annotate NCBO_services/ncbo_resourceIndex.xml @ 17:fc4c8a9b3152

branch merge
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 18 Jan 2012 11:06:11 +0100
parents 39bbdffcef51
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
1 <tool id="ncbo_resourceIndex" name="Search for resources matched up with terms in bio-ontologies depending on the given text" version="1.0.1">
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
2 <description>Search for resources matched up with terms in bio-ontologies depending on the given text</description>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
3 <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_resourceIndex_galaxy.jar $query $ontologyids $resourceId $mode $elementDetails $format $apikey > $output</command>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
4 <inputs>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
5 <param name="query" type="text" size="100" value="" label="Text to search for terms in the selected bio-ontologys"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
6 <param name="ontologyids" type="select" multiple="true" label="Indicates the list of ontologies to search for during the search process">
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
7 <option value="all" selected="true">ALL</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
8 <option value="1394">Syndromic Surveillance Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
9 <option value="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
10 <option value="1158">Cell Behavior Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
11 <option value="1033">NMR-instrument specific component of metabolomics investigations</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
12 <option value="1351">Medical Subject Headings</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
13 <option value="1146">Electrocardiography Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
14 <option value="1041">Protein modification</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
15 <option value="1058">SNP-Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
16 <option value="1099">African Traditional Medicine</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
17 <option value="1134">BioTop</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
18 <option value="1247">GeoSpecies Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
19 <option value="1024">Loggerhead nesting</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
20 <option value="1257">MeGO</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
21 <option value="1135">Pseudogene</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
22 <option value="1126">Family Health History Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
23 <option value="1108">Plant structure</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
24 <option value="1114">Bilateria anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
25 <option value="1100">Ontology for Genetic Interval</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
26 <option value="1044">Sample processing and separation techniques</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
27 <option value="1347">MedlinePlus Health Topics</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
28 <option value="1152">Minimal anatomical terminology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
29 <option value="1063">Common Anatomy Reference Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
30 <option value="1089">BIRNLex</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
31 <option value="1116">Bleeding History Phenotype</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
32 <option value="1104">Biomedical Resource Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
33 <option value="1350">Logical Observation Identifier Names and Codes</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
34 <option value="1082">Gene Regulation Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
35 <option value="1047">Cereal plant development</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
36 <option value="1349">Physician Data Query</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
37 <option value="1190">Parasite Life Cycle</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
38 <option value="1192">Proteomics Pipeline Infrastructure for CPTAC</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
39 <option value="1352">National Drug File</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
40 <option value="1059">Computer-based Patient Record Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
41 <option value="1052">Protein Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
42 <option value="1341">COSTART</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
43 <option value="1344">International Classification of Primary Care</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
44 <option value="1061">Suggested Ontology for Pharmacogenomics</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
45 <option value="1353">SNOMED Clinical Terms</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
46 <option value="1224">Symptom Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
47 <option value="1013">eVOC (Expressed Sequence Annotation for Humans)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
48 <option value="1149">DermLex: The Dermatology Lexicon</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
49 <option value="1311">Malaria Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
50 <option value="1335">Parasite Experiment Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
51 <option value="1370">Amphibian taxonomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
52 <option value="1354">WHO Adverse Reaction Terminology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
53 <option value="1148">BioPortal Metadata</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
54 <option value="1038">Plant growth and developmental stage</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
55 <option value="1132">NCBI organismal classification</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
56 <option value="1328">Ontology of homology and related concepts in biology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
57 <option value="1290">ABA Adult Mouse Brain</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
58 <option value="1055">Galen</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
59 <option value="1332">Basic Formal Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
60 <option value="1183">Lipid Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
61 <option value="1026">Multiple alignment</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
62 <option value="1130">Cancer Research and Management ACGT Master Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
63 <option value="1060">Epoch Clinical Trial Ontologies</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
64 <option value="1369">PhysicalFields</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
65 <option value="1086">Ontology for disease genetic investigation</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
66 <option value="1122">Skin Physiology Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
67 <option value="1142">Cardiac Electrophysiology Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
68 <option value="1128">Comparative Data Analysis Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
69 <option value="1088">MaHCO - An MHC Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
70 <option value="1249">Smoking Behavior Risk Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
71 <option value="1039">Proteomics data and process provenance</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
72 <option value="1040">Protein-protein interaction</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
73 <option value="1068">Subcellular Anatomy Ontology (SAO)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
74 <option value="1087">Ontology of Geographical Region</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
75 <option value="1094">Pathogen transmission</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
76 <option value="1131">MGED Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
77 <option value="1106">Gene Regulation Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
78 <option value="1054">Amino Acid</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
79 <option value="1056">Basic Vertebrate Anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
80 <option value="1083">NanoParticle Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
81 <option value="1053">Foundational Model of Anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
82 <option value="1092">Infectious disease</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
83 <option value="1393">Information Artifact Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
84 <option value="1395">MDSS Mo</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
85 <option value="1397">Gazetteer</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
86 <option value="1398">Ontology of Language Disorder in Autism</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
87 <option value="1399">Pilot Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
88 <option value="1406">linkingkin2pep</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
89 <option value="1409">PKO_Re</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
90 <option value="1410">Kinetic Simulation Algorithm Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
91 <option value="1415">Common Terminology Criteria for Adverse Events</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
92 <option value="1418">TOK_Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
93 <option value="1419">Taxonomic rank vocabulary</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
94 <option value="1422">MedDRA</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
95 <option value="1424">National Drug Data File</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
96 <option value="1425">ICD-10-PCS</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
97 <option value="1426">Master Drug Data Base</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
98 <option value="1429">ICPC-2 PLUS</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
99 <option value="1430">AIR</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
100 <option value="1438">Breast tissue cell lines</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
101 <option value="1439">General Formal Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
102 <option value="1440">General Formal Ontology: Biology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
103 <option value="1343">Health Level Seven</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
104 <option value="1484">International Classification of External Causes of Injuries</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
105 <option value="1487">Body System</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
106 <option value="1490">Platynereis stage ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
107 <option value="1491">IMGT-ONTOLOGY</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
108 <option value="1494">Tissue Microarray Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
109 <option value="1497">PMA 2010</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
110 <option value="1500">RNA ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
111 <option value="1501">Neomark Oral Cancer-Centred Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
112 <option value="1504">Current Procedural Terminology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
113 <option value="1505">Ontology for MicroRNA Target Prediction</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
114 <option value="1506">Gene Ontology Extension</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
115 <option value="1507">Cell Cycle Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
116 <option value="1509">ICPS Network</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
117 <option value="1510">Metathesaurus CPT Hierarchical Terms</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
118 <option value="1515">Interaction Network Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
119 <option value="1516">ICD10</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
120 <option value="1521">Neural Motor Recovery Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
121 <option value="1522">BioPAX</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
122 <option value="1523">OBOE SBC</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
123 <option value="1524">OBOE</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
124 <option value="1526">CRISP Thesaurus, 2006</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
125 <option value="1527">VANDF</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
126 <option value="1528">HUGO</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
127 <option value="1529">HCPCS</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
128 <option value="1530">Animal natural history and life history</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
129 <option value="1534">apollo-akesios</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
130 <option value="1537">Brucellosis Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
131 <option value="1538">Role Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
132 <option value="1539">Neural-Immune Gene Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
133 <option value="1540">Ontology for Drug Discovery Investigations</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
134 <option value="1541">Cell line ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
135 <option value="1545">Wheat trait </option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
136 <option value="1547">BRENDA tissue / enzyme source</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
137 <option value="1552">Reproductive traits ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
138 <option value="1553">ICD10CM</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
139 <option value="1560">Cognitive Paradigm Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
140 <option value="1423">RxNORM</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
141 <option value="1517">Human developmental anatomy, abstract version, v2</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
142 <option value="1016">Drosophila development</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
143 <option value="1062">PRotein Ontology (PRO)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
144 <option value="1000">Mouse adult gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
145 <option value="1065">Tick gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
146 <option value="1123">Ontology for Biomedical Investigations</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
147 <option value="1078">Spatial Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
148 <option value="1007">Chemical entities of biological interest</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
149 <option value="1049">C. elegans development</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
150 <option value="1070">Gene Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
151 <option value="1136">Experimental Factor Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
152 <option value="1141">Ontology of Physics for Biology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
153 <option value="1005">BRENDA tissue / enzyme source</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
154 <option value="1321">Neural ElectroMagnetic Ontologies</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
155 <option value="1043">Physico-chemical process</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
156 <option value="1064">Fly taxonomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
157 <option value="1076">Ontology of Clinical Research (OCRe)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
158 <option value="1110">Teleost Anatomy Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
159 <option value="1362">Hymenoptera Anatomy Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
160 <option value="1030">Mosquito gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
161 <option value="1029">Molecule role (INOH Protein name/family name ontology)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
162 <option value="1144">Dendritic cell</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
163 <option value="1125">Human Phenotype Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
164 <option value="1023">Biological imaging methods</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
165 <option value="1021">Human developmental anatomy, abstract version</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
166 <option value="1046">Systems Biology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
167 <option value="1051">Zebrafish anatomy and development</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
168 <option value="1037">Cereal plant trait</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
169 <option value="1107">Phenotypic quality</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
170 <option value="1081">Teleost taxonomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
171 <option value="1048">C. elegans gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
172 <option value="1050">Maize gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
173 <option value="1036">Plant environmental conditions</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
174 <option value="1109">Sequence types and features</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
175 <option value="1022">Human developmental anatomy, timed version</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
176 <option value="1095">Xenopus anatomy and development</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
177 <option value="1027">Medaka fish anatomy and development</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
178 <option value="1011">Event (INOH pathway ontology)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
179 <option value="1010">Mouse gross anatomy and development</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
180 <option value="1015">Drosophila gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
181 <option value="1090">Amphibian gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
182 <option value="1019">Fungal gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
183 <option value="1067">C. elegans phenotype</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
184 <option value="1069">Environment Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
185 <option value="1112">Units of measurement</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
186 <option value="1091">Spider Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
187 <option value="1017">FlyBase Controlled Vocabulary</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
188 <option value="1348">Online Mendelian Inheritance in Man</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
189 <option value="1172">Vaccine Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
190 <option value="1222">Ascomycete phenotype ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
191 <option value="1105">Mass spectrometry</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
192 <option value="1237">Situation-Based Access Control</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
193 <option value="1008">Dictyostelium discoideum anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
194 <option value="1150">Rat Strain Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
195 <option value="1101">International Classification of Diseases</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
196 <option value="1314">Cell Line Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
197 <option value="1009">Human disease</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
198 <option value="1084">NIFSTD</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
199 <option value="1025">Mammalian phenotype</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
200 <option value="1035">Pathway ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
201 <option value="1012">Evidence codes</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
202 <option value="1115">Yeast phenotypes</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
203 <option value="1001">Cereal plant gross anatomy</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
204 <option value="1006">Cell type</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
205 <option value="1077">Mosquito insecticide resistance</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
206 <option value="1085">Ontology of Glucose Metabolism Disorder</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
207 <option value="1057">RadLex</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
208 <option value="1031">Mouse pathology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
209 <option value="1032">NCI Thesaurus</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
210 <option value="1381">NIF Dysfunction</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
211 <option value="1401">International Classification for Nursing Practice</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
212 <option value="1402">NIF Cell</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
213 <option value="1404">Uber anatomy ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
214 <option value="1407">Terminology for the Description of Dynamics</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
215 <option value="1411">International Classification of Functioning, Disability and Health (ICF)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
216 <option value="1413">Software Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
217 <option value="1414">Ontology for General Medical Science</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
218 <option value="1444">Chemical Information Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
219 <option value="1461">Translational Medicine Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
220 <option value="1488">SysMO-JERM</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
221 <option value="1489">Adverse Event Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
222 <option value="1498">EDAM</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
223 <option value="1532">SemanticScience Integrated Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
224 <option value="1550">PHARE</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
225 <option value="1555">Vertebrate Anatomy Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
226 <option value="1565">Ontology of Medically Related Social Entities</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
227 <option value="1567">Pharmacovigilance Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
228 <option value="1568">Anatomical Entity Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
229 <option value="1569">Host Pathogen Interactions Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
230 <option value="1570">Traditional Medicine Constitution Value Set</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
231 <option value="1571">Traditional Medicine Other Factors Value Set</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
232 <option value="1572">Traditional Medicine Signs and Symptoms Value Set</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
233 <option value="1573">Traditional Medicine Meridian Value Sets</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
234 <option value="1574">vertebrate Homologous Organ Groups</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
235 <option value="1575">ExO</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
236 <option value="1576">FDA Medical Devices (2010)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
237 <option value="1578">HOM_ElixhauserScores</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
238 <option value="1580">Adverse Event Reporting ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
239 <option value="1581">HEALTH_INDICATORS</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
240 <option value="1582">COA</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
241 <option value="1583">Clinical Measurement Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
242 <option value="1584">Measurement Method Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
243 <option value="1585">Experimental Conditions Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
244 <option value="1587">Plant Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
245 <option value="1588">Ontology of General Purpose Datatypes</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
246 <option value="1596">MajDxCatgrs-DxRltdGrps</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
247 <option value="1613">Bone Dysplasia Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
248 <option value="1614">IxnO</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
249 <option value="1615">Systems Chemical Biology/Chemogenomics </option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
250 <option value="1616">Phylogenetic Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
251 <option value="1621">Neuro Behavior Ontology</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
252 </param>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
253 <param name="resourceId" type="select" multiple="true" label="Indicates the list of resources Ids to search for during the Resource Index search process">
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
254 <option value="all" selected="true">ALL</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
255 <option value="PGGE">PharmGKB [Gene]</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
256 <option value="BSM">Biositemaps</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
257 <option value="CDD">Conserved Domain Database (CDD)</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
258 <option value="CT">ClinicalTrials.gov</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
259 <option value="GM">ARRS GoldMiner</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
260 <option value="PC">Pathway Commons</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
261 <option value="DBK">DrugBank</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
262 <option value="AERS">Adverse Event Reporting System Data</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
263 <option value="PM">PubMed</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
264 <option value="MICAD">MICAD</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
265 <option value="OMIM">Online Mendelian Inheritance in Man</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
266 <option value="GAP">Database of Genotypes and Phenotypes</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
267 <option value="PCM">PubChem</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
268 <option value="PGDI">PharmGKB [Disease]</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
269 <option value="WP">WikiPathways</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
270 <option value="SMD">Stanford Microarray Database</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
271 <option value="AE">ArrayExpress</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
272 <option value="RXRD">ResearchCrossroads</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
273 <option value="GEO">Gene Expression Omnibus DataSets</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
274 <option value="REAC">Reactome</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
275 <option value="UPKB">UniProt KB</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
276 <option value="CANANO">caNanoLab</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
277 <option value="PGDR">PharmGKB [Drug]</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
278 </param>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
279 <param name="mode" type="select" label="Gets the union or intersection of the annotations done with the given text if we find more than one concept in the bio-ontologies ">
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
280 <option value="unioin" selected="true">Union</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
281 <option value="intersection">Intersection</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
282 </param>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
283 <param name="elementDetails" type="boolean" value="true" label="Tick the box whether the returned resource elements should be detailled or not"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
284 <param name="format" type="select" label="Gets the results in a particular format">
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
285 <option value="xml" selected="true">XML</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
286 <option value="text">Text</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
287 <option value="tabDelimited">Tab Delimited</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
288 <option value="rdf">RDF</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
289 <option value="owl">OWL</option>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
290 </param>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
291 <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
292 </inputs>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
293 <outputs>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
294 <data format="text" name="output"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
295 </outputs>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
296 <tests>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
297 <test>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
298 <param name="query"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
299 <param name="ontologyids"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
300 <param name="resouceId"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
301 <param name="apikey"/>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
302 </test>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
303 </tests>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
304 <help>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
305
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
306 **Usage**
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
307 Enter bioportal API key, a text, a list of bioontolgies Ids,a list of resources to search for, the mode, tick if you want detailed element and the format of the results, and the Resource Index interface retrieves the resources matched up with the bioontology terms associated with the text provided.
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
308 Example of search text: Melanoma
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
309
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
310 **Contact**
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
311
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
312 Please send any request or comment to jose.minyarro@um.es
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
313
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
314 **More information**
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
315
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
316 http://bioportal.bioontology.org
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
317
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
318 </help>
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
319
39bbdffcef51 Uploaded
jose-minyarro
parents:
diff changeset
320 </tool>