Mercurial > repos > mikel-egana-aranguren > ncbo_services
changeset 3:097aa7000159
Interface improved
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Thu, 12 Jan 2012 10:27:50 +0100 |
| parents | 86a5e3f4f32f |
| children | 1aa0a6639913 d3d6bdbcf3ea |
| files | NCBO_services/get_ontology.xml |
| diffstat | 1 files changed, 274 insertions(+), 4 deletions(-) [+] |
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--- a/NCBO_services/get_ontology.xml Sat Dec 31 17:30:24 2011 +0100 +++ b/NCBO_services/get_ontology.xml Thu Jan 12 10:27:50 2012 +0100 @@ -1,9 +1,279 @@ -<tool id="get_ontology" name="Get ontology by id" version="1.0.2"> +<tool id="get_ontology" name="Get ontology by id" version="1.0.3"> <description>Retrieves an ontology from bioportal using its id</description> - <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_galaxy.jar $api_key $ontology_id > $output </command> +<!-- <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_galaxy.jar $api_key $ontology_id > $output </command> --> + <command> + #if $id_opts.id_opts_menu=="id_by_hand" #java -jar ${__tool_data_path__}/shared/jars/ncbo_galaxy.jar $api_key $id_opts.ontology_id > $output + #else #java -jar ${__tool_data_path__}/shared/jars/ncbo_galaxy.jar $api_key $id_opts.ontology_id > $output + #end if + </command> + <inputs> <param name="api_key" type="text" size="100" label="BioPortal API key" /> - <param name="ontology_id" type="text" size="100" label="Ontology ID from bioportal" /> + +<!-- <param name="ontology_id" type="text" size="100" label="Provide ontology id ... " /> --> + + <conditional name="id_opts"> + <!--<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"> + <option value="id_by_hand">Provide id by hand</option> + <option value="choose_from_list">Choose ontology from list</option> + </param>--> + + <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"/> + + <when value="id_by_hand"> + <param name="ontology_id" type="text" size="100" label="Provide ontology id" /> + </when> + + <when value="choose_from_list"> + <!-- Copied from Jose Miñarro --> + <param name="ontology_id" type="select" multiple="false" label="Choose ontology from this list"> + <option value="1394">Syndromic Surveillance Ontology</option> + <option value="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> + <option value="1158">Cell Behavior Ontology</option> + <option value="1033">NMR-instrument specific component of metabolomics investigations</option> + <option value="1351">Medical Subject Headings</option> + <option value="1146">Electrocardiography Ontology</option> + <option value="1041">Protein modification</option> + <option value="1058">SNP-Ontology</option> + <option value="1099">African Traditional Medicine</option> + <option value="1134">BioTop</option> + <option value="1247">GeoSpecies Ontology</option> + <option value="1024">Loggerhead nesting</option> + <option value="1257">MeGO</option> + <option value="1135">Pseudogene</option> + <option value="1126">Family Health History Ontology</option> + <option value="1108">Plant structure</option> + <option value="1114">Bilateria anatomy</option> + <option value="1100">Ontology for Genetic Interval</option> + <option value="1044">Sample processing and separation techniques</option> + <option value="1347">MedlinePlus Health Topics</option> + <option value="1152">Minimal anatomical terminology</option> + <option value="1063">Common Anatomy Reference Ontology</option> + <option value="1089">BIRNLex</option> + <option value="1116">Bleeding History Phenotype</option> + <option value="1104">Biomedical Resource Ontology</option> + <option value="1350">Logical Observation Identifier Names and Codes</option> + <option value="1082">Gene Regulation Ontology</option> + <option value="1047">Cereal plant development</option> + <option value="1349">Physician Data Query</option> + <option value="1190">Parasite Life Cycle</option> + <option value="1192">Proteomics Pipeline Infrastructure for CPTAC</option> + <option value="1352">National Drug File</option> + <option value="1059">Computer-based Patient Record Ontology</option> + <option value="1052">Protein Ontology</option> + <option value="1341">COSTART</option> + <option value="1344">International Classification of Primary Care</option> + <option value="1061">Suggested Ontology for Pharmacogenomics</option> + <option value="1353">SNOMED Clinical Terms</option> + <option value="1224">Symptom Ontology</option> + <option value="1013">eVOC (Expressed Sequence Annotation for Humans)</option> + <option value="1149">DermLex: The Dermatology Lexicon</option> + <option value="1311">Malaria Ontology</option> + <option value="1335">Parasite Experiment Ontology</option> + <option value="1370">Amphibian taxonomy</option> + <option value="1354">WHO Adverse Reaction Terminology</option> + <option value="1148">BioPortal Metadata</option> + <option value="1038">Plant growth and developmental stage</option> + <option value="1132">NCBI organismal classification</option> + <option value="1328">Ontology of homology and related concepts in biology</option> + <option value="1290">ABA Adult Mouse Brain</option> + <option value="1055">Galen</option> + <option value="1332">Basic Formal Ontology</option> + <option value="1183">Lipid Ontology</option> + <option value="1026">Multiple alignment</option> + <option value="1130">Cancer Research and Management ACGT Master Ontology</option> + <option value="1060">Epoch Clinical Trial Ontologies</option> + <option value="1369">PhysicalFields</option> + <option value="1086">Ontology for disease genetic investigation</option> + <option value="1122">Skin Physiology Ontology</option> + <option value="1142">Cardiac Electrophysiology Ontology</option> + <option value="1128">Comparative Data Analysis Ontology</option> + <option value="1088">MaHCO - An MHC Ontology</option> + <option value="1249">Smoking Behavior Risk Ontology</option> + <option value="1039">Proteomics data and process provenance</option> + <option value="1040">Protein-protein interaction</option> + <option value="1068">Subcellular Anatomy Ontology (SAO)</option> + <option value="1087">Ontology of Geographical Region</option> + <option value="1094">Pathogen transmission</option> + <option value="1131">MGED Ontology</option> + <option value="1106">Gene Regulation Ontology</option> + <option value="1054">Amino Acid</option> + <option value="1056">Basic Vertebrate Anatomy</option> + <option value="1083">NanoParticle Ontology</option> + <option value="1053">Foundational Model of Anatomy</option> + <option value="1092">Infectious disease</option> + <option value="1393">Information Artifact Ontology</option> + <option value="1395">MDSS Mo</option> + <option value="1397">Gazetteer</option> + <option value="1398">Ontology of Language Disorder in Autism</option> + <option value="1399">Pilot Ontology</option> + <option value="1406">linkingkin2pep</option> + <option value="1409">PKO_Re</option> + <option value="1410">Kinetic Simulation Algorithm Ontology</option> + <option value="1415">Common Terminology Criteria for Adverse Events</option> + <option value="1418">TOK_Ontology</option> + <option value="1419">Taxonomic rank vocabulary</option> + <option value="1422">MedDRA</option> + <option value="1424">National Drug Data File</option> + <option value="1425">ICD-10-PCS</option> + <option value="1426">Master Drug Data Base</option> + <option value="1429">ICPC-2 PLUS</option> + <option value="1430">AIR</option> + <option value="1438">Breast tissue cell lines</option> + <option value="1439">General Formal Ontology</option> + <option value="1440">General Formal Ontology: Biology</option> + <option value="1343">Health Level Seven</option> + <option value="1484">International Classification of External Causes of Injuries</option> + <option value="1487">Body System</option> + <option value="1490">Platynereis stage ontology</option> + <option value="1491">IMGT-ONTOLOGY</option> + <option value="1494">Tissue Microarray Ontology</option> + <option value="1497">PMA 2010</option> + <option value="1500">RNA ontology</option> + <option value="1501">Neomark Oral Cancer-Centred Ontology</option> + <option value="1504">Current Procedural Terminology</option> + <option value="1505">Ontology for MicroRNA Target Prediction</option> + <option value="1506">Gene Ontology Extension</option> + <option value="1507">Cell Cycle Ontology</option> + <option value="1509">ICPS Network</option> + <option value="1510">Metathesaurus CPT Hierarchical Terms</option> + <option value="1515">Interaction Network Ontology</option> + <option value="1516">ICD10</option> + <option value="1521">Neural Motor Recovery Ontology</option> + <option value="1522">BioPAX</option> + <option value="1523">OBOE SBC</option> + <option value="1524">OBOE</option> + <option value="1526">CRISP Thesaurus, 2006</option> + <option value="1527">VANDF</option> + <option value="1528">HUGO</option> + <option value="1529">HCPCS</option> + <option value="1530">Animal natural history and life history</option> + <option value="1534">apollo-akesios</option> + <option value="1537">Brucellosis Ontology</option> + <option value="1538">Role Ontology</option> + <option value="1539">Neural-Immune Gene Ontology</option> + <option value="1540">Ontology for Drug Discovery Investigations</option> + <option value="1541">Cell line ontology</option> + <option value="1545">Wheat trait </option> + <option value="1547">BRENDA tissue / enzyme source</option> + <option value="1552">Reproductive traits ontology</option> + <option value="1553">ICD10CM</option> + <option value="1560">Cognitive Paradigm Ontology</option> + <option value="1423">RxNORM</option> + <option value="1517">Human developmental anatomy, abstract version, v2</option> + <option value="1016">Drosophila development</option> + <option value="1062">PRotein Ontology (PRO)</option> + <option value="1000">Mouse adult gross anatomy</option> + <option value="1065">Tick gross anatomy</option> + <option value="1123">Ontology for Biomedical Investigations</option> + <option value="1078">Spatial Ontology</option> + <option value="1007">Chemical entities of biological interest</option> + <option value="1049">C. elegans development</option> + <option value="1070">Gene Ontology</option> + <option value="1136">Experimental Factor Ontology</option> + <option value="1141">Ontology of Physics for Biology</option> + <option value="1005">BRENDA tissue / enzyme source</option> + <option value="1321">Neural ElectroMagnetic Ontologies</option> + <option value="1043">Physico-chemical process</option> + <option value="1064">Fly taxonomy</option> + <option value="1076">Ontology of Clinical Research (OCRe)</option> + <option value="1110">Teleost Anatomy Ontology</option> + <option value="1362">Hymenoptera Anatomy Ontology</option> + <option value="1030">Mosquito gross anatomy</option> + <option value="1029">Molecule role (INOH Protein name/family name ontology)</option> + <option value="1144">Dendritic cell</option> + <option value="1125">Human Phenotype Ontology</option> + <option value="1023">Biological imaging methods</option> + <option value="1021">Human developmental anatomy, abstract version</option> + <option value="1046">Systems Biology</option> + <option value="1051">Zebrafish anatomy and development</option> + <option value="1037">Cereal plant trait</option> + <option value="1107">Phenotypic quality</option> + <option value="1081">Teleost taxonomy</option> + <option value="1048">C. elegans gross anatomy</option> + <option value="1050">Maize gross anatomy</option> + <option value="1036">Plant environmental conditions</option> + <option value="1109">Sequence types and features</option> + <option value="1022">Human developmental anatomy, timed version</option> + <option value="1095">Xenopus anatomy and development</option> + <option value="1027">Medaka fish anatomy and development</option> + <option value="1011">Event (INOH pathway ontology)</option> + <option value="1010">Mouse gross anatomy and development</option> + <option value="1015">Drosophila gross anatomy</option> + <option value="1090">Amphibian gross anatomy</option> + <option value="1019">Fungal gross anatomy</option> + <option value="1067">C. elegans phenotype</option> + <option value="1069">Environment Ontology</option> + <option value="1112">Units of measurement</option> + <option value="1091">Spider Ontology</option> + <option value="1017">FlyBase Controlled Vocabulary</option> + <option value="1348">Online Mendelian Inheritance in Man</option> + <option value="1172">Vaccine Ontology</option> + <option value="1222">Ascomycete phenotype ontology</option> + <option value="1105">Mass spectrometry</option> + <option value="1237">Situation-Based Access Control</option> + <option value="1008">Dictyostelium discoideum anatomy</option> + <option value="1150">Rat Strain Ontology</option> + <option value="1101">International Classification of Diseases</option> + <option value="1314">Cell Line Ontology</option> + <option value="1009">Human disease</option> + <option value="1084">NIFSTD</option> + <option value="1025">Mammalian phenotype</option> + <option value="1035">Pathway ontology</option> + <option value="1012">Evidence codes</option> + <option value="1115">Yeast phenotypes</option> + <option value="1001">Cereal plant gross anatomy</option> + <option value="1006">Cell type</option> + <option value="1077">Mosquito insecticide resistance</option> + <option value="1085">Ontology of Glucose Metabolism Disorder</option> + <option value="1057">RadLex</option> + <option value="1031">Mouse pathology</option> + <option value="1032">NCI Thesaurus</option> + <option value="1381">NIF Dysfunction</option> + <option value="1401">International Classification for Nursing Practice</option> + <option value="1402">NIF Cell</option> + <option value="1404">Uber anatomy ontology</option> + <option value="1407">Terminology for the Description of Dynamics</option> + <option value="1411">International Classification of Functioning, Disability and Health (ICF)</option> + <option value="1413">Software Ontology</option> + <option value="1414">Ontology for General Medical Science</option> + <option value="1444">Chemical Information Ontology</option> + <option value="1461">Translational Medicine Ontology</option> + <option value="1488">SysMO-JERM</option> + <option value="1489">Adverse Event Ontology</option> + <option value="1498">EDAM</option> + <option value="1532">SemanticScience Integrated Ontology</option> + <option value="1550">PHARE</option> + <option value="1555">Vertebrate Anatomy Ontology</option> + <option value="1565">Ontology of Medically Related Social Entities</option> + <option value="1567">Pharmacovigilance Ontology</option> + <option value="1568">Anatomical Entity Ontology</option> + <option value="1569">Host Pathogen Interactions Ontology</option> + <option value="1570">Traditional Medicine Constitution Value Set</option> + <option value="1571">Traditional Medicine Other Factors Value Set</option> + <option value="1572">Traditional Medicine Signs and Symptoms Value Set</option> + <option value="1573">Traditional Medicine Meridian Value Sets</option> + <option value="1574">vertebrate Homologous Organ Groups</option> + <option value="1575">ExO</option> + <option value="1576">FDA Medical Devices (2010)</option> + <option value="1578">HOM_ElixhauserScores</option> + <option value="1580">Adverse Event Reporting ontology</option> + <option value="1581">HEALTH_INDICATORS</option> + <option value="1582">COA</option> + <option value="1583">Clinical Measurement Ontology</option> + <option value="1584">Measurement Method Ontology</option> + <option value="1585">Experimental Conditions Ontology</option> + <option value="1587">Plant Ontology</option> + <option value="1588">Ontology of General Purpose Datatypes</option> + <option value="1596">MajDxCatgrs-DxRltdGrps</option> + <option value="1613">Bone Dysplasia Ontology</option> + <option value="1614">IxnO</option> + <option value="1615">Systems Chemical Biology/Chemogenomics </option> + <option value="1616"> Phylogenetic Ontology</option> + <option value="1621">Neuro Behavior Ontology</option> + </param> + </when> + </conditional> </inputs> <outputs> <data format="text" name="output" /> @@ -18,7 +288,7 @@ **Usage** - Enter bioportal API key and ontology id (e.g. 1522 for BioPAX), and the ontology will be retrieved. + Enter bioportal API key and ontology id (e.g. 1522 for BioPAX), or select from list, and the ontology will be retrieved. **Contact**