosis Ontology</option>
139 <option value="e-1538">Role Ontology</option>
140 <option value="e-1539">Neural-Immune Gene Ontology</option>
141 <option value="e-1540">Ontology for Drug Discovery Investigations</option>
142 <option value="e-1541">Cell line ontology</option>
143 <option value="e-1545">Wheat trait </option>
144 <option value="e-1547">BRENDA tissue / enzyme source</option>
145 <option value="e-1552">Reproductive traits ontology</option>
146 <option value="e-1553">ICD10CM</option>
147 <option value="e-1560">Cognitive Paradigm Ontology</option>
148 <option value="e-1423">RxNORM</option>
149 <option value="e-1517">Human developmental anatomy, abstract version, v2</option>
150 <option value="e-1016">Drosophila development</option>
151 <option value="e-1062">PRotein Ontology (PRO)</option>
152 <option value="e-1000">Mouse adult gross anatomy</option>
153 <option value="e-1065">Tick gross anatomy</option>
154 <option value="e-1123">Ontology for Biomedical Investigations</option>
155 <option value="e-1078">Spatial Ontology</option>
156 <option value="e-1007">Chemical entities of biological interest</option>
157 <option value="e-1049">C. elegans development</option>
158 <option value="e-1070">Gene Ontology</option>
159 <option value="e-1136">Experimental Factor Ontology</option>
160 <option value="e-1141">Ontology of Physics for Biology</option>
161 <option value="e-1005">BRENDA tissue / enzyme source</option>
162 <option value="e-1321">Neural ElectroMagnetic Ontologies</option>
163 <option value="e-1043">Physico-chemical process</option>
164 <option value="e-1064">Fly taxonomy</option>
165 <option value="e-1076">Ontology of Clinical Research (OCRe)</option>
166 <option value="e-1110">Teleost Anatomy Ontology</option>
167 <option value="e-1362">Hymenoptera Anatomy Ontology</option>
168 <option value="e-1030">Mosquito gross anatomy</option>
169 <option value="e-1029">Molecule role (INOH Protein name/family name ontology)</option>
170 <option value="e-1144">Dendritic cell</option>
171 <option value="e-1125">Human Phenotype Ontology</option>
172 <option value="e-1023">Biological imaging methods</option>
173 <option value="e-1021">Human developmental anatomy, abstract version</option>
174 <option value="e-1046">Systems Biology</option>
175 <option value="e-1051">Zebrafish anatomy and development</option>
176 <option value="e-1037">Cereal plant trait</option>
177 <option value="e-1107">Phenotypic quality</option>
178 <option value="e-1081">Teleost taxonomy</option>
179 <option value="e-1048">C. elegans gross anatomy</option>
180 <option value="e-1050">Maize gross anatomy</option>
181 <option value="e-1036">Plant environmental conditions</option>
182 <option value="e-1109">Sequence types and features</option>
183 <option value="e-1022">Human developmental anatomy, timed version</option>
184 <option value="e-1095">Xenopus anatomy and development</option>
185 <option value="e-1027">Medaka fish anatomy and development</option>
186 <option value="e-1011">Event (INOH pathway ontology)</option>
187 <option value="e-1010">Mouse gross anatomy and development</option>
188 <option value="e-1015">Drosophila gross anatomy</option>
189 <option value="e-1090">Amphibian gross anatomy</option>
190 <option value="e-1019">Fungal gross anatomy</option>
191 <option value="e-1067">C. elegans phenotype</option>
192 <option value="e-1069">Environment Ontology</option>
193 <option value="e-1112">Units of measurement</option>
194 <option value="e-1091">Spider Ontology</option>
195 <option value="e-1017">FlyBase Controlled Vocabulary</option>
196 <option value="e-1348">Online Mendelian Inheritance in Man</option>
197 <option value="e-1172">Vaccine Ontology</option>
198 <option value="e-1222">Ascomycete phenotype ontology</option>
199 <option value="e-1105">Mass spectrometry</option>
200 <option value="e-1237">Situation-Based Access Control</option>
201 <option value="e-1008">Dictyostelium discoideum anatomy</option>
202 <option value="e-1150">Rat Strain Ontology</option>
203 <option value="e-1101">International Classification of Diseases</option>
204 <option value="e-1314">Cell Line Ontology</option>
205 <option value="e-1009">Human disease</option>
206 <option value="e-1084">NIFSTD</option>
207 <option value="e-1025">Mammalian phenotype</option>
208 <option value="e-1035">Pathway ontology</option>
209 <option value="e-1012">Evidence codes</option>
210 <option value="e-1115">Yeast phenotypes</option>
211 <option value="e-1001">Cereal plant gross anatomy</option>
212 <option value="e-1006">Cell type</option>
213 <option value="e-1077">Mosquito insecticide resistance</option>
214 <option value="e-1085">Ontology of Glucose Metabolism Disorder</option>
215 <option value="e-1057">RadLex</option>
216 <option value="e-1031">Mouse pathology</option>
217 <option value="e-1032">NCI Thesaurus</option>
218 <option value="e-1381">NIF Dysfunction</option>
219 <option value="e-1401">International Classification for Nursing Practice</option>
220 <option value="e-1402">NIF Cell</option>
221 <option value="e-1404">Uber anatomy ontology</option>
222 <option value="e-1407">Terminology for the Description of Dynamics</option>
223 <option value="e-1411">International Classification of Functioning, Disability and Health (ICF)</option>
224 <option value="e-1413">Software Ontology</option>
225 <option value="e-1414">Ontology for General Medical Science</option>
226 <option value="e-1444">Chemical Information Ontology</option>
227 <option value="e-1461">Translational Medicine Ontology</option>
228 <option value="e-1488">SysMO-JERM</option>
229 <option value="e-1489">Adverse Event Ontology</option>
230 <option value="e-1498">EDAM</option>
231 <option value="e-1532">SemanticScience Integrated Ontology</option>
232 <option value="e-1550">PHARE</option>
233 <option value="e-1555">Vertebrate Anatomy Ontology</option>
234 <option value="e-1565">Ontology of Medically Related Social Entities</option>
235 <option value="e-1567">Pharmacovigilance Ontology</option>
236 <option value="e-1568">Anatomical Entity Ontology</option>
237 <option value="e-1569">Host Pathogen Interactions Ontology</option>
238 <option value="e-1570">Traditional Medicine Constitution Value Set</option>
239 <option value="e-1571">Traditional Medicine Other Factors Value Set</option>
240 <option value="e-1572">Traditional Medicine Signs and Symptoms Value Set</option>
241 <option value="e-1573">Traditional Medicine Meridian Value Sets</option>
242 <option value="e-1574">vertebrate Homologous Organ Groups</option>
243 <option value="e-1575">ExO</option>
244 <option value="e-1576">FDA Medical Devices (2010)</option>
245 <option value="e-1578">HOM_ElixhauserScores</option>
246 <option value="e-1580">Adverse Event Reporting ontology</option>
247 <option value="e-1581">HEALTH_INDICATORS</option>
248 <option value="e-1582">COA</option>
249 <option value="e-1583">Clinical Measurement Ontology</option>
250 <option value="e-1584">Measurement Method Ontology</option>
251 <option value="e-1585">Experimental Conditions Ontology</option>
252 <option value="e-1587">Plant Ontology</option>
253 <option value="e-1588">Ontology of General Purpose Datatypes</option>
254 <option value="e-1596">MajDxCatgrs-DxRltdGrps</option>
255 <option value="e-1613">Bone Dysplasia Ontology</option>
256 <option value="e-1614">IxnO</option>
257 <option value="e-1615">Systems Chemical Biology/Chemogenomics </option>
258 <option value="e-1616">Phylogenetic Ontology</option>
259 <option value="e-1621">Neuro Behavior Ontology</option>
260 </param>
261 <param name="ontologiesToKeepInResult" type="select" multiple="true" label="Indicates the list of ontologies to keep in the result of the annotation process">
262 <option value="k-all" selected="true">ALL</option>
263 <option value="k-1394">Syndromic Surveillance Ontology</option>
264 <option value="k-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
265 <option value="k-1158">Cell Behavior Ontology</option>
266 <option value="k-1033">NMR-instrument specific component of metabolomics investigations</option>
267 <option value="k-1351">Medical Subject Headings</option>
268 <option value="k-1146">Electrocardiography Ontology</option>
269 <option value="k-1041">Protein modification</option>
270 <option value="k-1058">SNP-Ontology</option>
271 <option value="k-1099">African Traditional Medicine</option>
272 <option value="k-1134">BioTop</option>
273 <option value="k-1247">GeoSpecies Ontology</option>
274 <option value="k-1024">Loggerhead nesting</option>
275 <option value="k-1257">MeGO</option>
276 <option value="k-1135">Pseudogene</option>
277 <option value="k-1126">Family Health History Ontology</option>
278 <option value="k-1108">Plant structure</option>
279 <option value="k-1114">Bilateria anatomy</option>
280 <option value="k-1100">Ontology for Genetic Interval</option>
281 <option value="k-1044">Sample processing and separation techniques</option>
282 <option value="k-1347">MedlinePlus Health Topics</option>
283 <option value="k-1152">Minimal anatomical terminology</option>
284 <option value="k-1063">Common Anatomy Reference Ontology</option>
285 <option value="k-1089">BIRNLex</option>
286 <option value="k-1116">Bleeding History Phenotype</option>
287 <option value="k-1104">Biomedical Resource Ontology</option>
288 <option value="k-1350">Logical Observation Identifier Names and Codes</option>
289 <option value="k-1082">Gene Regulation Ontology</option>
290 <option value="k-1047">Cereal plant development</option>
291 <option value="k-1349">Physician Data Query</option>
292 <option value="k-1190">Parasite Life Cycle</option>
293 <option value="k-1192">Proteomics Pipeline Infrastructure for CPTAC</option>
294 <option value="k-1352">National Drug File</option>
295 <option value="k-1059">Computer-based Patient Record Ontology</option>
296 <option value="k-1052">Protein Ontology</option>
297 <option value="k-1341">COSTART</option>
298 <option value="k-1344">International Classification of Primary Care</option>
299 <option value="k-1061">Suggested Ontology for Pharmacogenomics</option>
300 <option value="k-1353">SNOMED Clinical Terms</option>
301 <option value="k-1224">Symptom Ontology</option>
302 <option value="k-1013">eVOC (Expressed Sequence Annotation for Humans)</option>
303 <option value="k-1149">DermLex: The Dermatology Lexicon</option>
304 <option value="k-1311">Malaria Ontology</option>
305 <option value="k-1335">Parasite Experiment Ontology</option>
306 <option value="k-1370">Amphibian taxonomy</option>
307 <option value="k-1354">WHO Adverse Reaction Terminology</option>
308 <option value="k-1148">BioPortal Metadata</option>
309 <option value="k-1038">Plant growth and developmental stage</option>
310 <option value="k-1132">NCBI organismal classification</option>
311 <option value="k-1328">Ontology of homology and related concepts in biology</option>
312 <option value="k-1290">ABA Adult Mouse Brain</option>
313 <option value="k-1055">Galen</option>
314 <option value="k-1332">Basic Formal Ontology</option>
315 <option value="k-1183">Lipid Ontology</option>
316 <option value="k-1026">Multiple alignment</option>
317 <option value="k-1130">Cancer Research and Management ACGT Master Ontology</option>
318 <option value="k-1060">Epoch Clinical Trial Ontologies</option>
319 <option value="k-1369">PhysicalFields</option>
320 <option value="k-1086">Ontology for disease genetic investigation</option>
321 <option value="k-1122">Skin Physiology Ontology</option>
322 <option value="k-1142">Cardiac Electrophysiology Ontology</option>
323 <option value="k-1128">Comparative Data Analysis Ontology</option>
324 <option value="k-1088">MaHCO - An MHC Ontology</option>
325 <option value="k-1249">Smoking Behavior Risk Ontology</option>
326 <option value="k-1039">Proteomics data and process provenance</option>
327 <option value="k-1040">Protein-protein interaction</option>
328 <option value="k-1068">Subcellular Anatomy Ontology (SAO)</option>
329 <option value="k-1087">Ontology of Geographical Region</option>
330 <option value="k-1094">Pathogen transmission</option>
331 <option value="k-1131">MGED Ontology</option>
332 <option value="k-1106">Gene Regulation Ontology</option>
333 <option value="k-1054">Amino Acid</option>
334 <option value="k-1056">Basic Vertebrate Anatomy</option>
335 <option value="k-1083">NanoParticle Ontology</option>
336 <option value="k-1053">Foundational Model of Anatomy</option>
337 <option value="k-1092">Infectious disease</option>
338 <option value="k-1393">Information Artifact Ontology</option>
339 <option value="k-1395">MDSS Mo</option>
340 <option value="k-1397">Gazetteer</option>
341 <option value="k-1398">Ontology of Language Disorder in Autism</option>
342 <option value="k-1399">Pilot Ontology</option>
343 <option value="k-1406">linkingkin2pep</option>
344 <option value="k-1409">PKO_Re</option>
345 <option value="k-1410">Kinetic Simulation Algorithm Ontology</option>
346 <option value="k-1415">Common Terminology Criteria for Adverse Events</option>
347 <option value="k-1418">TOK_Ontology</option>
348 <option value="k-1419">Taxonomic rank vocabulary</option>
349 <option value="k-1422">MedDRA</option>
350 <option value="k-1424">National Drug Data File</option>
351 <option value="k-1425">ICD-10-PCS</option>
352 <option value="k-1426">Master Drug Data Base</option>
353 <option value="k-1429">ICPC-2 PLUS</option>
354 <option value="k-1430">AIR</option>
355 <option value="k-1438">Breast tissue cell lines</option>
356 <option value="k-1439">General Formal Ontology</option>
357 <option value="k-1440">General Formal Ontology: Biology</option>
358 <option value="k-1343">Health Level Seven</option>
359 <option value="k-1484">International Classification of External Causes of Injuries</option>
360 <option value="k-1487">Body System</option>
361 <option value="k-1490">Platynereis stage ontology</option>
362 <option value="k-1491">IMGT-ONTOLOGY</option>
363 <option value="k-1494">Tissue Microarray Ontology</option>
364 <option value="k-1497">PMA 2010</option>
365 <option value="k-1500">RNA ontology</option>
366 <option value="k-1501">Neomark Oral Cancer-Centred Ontology</option>
367 <option value="k-1504">Current Procedural Terminology</option>
368 <option value="k-1505">Ontology for MicroRNA Target Prediction</option>
369 <option value="k-1506">Gene Ontology Extension</option>
370 <option value="k-1507">Cell Cycle Ontology</option>
371 <option value="k-1509">ICPS Network</option>
372 <option value="k-1510">Metathesaurus CPT Hierarchical Terms</option>
373 <option value="k-1515">Interaction Network Ontology</option>
374 <option value="k-1516">ICD10</option>
375 <option value="k-1521">Neural Motor Recovery Ontology</option>
376 <option value="k-1522">BioPAX</option>
377 <option value="k-1523">OBOE SBC</option>
378 <option value="k-1524">OBOE</option>
379 <option value="k-1526">CRISP Thesaurus, 2006</option>
380 <option value="k-1527">VANDF</option>
381 <option value="k-1528">HUGO</option>
382 <option value="k-1529">HCPCS</option>
383 <option value="k-1530">Animal natural history and life history</option>
384 <option value="k-1534">apollo-akesios</option>
385 <option value="k-1537">Brucellosis Ontology</option>
386 <option value="k-1538">Role Ontology</option>
387 <option value="k-1539">Neural-Immune Gene Ontology</option>
388 <option value="k-1540">Ontology for Drug Discovery Investigations</option>
389 <option value="k-1541">Cell line ontology</option>
390 <option value="k-1545">Wheat trait </option>
391 <option value="k-1547">BRENDA tissue / enzyme source</option>
392 <option value="k-1552">Reproductive traits ontology</option>
393 <option value="k-1553">ICD10CM</option>
394 <option value="k-1560">Cognitive Paradigm Ontology</option>
395 <option value="k-1423">RxNORM</option>
396 <option value="k-1517">Human developmental anatomy, abstract version, v2</option>
397 <option value="k-1016">Drosophila development</option>
398 <option value="k-1062">PRotein Ontology (PRO)</option>
399 <option value="k-1000">Mouse adult gross anatomy</option>
400 <option value="k-1065">Tick gross anatomy</option>
401 <option value="k-1123">Ontology for Biomedical Investigations</option>
402 <option value="k-1078">Spatial Ontology</option>
403 <option value="k-1007">Chemical entities of biological interest</option>
404 <option value="k-1049">C. elegans development</option>
405 <option value="k-1070">Gene Ontology</option>
406 <option value="k-1136">Experimental Factor Ontology</option>
407 <option value="k-1141">Ontology of Physics for Biology</option>
408 <option value="k-1005">BRENDA tissue / enzyme source</option>
409 <option value="k-1321">Neural ElectroMagnetic Ontologies</option>
410 <option value="k-1043">Physico-chemical process</option>
411 <option value="k-1064">Fly taxonomy</option>
412 <option value="k-1076">Ontology of Clinical Research (OCRe)</option>
413 <option value="k-1110">Teleost Anatomy Ontology</option>
414 <option value="k-1362">Hymenoptera Anatomy Ontology</option>
415 <option value="k-1030">Mosquito gross anatomy</option>
416 <option value="k-1029">Molecule role (INOH Protein name/family name ontology)</option>
417 <option value="k-1144">Dendritic cell</option>
418 <option value="k-1125">Human Phenotype Ontology</option>
419 <option value="k-1023">Biological imaging methods</option>
420 <option value="k-1021">Human developmental anatomy, abstract version</option>
421 <option value="k-1046">Systems Biology</option>
422 <option value="k-1051">Zebrafish anatomy and development</option>
423 <option value="k-1037">Cereal plant trait</option>
424 <option value="k-1107">Phenotypic quality</option>
425 <option value="k-1081">Teleost taxonomy</option>
426 <option value="k-1048">C. elegans gross anatomy</option>
427 <option value="k-1050">Maize gross anatomy</option>
428 <option value="k-1036">Plant environmental conditions</option>
429 <option value="k-1109">Sequence types and features</option>
430 <option value="k-1022">Human developmental anatomy, timed version</option>
431 <option value="k-1095">Xenopus anatomy and development</option>
432 <option value="k-1027">Medaka fish anatomy and development</option>
433 <option value="k-1011">Event (INOH pathway ontology)</option>
434 <option value="k-1010">Mouse gross anatomy and development</option>
435 <option value="k-1015">Drosophila gross anatomy</option>
436 <option value="k-1090">Amphibian gross anatomy</option>
437 <option value="k-1019">Fungal gross anatomy</option>
438 <option value="k-1067">C. elegans phenotype</option>
439 <option value="k-1069">Environment Ontology</option>
440 <option value="k-1112">Units of measurement</option>
441 <option value="k-1091">Spider Ontology</option>
442 <option value="k-1017">FlyBase Controlled Vocabulary</option>
443 <option value="k-1348">Online Mendelian Inheritance in Man</option>
444 <option value="k-1172">Vaccine Ontology</option>
445 <option value="k-1222">Ascomycete phenotype ontology</option>
446 <option value="k-1105">Mass spectrometry</option>
447 <option value="k-1237">Situation-Based Access Control</option>
448 <option value="k-1008">Dictyostelium discoideum anatomy</option>
449 <option value="k-1150">Rat Strain Ontology</option>
450 <option value="k-1101">International Classification of Diseases</option>
451 <option value="k-1314">Cell Line Ontology</option>
452 <option value="k-1009">Human disease</option>
453 <option value="k-1084">NIFSTD</option>
454 <option value="k-1025">Mammalian phenotype</option>
455 <option value="k-1035">Pathway ontology</option>
456 <option value="k-1012">Evidence codes</option>
457 <option value="k-1115">Yeast phenotypes</option>
458 <option value="k-1001">Cereal plant gross anatomy</option>
459 <option value="k-1006">Cell type</option>
460 <option value="k-1077">Mosquito insecticide resistance</option>
461 <option value="k-1085">Ontology of Glucose Metabolism Disorder</option>
462 <option value="k-1057">RadLex</option>
463 <option value="k-1031">Mouse pathology</option>
464 <option value="k-1032">NCI Thesaurus</option>
465 <option value="k-1381">NIF Dysfunction</option>
466 <option value="k-1401">International Classification for Nursing Practice</option>
467 <option value="k-1402">NIF Cell</option>
468 <option value="k-1404">Uber anatomy ontology</option>
469 <option value="k-1407">Terminology for the Description of Dynamics</option>
470 <option value="k-1411">International Classification of Functioning, Disability and Health (ICF)</option>
471 <option value="k-1413">Software Ontology</option>
472 <option value="k-1414">Ontology for General Medical Science</option>
473 <option value="k-1444">Chemical Information Ontology</option>
474 <option value="k-1461">Translational Medicine Ontology</option>
475 <option value="k-1488">SysMO-JERM</option>
476 <option value="k-1489">Adverse Event Ontology</option>
477 <option value="k-1498">EDAM</option>
478 <option value="k-1532">SemanticScience Integrated Ontology</option>
479 <option value="k-1550">PHARE</option>
480 <option value="k-1555">Vertebrate Anatomy Ontology</option>
481 <option value="k-1565">Ontology of Medically Related Social Entities</option>
482 <option value="k-1567">Pharmacovigilance Ontology</option>
483 <option value="k-1568">Anatomical Entity Ontology</option>
484 <option value="k-1569">Host Pathogen Interactions Ontology</option>
485 <option value="k-1570">Traditional Medicine Constitution Value Set</option>
486 <option value="k-1571">Traditional Medicine Other Factors Value Set</option>
487 <option value="k-1572">Traditional Medicine Signs and Symptoms Value Set</option>
488 <option value="k-1573">Traditional Medicine Meridian Value Sets</option>
489 <option value="k-1574">vertebrate Homologous Organ Groups</option>
490 <option value="k-1575">ExO</option>
491 <option value="k-1576">FDA Medical Devices (2010)</option>
492 <option value="k-1578">HOM_ElixhauserScores</option>
493 <option value="k-1580">Adverse Event Reporting ontology</option>
494 <option value="k-1581">HEALTH_INDICATORS</option>
495 <option value="k-1582">COA</option>
496 <option value="k-1583">Clinical Measurement Ontology</option>
497 <option value="k-1584">Measurement Method Ontology</option>
498 <option value="k-1585">Experimental Conditions Ontology</option>
499 <option value="k-1587">Plant Ontology</option>
500 <option value="k-1588">Ontology of General Purpose Datatypes</option>
501 <option value="k-1596">MajDxCatgrs-DxRltdGrps</option>
502 <option value="k-1613">Bone Dysplasia Ontology</option>
503 <option value="k-1614">IxnO</option>
504 <option value="k-1615">Systems Chemical Biology/Chemogenomics </option>
505 <option value="k-1616">Phylogenetic Ontology</option>
506 <option value="k-1621">Neuro Behavior Ontology</option>
507 </param>
508 <param name="semanticTypes" type="select" multiple="true" label="Indicates the list of semantic types to use in the annotation process">
509 <option value="T-all" selected="true">ALL</option>
510 <option value="T000">UMLS concept</option>
511 <option value="T998">Jax Mouse/Human Gene dictionary concept</option>
512 <option value="T999">NCBO BioPortal concept</option>
513 <option value="T116">Amino Acid, Peptide, or Protein</option>
514 <option value="T121">Pharmacologic Substance</option>
515 <option value="T130">Indicator, Reagent, or Diagnostic Aid</option>
516 <option value="T119">Lipid</option>
517 <option value="T126">Enzyme</option>
518 <option value="T123">Biologically Active Substance</option>
519 <option value="T109">Organic Chemical</option>
520 <option value="T131">Hazardous or Poisonous Substance</option>
521 <option value="T110">Steroid</option>
522 <option value="T125">Hormone</option>
523 <option value="T114">Nucleic Acid, Nucleoside, or Nucleotide</option>
524 <option value="T111">Eicosanoid</option>
525 <option value="T118">Carbohydrate</option>
526 <option value="T124">Neuroreactive Substance or Biogenic Amine</option>
527 <option value="T127">Vitamin</option>
528 <option value="T195">Antibiotic</option>
529 <option value="T129">Immunologic Factor</option>
530 <option value="T024">Tissue</option>
531 <option value="T115">Organophosphorus Compound</option>
532 <option value="T073">Manufactured Object</option>
533 <option value="T081">Quantitative Concept</option>
534 <option value="T170">Intellectual Product</option>
535 <option value="T029">Body Location or Region</option>
536 <option value="T184">Sign or Symptom</option>
537 <option value="T033">Finding</option>
538 <option value="T037">Injury or Poisoning</option>
539 <option value="T191">Neoplastic Process</option>
540 <option value="T023">Body Part, Organ, or Organ Component</option>
541 <option value="T005">Virus</option>
542 <option value="T047">Disease or Syndrome</option>
543 <option value="T019">Congenital Abnormality</option>
544 <option value="T169">Functional Concept</option>
545 <option value="T190">Anatomical Abnormality</option>
546 <option value="T022">Body System</option>
547 <option value="T018">Embryonic Structure</option>
548 <option value="T101">Patient or Disabled Group</option>
549 <option value="T093">Health Care Related Organization</option>
550 <option value="T089">Regulation or Law</option>
551 <option value="T061">Therapeutic or Preventive Procedure</option>
552 <option value="T062">Research Activity</option>
553 <option value="T046">Pathologic Function</option>
554 <option value="T041">Mental Process</option>
555 <option value="T055">Individual Behavior</option>
556 <option value="T004">Fungus</option>
557 <option value="T060">Diagnostic Procedure</option>
558 <option value="T070">Natural Phenomenon or Process</option>
559 <option value="T197">Inorganic Chemical</option>
560 <option value="T057">Occupational Activity</option>
561 <option value="T083">Geographic Area</option>
562 <option value="T074">Medical Device</option>
563 <option value="T002">Plant</option>
564 <option value="T065">Educational Activity</option>
565 <option value="T092">Organization</option>
566 <option value="T009">Invertebrate</option>
567 <option value="T025">Cell</option>
568 <option value="T196">Element, Ion, or Isotope</option>
569 <option value="T067">Phenomenon or Process</option>
570 <option value="T080">Qualitative Concept</option>
571 <option value="T102">Group Attribute</option>
572 <option value="T098">Population Group</option>
573 <option value="T040">Organism Function</option>
574 <option value="T034">Laboratory or Test Result</option>
575 <option value="T201">Clinical Attribute</option>
576 <option value="T097">Professional or Occupational Group</option>
577 <option value="T064">Governmental or Regulatory Activity</option>
578 <option value="T054">Social Behavior</option>
579 <option value="T003">Alga</option>
580 <option value="T007">Bacterium</option>
581 <option value="T044">Molecular Function</option>
582 <option value="T053">Behavior</option>
583 <option value="T069">Environmental Effect of Humans</option>
584 <option value="T042">Organ or Tissue Function</option>
585 <option value="T103">Chemical</option>
586 <option value="T122">Biomedical or Dental Material</option>
587 <option value="T015">Mammal</option>
588 <option value="T020">Acquired Abnormality</option>
589 <option value="T030">Body Space or Junction</option>
590 <option value="T026">Cell Component</option>
591 <option value="T043">Cell Function</option>
592 <option value="T059">Laboratory Procedure</option>
593 <option value="T052">Activity</option>
594 <option value="T056">Daily or Recreational Activity</option>
595 <option value="T079">Temporal Concept</option>
596 <option value="T091">Biomedical Occupation or Discipline</option>
597 <option value="T192">Receptor</option>
598 <option value="T031">Body Substance</option>
599 <option value="T048">Mental or Behavioral Dysfunction</option>
600 <option value="T058">Health Care Activity</option>
601 <option value="T120">Chemical Viewed Functionally</option>
602 <option value="T100">Age Group</option>
603 <option value="T104">Chemical Viewed Structurally</option>
604 <option value="T171">Language</option>
605 <option value="T032">Organism Attribute</option>
606 <option value="T095">Self-help or Relief Organization</option>
607 <option value="T078">Idea or Concept</option>
608 <option value="T090">Occupation or Discipline</option>
609 <option value="T167">Substance</option>
610 <option value="T068">Human-caused Phenomenon or Process</option>
611 <option value="T168">Food</option>
612 <option value="T028">Gene or Genome</option>
613 <option value="T014">Reptile</option>
614 <option value="T050">Experimental Model of Disease</option>
615 <option value="T045">Genetic Function</option>
616 <option value="T011">Amphibian</option>
617 <option value="T013">Fish</option>
618 <option value="T094">Professional Society</option>
619 <option value="T087">Amino Acid Sequence</option>
620 <option value="T066">Machine Activity</option>
621 <option value="T185">Classification</option>
622 <option value="T006">Rickettsia or Chlamydia</option>
623 <option value="T049">Cell or Molecular Dysfunction</option>
624 <option value="T008">Animal</option>
625 <option value="T051">Event</option>
626 <option value="T038">Biologic Function</option>
627 <option value="T194">Archaeon</option>
628 <option value="T086">Nucleotide Sequence</option>
629 <option value="T039">Physiologic Function</option>
630 <option value="T012">Bird</option>
631 <option value="T063">Molecular Biology Research Technique</option>
632 <option value="T017">Anatomical Structure</option>
633 <option value="T082">Spatial Concept</option>
634 <option value="T088">Carbohydrate Sequence</option>
635 <option value="T099">Family Group</option>
636 <option value="T001">Organism</option>
637 <option value="T075">Research Device</option>
638 <option value="T096">Group</option>
639 <option value="T016">Human</option>
640 <option value="T072">Physical Object</option>
641 <option value="T071">Entity</option>
642 <option value="T200">Clinical Drug</option>
643 <option value="T085">Molecular Sequence</option>
644 <option value="T077">Conceptual Entity</option>
645 <option value="T010">Vertebrate</option>
646 <option value="T203">Drug Delivery Device</option>
647 <option value="T021">Fully Formed Anatomical Structure</option>
648 <option value="T204">Eukaryote</option>
649 </param>
650 <param name="levelMax" type="integer" value="0" min="0" label="Indicates the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step"/>
651 <param name="mappingTypes" type="select" multiple="true" label="the list of mapping type to use during the mapping expansion step">
652 <option value="m-all" selected="true">ALL</option>
653 <option value="m-null">None</option>
654 <option value="m-Automatic">Automatic</option>
655 <option value="m-Manual">Manual</option>
656 </param>
657 <param name="textToAnnotate" type="text" size="100" value="" label="Text to annotate"/>
658 <param name="format" type="select" label="File output format">
659 <option value="xml" selected="true">XML</option>
660 <option value="text">Text</option>
661 <option value="tabDelimited">Tab Delimited</option>
662 </param>
663 <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/>
664 </inputs>
665 <outputs>
666 <data format="text" name="output" />
667 </outputs>
668 <tests>
669 <test>
670 <param name="longestOnly"/>
671 <param name="wholeWordOnly"/>
672 <param name="filterNumber"/>
673 <param name="stopWords"/>
674 <param name="withDefaultStopWords"/>
675 <param name="isTopWordsCaseSensitive"/>
676 <param name="mintermSize"/>
677 <param name="scored"/>
678 <param name="withSynony"/>
679 <param name="ontologiesToExpand"/>
680 <param name="ontologiesToKeepInResult"/>
681 <param name="semanticTypes"/>
682 <param name="levelMax"/>
683 <param name="mappintTypes"/>
684 <param name="textToAnnotate"/>
685 <param name="format"/>
686 <param name="apikey"/>
687 </test>
688 </tests>
689 <help>
690
691 **Usage**
692 Enter bioportal API key, a text to annotate and specify the parameters, and the annotations will be retrieved.
693
694 **Contact**
695
696 Please send any request or comment to jose.minyarro@um.es
697
698 **More information**
699
700 http://bioportal.bioontology.org
701
702 </help>
703
704 </tool>