Mercurial > repos > mikel-egana-aranguren > ncbo_services
changeset 27:e2b16720ef25 draft
Directories re-arranged for easier installation via mercurial
| author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Mon, 08 Oct 2012 14:25:04 +0200 |
| parents | 354aa87772e0 |
| children | ebf11126df7c |
| files | NCBO_services/README NCBO_services/extract.jar NCBO_services/extract.java NCBO_services/extract.xml NCBO_services/get_ontology.jar NCBO_services/get_ontology.java NCBO_services/get_ontology.xml NCBO_services/get_ontology_view.jar NCBO_services/get_ontology_view.java NCBO_services/get_ontology_view.xml NCBO_services/ncbo_annotator.xml NCBO_services/ncbo_annotator_galaxy.jar NCBO_services/ncbo_recommender.xml NCBO_services/ncbo_recommender_galaxy.jar NCBO_services/ncbo_resourceIndex.xml NCBO_services/ncbo_resourceIndex_galaxy.jar NCBO_services/ncbo_search.xml NCBO_services/ncbo_search_galaxy.jar README extract.jar extract.java extract.xml get_ontology.jar get_ontology.java get_ontology.xml get_ontology_view.jar get_ontology_view.java get_ontology_view.xml ncbo_annotator.xml ncbo_annotator_galaxy.jar ncbo_recommender.xml ncbo_recommender_galaxy.jar ncbo_resourceIndex.xml ncbo_resourceIndex_galaxy.jar ncbo_search.xml ncbo_search_galaxy.jar |
| diffstat | 36 files changed, 2311 insertions(+), 2311 deletions(-) [+] |
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--- a/NCBO_services/README Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - - - - ============= - NCBO Services - ============= - - - -INSTALLATION -============ - -1.- Stop Galaxy. - -2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/ - -3.- Create directory /galaxy-dist/tools/NCBO_services/ - -4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/ - -5.- Add the following lines to /galaxy-dist/tool_conf.xml: - - <section name="NCBO services" id="NCBO_services"> - <tool file="NCBO_services/get_ontology.xml"/> - <tool file="NCBO_services/extract.xml"/> - <tool file="NCBO_services/get_ontology_view.xml"/> - <tool file="NCBO_services/ncbo_annotator.xml"/> - <tool file="NCBO_services/ncbo_recommender.xml"/> - <tool file="NCBO_services/ncbo_search.xml"/> - <tool file="NCBO_services/ncbo_resourceIndex.xml"/> - </section> - -6.- Start Galaxy. - - - -USAGE -===== - -Each tool has a different functionality, but all of them need a -bioportal API key. The API key can be obtained by creating an account at -bioportal (http://bioportal.bioontology.org/). - - - -CONTACT -======= - -Please send any request or comment to mikel.egana.aranguren@gmail.com or -jose.minya@gmail.com. - - - -ACKNOWLEDGEMENTS -================ - -The work on get_ontology, extract and get_ontology_view is funded by the -Marie Curie Cofund program of the EU, FP7. - - - -COPYRIGHT AND LICENSE -===================== - -get_ontology, extract and get_ontology_view are copyright of Mikel -Egaña Aranguren (2012), and they are distributed under a GPL 3 license -(http://www.gnu.org/licenses/) - - - - - - - - - - - - - - -
--- a/NCBO_services/extract.java Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -package es.upm.fi.dia.oeg.ncbo.galaxy; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.OutputStreamWriter; - -import org.apache.http.HttpEntity; -import org.apache.http.HttpResponse; -import org.apache.http.client.ClientProtocolException; -import org.apache.http.client.HttpClient; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.impl.client.DefaultHttpClient; - -public class extract { - - /** - * @param args - * @throws IOException - * @throws ClientProtocolException - */ - public static void main(String[] args) throws ClientProtocolException, IOException { - -// http://www.bioontology.org/wiki/index.php/View_Extraction -// ./viewextractor/{ontology version id}[?{args}]&apikey={YourAPIKey} - - String api_key = args [0]; - String ontologyversionid = args [1]; // 35686 - String conceptid = args [2]; // E800-E999.9 - String filterrelations = args [3]; // PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass,[R]SIB,SI - String ontologyname = args [4]; // http://who.int/icd9 - - HttpClient client = new DefaultHttpClient(); - -// HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/35686/" + -// "?conceptid=E800-E999.9&filterrelations=PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass," + -// "[R]SIB,SIB&existontology=true&ontologyname=http://who.int/icd9&apikey=74c12fc6-9423-455a-a619-b94f47d1951b"); - - HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/" + ontologyversionid + - "/?conceptid="+ conceptid +"&filterrelations=" + filterrelations + - "&existontology=true&ontologyname="+ ontologyname + "&apikey=" + api_key); - - HttpResponse response = client.execute(get); - HttpEntity entity = response.getEntity(); - if (entity != null) { - InputStream instream = entity.getContent(); - InputStreamReader is=new InputStreamReader(instream); - BufferedReader br=new BufferedReader(is); - String read=br.readLine(); - BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out)); - while(read!=null){ -// System.out.println(read); - bw.write(read); - bw.newLine(); - read=br.readLine(); - } - bw.close(); - instream.close(); - } - - } - -}
--- a/NCBO_services/extract.xml Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -<tool id="extract" name="Extract a branch from an ontology" version="1.0.1"> - <description>Retrieves a subtree from an ontology using a root concept</description> - <command>java -jar ${__tool_data_path__}/shared/jars/extract.jar $api_key $ontologyversionid $conceptid $filterrelations $ontologyname > $output </command> - - <inputs> - <param name="api_key" type="text" size="100" label="BioPortal API key" /> - <param name="ontologyversionid" type="text" size="100" label="Ontology version ID" /> - <param name="conceptid" type="text" size="100" label="Concept id" /> - <param name="filterrelations" type="text" value="None" size="100" label="Filter relations" /> - <param name="ontologyname" type="text" size="100" label="Ontology name" /> - </inputs> - <outputs> - <data format="text" name="output" /> - </outputs> - <tests> - <test> - <param name="api_key"/> - </test> - </tests> - <help> - -**What it does** - -It extracts a subtree from an ontology contained in BioPortal, and retrieves such subtree as an OWL ontology. - -**Parameters** - -* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. -* Ontology version ID: it can be obtained from BioPortal, in the Ontology page, on the versions column, by looking at the version URL. For example, it is 46754 for the Gene Ontology. -* Concept ID: the root term. For example, GO:0051179. -* Filter relations: for example "is_a,part_of". -* Ontology name: the URI for the new ontology. For example http://go_redux_is_a.owl. - -**Contact** - -Please send any request or comment to mikel.egana.aranguren@gmail.com. - -**More information** - -http://bioportal.bioontology.org - -http://www.bioontology.org/wiki/index.php/BioPortal_REST_services - - </help> - -</tool>
--- a/NCBO_services/get_ontology.java Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -package es.upm.fi.dia.oeg.ncbo.galaxy; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.OutputStreamWriter; - -import org.apache.http.HttpEntity; -import org.apache.http.HttpResponse; -import org.apache.http.client.ClientProtocolException; -import org.apache.http.client.HttpClient; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.client.methods.HttpPost; -import org.apache.http.impl.client.DefaultHttpClient; - -public class get_ontology { - - /** - * @param args - * @throws IOException - * @throws ClientProtocolException - */ - public static void main(String[] args) throws ClientProtocolException, IOException { - String api_key = args [0]; - String ontology_id = args [1]; // 1522 - HttpClient client = new DefaultHttpClient(); - - HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/virtual/download/" + ontology_id + "?apikey=" +api_key); - HttpResponse response = client.execute(get); - HttpEntity entity = response.getEntity(); - if (entity != null) { - InputStream instream = entity.getContent(); - InputStreamReader is=new InputStreamReader(instream); - BufferedReader br=new BufferedReader(is); - String read=br.readLine(); - BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out)); - while(read!=null){ -// System.out.println(read); - bw.write(read); - bw.newLine(); - read=br.readLine(); - } - bw.close(); - instream.close(); - } - } -}
--- a/NCBO_services/get_ontology.xml Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,384 +0,0 @@ -<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> - #if $id_opts.id_opts_menu=="id_by_hand" #java -jar ${__tool_data_path__}/shared/jars/get_ontology.jar $api_key $id_opts.ontology_id > $output - #else #java -jar ${__tool_data_path__}/shared/jars/get_ontology.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="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"> - <!-- Automatically generated with http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey --> - <param name="ontology_id" type="select" multiple="false" label="Choose ontology from this list"> - <option value="1158">Cell Behavior Ontology</option> - <option value="1016">Drosophila development</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="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="1058">SNP-Ontology</option> - <option value="1099">African Traditional Medicine</option> - <option value="1134">BioTop</option> - <option value="1078">Spatial Ontology</option> - <option value="1247">GeoSpecies Ontology</option> - <option value="1007">Chemical entities of biological interest</option> - <option value="1024">Loggerhead nesting</option> - <option value="1257">MeGO</option> - <option value="1135">Pseudogene</option> - <option value="1049">C. elegans development</option> - <option value="1070">Gene Ontology</option> - <option value="1126">Family Health History Ontology</option> - <option value="1108">Plant Anatomy</option> - <option value="1114">Bilateria anatomy</option> - <option value="1100">Ontology for Genetic Interval</option> - <option value="1136">Experimental Factor Ontology</option> - <option value="1141">Ontology of Physics for Biology</option> - <option value="1044">Sample processing and separation techniques</option> - <option value="1347">MedlinePlus Health Topics</option> - <option value="1005">BRENDA tissue / enzyme source</option> - <option value="1152">Minimal anatomical terminology</option> - <option value="1063">Common Anatomy Reference Ontology</option> - <option value="1321">Neural ElectroMagnetic Ontologies</option> - <option value="1043">Physico-chemical process</option> - <option value="1064">Fly taxonomy</option> - <option value="1089">BIRNLex</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="1116">Bleeding History Phenotype</option> - <option value="1104">Biomedical Resource 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">Plant Trait Ontology</option> - <option value="1350">Logical Observation Identifier Names and Codes</option> - <option value="1082">Gene Regulation Ontology</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="1047">Cereal Plant Development</option> - <option value="1349">Physician Data Query</option> - <option value="1190">Ontology for Parasite LifeCycle</option> - <option value="1036">Plant environmental conditions</option> - <option value="1109">Sequence types and features</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="1304">Breast Cancer Grading Ontology</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="1022">Human developmental anatomy, timed version</option> - <option value="1014">Physico-chemical methods and properties</option> - <option value="1224">Symptom Ontology</option> - <option value="1095">Xenopus anatomy and development</option> - <option value="1042">OBO relationship types</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="1027">Medaka fish anatomy and development</option> - <option value="1354">WHO Adverse Reaction Terminology</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="1020">Habronattus courtship</option> - <option value="1148">BioPortal Metadata</option> - <option value="1038">Plant Growth and Development Stage</option> - <option value="1132">NCBI organismal classification</option> - <option value="1328">Ontology of homology and related concepts in biology</option> - <option value="1019">Fungal gross anatomy</option> - <option value="1290">ABA Adult Mouse Brain</option> - <option value="1067">C. elegans phenotype</option> - <option value="1069">Environment Ontology</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="1112">Units of measurement</option> - <option value="1369">PhysicalFields</option> - <option value="1086">Ontology for disease genetic investigation</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="1122">Skin Physiology Ontology</option> - <option value="1142">Cardiac Electrophysiology Ontology</option> - <option value="1128">Comparative Data Analysis Ontology</option> - <option value="1172">Vaccine Ontology</option> - <option value="1088">MaHCO - An MHC Ontology</option> - <option value="1245">Cell line ontology</option> - <option value="1222">Ascomycete phenotype ontology</option> - <option value="1249">Smoking Behavior Risk Ontology</option> - <option value="1039">Proteomics data and process provenance</option> - <option value="1105">Mass spectrometry</option> - <option value="1040">Protein-protein interaction</option> - <option value="1237">Situation-Based Access Control</option> - <option value="1008">Dictyostelium discoideum anatomy</option> - <option value="1068">Subcellular Anatomy Ontology (SAO)</option> - <option value="1087">Ontology of Geographical Region</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 ontology</option> - <option value="1094">Pathogen transmission</option> - <option value="1084">NIFSTD</option> - <option value="1025">Mammalian phenotype</option> - <option value="1131">MGED Ontology</option> - <option value="1035">Pathway ontology</option> - <option value="1106">Gene Regulation Ontology</option> - <option value="1054">Amino Acid</option> - <option value="1056">Basic Vertebrate Anatomy</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="1083">NanoParticle Ontology</option> - <option value="1053">Foundational Model of Anatomy</option> - <option value="1031">Mouse pathology</option> - <option value="1092">Infectious Disease Ontology</option> - <option value="1032">NCI Thesaurus</option> - <option value="1381">NIF Dysfunction</option> - <option value="1393">Information Artifact Ontology</option> - <option value="1394">Syndromic Surveillance 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="1401">International Classification for Nursing Practice</option> - <option value="1402">NIF Cell</option> - <option value="1404">Uber anatomy ontology</option> - <option value="1406">linkingkin2pep</option> - <option value="1407">Terminology for the Description of Dynamics</option> - <option value="1409">PKO_Re</option> - <option value="1410">Kinetic Simulation Algorithm Ontology</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="1415">Common Terminology Criteria for Adverse Events</option> - <option value="1417">Influenza Ontology</option> - <option value="1418">TOK_Ontology</option> - <option value="1419">Taxonomic rank vocabulary</option> - <option value="1422">MedDRA</option> - <option value="1423">RxNORM</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="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> - <option value="1428">Nursing Interventions Classification (NIC)</option> - <option value="1429">ICPC-2 PLUS</option> - <option value="1430">AI/RHEUM</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="1444">Chemical Information Ontology</option> - <option value="1343">Health Level Seven</option> - <option value="1461">Translational Medicine Ontology</option> - <option value="1484">International Classification of External Causes of Injuries</option> - <option value="1487">Body System</option> - <option value="1488">SysMO-JERM</option> - <option value="1489">Ontology of Adverse Events (OAE)</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="1498">Bioinformatics operations, types of data, data formats and topics</option> - <option value="1499">NCI Metathesaurus</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="1517">Human developmental anatomy, abstract version, v2</option> - <option value="1520">Leukocyte Surface Markers</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="1532">SemanticScience Integrated Ontology</option> - <option value="1533">BioAssay Ontology</option> - <option value="1534">apollo-akesios</option> - <option value="1535">Terminology of Anatomy of Human Histology</option> - <option value="1536">Terminology of Anatomy of Human Embryology</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="1544">Crop Ontology</option> - <option value="1545">Wheat trait </option> - <option value="1550">PHARE</option> - <option value="1552">Reproductive trait and phenotype ontology</option> - <option value="1553">ICD10CM</option> - <option value="1555">Vertebrate Anatomy Ontology</option> - <option value="1560">Cognitive Paradigm 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">CAO</option> - <option value="1583">Clinical Measurement Ontology</option> - <option value="1584">Measurement Method Ontology</option> - <option value="1585">Experimental Conditions Ontology</option> - <option value="1586">Orphanet Ontology of Rare Diseases</option> - <option value="1587">Plant Ontology</option> - <option value="1588">Ontology of General Purpose Datatypes</option> - <option value="1596">HOM_MDCs-DRGS</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> - <option value="1625">HOM-ICD9CM_PROCEDURES</option> - <option value="1626">Enzyme Mechanism Ontology</option> - <option value="1627">HOMERUN Ontology</option> - <option value="1629">HOM-UCARE</option> - <option value="1630">HOM-EPIC</option> - <option value="1631">HOM-HARVARD</option> - <option value="1632">Web-Service Interaction Ontology</option> - <option value="1633">Cognitive Atlas</option> - <option value="1638">Ontology of Data Mining</option> - <option value="1639">Epilepsy</option> - <option value="1640">Pediatric Terminology</option> - <option value="1641">HOM-ICD9CM-ECODES</option> - <option value="1642">HOM-DXPROCS_MDCDRG</option> - <option value="1643">HOM-ICD9_PROCS_OSHPD</option> - <option value="1645">HOM-MDCDRG_OSHPD</option> - <option value="1647">HOM-ICD9_DXandVCODES_OSHPD</option> - <option value="1648">HOM-DATASOURCE_OSHPD</option> - <option value="1649">HOM-OSHPD</option> - <option value="1650">Units Ontology</option> - <option value="1651">Sleep Domain Ontology</option> - <option value="1652">HOM-OSHPD_UseCase</option> - <option value="1653">HOM-PROCS2_OSHPD</option> - <option value="1654">HOM-DXVCODES2_OSHPD</option> - <option value="1655">PharmGKB-in-OWL</option> - <option value="1656">PhenomeBLAST ontology</option> - <option value="1657">Quadrupedal Gait</option> - <option value="1658">Hewan Invertebrata</option> - <option value="1659">Vertebrate Trait Ontology</option> - <option value="1660">HOM-DATASOURCE_EPIC</option> - <option value="1661">HOM-Transplant Ontology</option> - <option value="1665">Student Health Record</option> - <option value="1666">Emotion Ontology</option> - <option value="1667">HOM-DATASOURCE_OSHPDSC</option> - <option value="1668">HOM-OSHPD-SC</option> - <option value="1670">ICD_Oncology-3</option> - <option value="1671">Quantitative Imaging Biomarker Ontology</option> - <option value="1672">DIKB-Evidence-Ontology</option> - <option value="1675">CEEROntology</option> - <option value="1676">Randomized Controlled Trials (RCT) Ontology</option> - <option value="1679">JADNI test ontology2</option> - <option value="1680">BioActivity Ontology3</option> - <option value="1681">JADNI test ontology</option> - <option value="1682">Human disease in Bioactivity</option> - <option value="1683">BioActivity Ontology</option> - <option value="1684">BioActivity Ontology2</option> - <option value="1686">Neomark Oral Cancer Ontology</option> - <option value="1688">UniprotCoreBH</option> - <option value="1689">Fission Yeast Phenotype Ontology</option> - <option value="1691">yipd_test</option> - <option value="1692">test-purl</option> - <option value="1693">ICD9-ICD10-PCS (partial)</option> - <option value="1694">HOM-CPT</option> - <option value="1696">Synapse Ontology</option> - <option value="1697">HOM-ORTHO</option> - <option value="1698">HOM-DATASRC-ORTHO</option> - <option value="1699">VIVO</option> - <option value="1700">Test Pradip PURL</option> - <option value="1701">HOM-ORTHOSURGERY</option> - <option value="1702">Eurofut</option> - </param> - </when> - </conditional> - </inputs> - <outputs> - <data format="text" name="output" /> - </outputs> - <tests> - <test> - <param name="api_key"/> - <param name="id_opts.ontology_id"/> - </test> - </tests> - <help> - -**What it does** - -It retrieves an ontology from BioPortal. - -**Parameters** - -* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. -* Ontology ID: provide it by hand (e.g. 1522 for BioPAX), or select from list. - -**Contact** - -Please send any request or comment to mikel.egana.aranguren@gmail.com. - -**More information** - -http://bioportal.bioontology.org - -http://www.bioontology.org/wiki/index.php/BioPortal_REST_services - - - - </help> - -</tool>
--- a/NCBO_services/get_ontology_view.java Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -package es.upm.fi.dia.oeg.ncbo.galaxy; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.OutputStreamWriter; - -import org.apache.http.HttpEntity; -import org.apache.http.HttpResponse; -import org.apache.http.client.ClientProtocolException; -import org.apache.http.client.HttpClient; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.client.methods.HttpPost; -import org.apache.http.impl.client.DefaultHttpClient; - -public class get_ontology_view { - - /** - * @param args - * @throws IOException - * @throws ClientProtocolException - */ - public static void main(String[] args) throws ClientProtocolException, IOException { -// http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Download_a_specific_ontology_view_based_on_the_ontology_view_version_id -// Download a specific ontology view based on the ontology view version id - - String api_key = args [0]; - String ontology_view_id = args [1]; - - HttpClient client = new DefaultHttpClient(); -// http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey - HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/ontologies/download/" + ontology_view_id + "?apikey=" + api_key); - - HttpResponse response = client.execute(get); - HttpEntity entity = response.getEntity(); - if (entity != null) { - InputStream instream = entity.getContent(); - InputStreamReader is=new InputStreamReader(instream); - BufferedReader br=new BufferedReader(is); - String read=br.readLine(); - BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out)); - while(read!=null){ -// System.out.println(read); - bw.write(read); - bw.newLine(); - read=br.readLine(); - } - bw.close(); - instream.close(); - } - } -}
--- a/NCBO_services/get_ontology_view.xml Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -<tool id="get_ontology_view" name="Get a concrete view of an ontology" version="1.0.1"> - <description>Retrieves a view of an ontology using the view id</description> - <command>java -jar ${__tool_data_path__}/shared/jars/get_ontology_view.jar $api_key $ontologyviewid > $output </command> - - <inputs> - <param name="api_key" type="text" size="100" label="BioPortal API key" /> - <param name="ontologyviewid" type="text" size="100" label="Ontology view ID" /> - </inputs> - <outputs> - <data format="text" name="output" /> - </outputs> - <tests> - <test> - <param name="api_key"/> - </test> - </tests> - <help> - -**What it does** - -It retrieves a view from an ontology contained in BioPortal. - -**Parameters** - -* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. -* Ontology view ID: it can be obtained from BioPortal, in the Ontology page, on the views section, by looking at the view URL. For example, it is 41014 for the generic Gene Ontology slim. - -**Contact** - -Please send any request or comment to mikel.egana.aranguren@gmail.com. - -**More information** - -http://bioportal.bioontology.org - -http://www.bioontology.org/wiki/index.php/BioPortal_REST_services - - </help> - -</tool>
--- a/NCBO_services/ncbo_annotator.xml Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,704 +0,0 @@ -<tool id="ncbo_annotator" name="Annotates a text with bio-ontology terms" version="1.0.1"> - <description>Annotates biological texts with the terms of the bio-ontologies from BioPortal</description> - <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> - <inputs> - <param name="longestOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only the longest word"/> - <param name="wholeWordOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only whole words"/> - <param name="filterNumber" type="boolean" value="true" label="Tick the box if the Annotator should filter numbers before annotating the text"/> - <param name="stopWords" type="text" value="" size="100" label="List the words that the Annotator should omit from the text"/> - <param name="withDefaultStopWords" type="boolean" value="true" label="Tick the box if the Annotator should use the default list of stop words"/> - <param name="isTopWordsCaseSensitive" type="boolean" value="false" label="Tick the box whether the stop words are case sensitive or not"/> - <param name="mintermSize" type="integer" value="3" min="0" max="100" label="Indicates the minimum length for the terms to annotate"/> - <param name="scored" type="boolean" value="true" label="Tick the box whether the Annotator should assign a numeric accuracy to each annotation or not"/> - <param name="withSynonyms" type="boolean" value="true" label="Tick the box if the Annotator should use synonyms in the direct annotation"/> - <param name="ontologiesToExpand" type="select" multiple="true" label="Indicates the list of ontologies to use with the mapping semantic expansion component"> - <option value="e-all" selected="true">ALL</option> - <option value="e-1394">Syndromic Surveillance Ontology</option> - <option value="e-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> - <option value="e-1158">Cell Behavior Ontology</option> - <option value="e-1033">NMR-instrument specific component of metabolomics investigations</option> - <option value="e-1351">Medical Subject Headings</option> - <option value="e-1146">Electrocardiography Ontology</option> - <option value="e-1041">Protein modification</option> - <option value="e-1058">SNP-Ontology</option> - <option value="e-1099">African Traditional Medicine</option> - <option value="e-1134">BioTop</option> - <option value="e-1247">GeoSpecies Ontology</option> - <option value="e-1024">Loggerhead nesting</option> - <option value="e-1257">MeGO</option> - <option value="e-1135">Pseudogene</option> - <option value="e-1126">Family Health History Ontology</option> - <option value="e-1108">Plant structure</option> - <option value="e-1114">Bilateria anatomy</option> - <option value="e-1100">Ontology for Genetic Interval</option> - <option value="e-1044">Sample processing and separation techniques</option> - <option value="e-1347">MedlinePlus Health Topics</option> - <option value="e-1152">Minimal anatomical terminology</option> - <option value="e-1063">Common Anatomy Reference Ontology</option> - <option value="e-1089">BIRNLex</option> - <option value="e-1116">Bleeding History Phenotype</option> - <option value="e-1104">Biomedical Resource Ontology</option> - <option value="e-1350">Logical Observation Identifier Names and Codes</option> - <option value="e-1082">Gene Regulation Ontology</option> - <option value="e-1047">Cereal plant development</option> - <option value="e-1349">Physician Data Query</option> - <option value="e-1190">Parasite Life Cycle</option> - <option value="e-1192">Proteomics Pipeline Infrastructure for CPTAC</option> - <option value="e-1352">National Drug File</option> - <option value="e-1059">Computer-based Patient Record Ontology</option> - <option value="e-1052">Protein Ontology</option> - <option value="e-1341">COSTART</option> - <option value="e-1344">International Classification of Primary Care</option> - <option value="e-1061">Suggested Ontology for Pharmacogenomics</option> - <option value="e-1353">SNOMED Clinical Terms</option> - <option value="e-1224">Symptom Ontology</option> - <option value="e-1013">eVOC (Expressed Sequence Annotation for Humans)</option> - <option value="e-1149">DermLex: The Dermatology Lexicon</option> - <option value="e-1311">Malaria Ontology</option> - <option value="e-1335">Parasite Experiment Ontology</option> - <option value="e-1370">Amphibian taxonomy</option> - <option value="e-1354">WHO Adverse Reaction Terminology</option> - <option value="e-1148">BioPortal Metadata</option> - <option value="e-1038">Plant growth and developmental stage</option> - <option value="e-1132">NCBI organismal classification</option> - <option value="e-1328">Ontology of homology and related concepts in biology</option> - <option value="e-1290">ABA Adult Mouse Brain</option> - <option value="e-1055">Galen</option> - <option value="e-1332">Basic Formal Ontology</option> - <option value="e-1183">Lipid Ontology</option> - <option value="e-1026">Multiple alignment</option> - <option value="e-1130">Cancer Research and Management ACGT Master Ontology</option> - <option value="e-1060">Epoch Clinical Trial Ontologies</option> - <option value="e-1369">PhysicalFields</option> - <option value="e-1086">Ontology for disease genetic investigation</option> - <option value="e-1122">Skin Physiology Ontology</option> - <option value="e-1142">Cardiac Electrophysiology Ontology</option> - <option value="e-1128">Comparative Data Analysis Ontology</option> - <option value="e-1088">MaHCO - An MHC Ontology</option> - <option value="e-1249">Smoking Behavior Risk Ontology</option> - <option value="e-1039">Proteomics data and process provenance</option> - <option value="e-1040">Protein-protein interaction</option> - <option value="e-1068">Subcellular Anatomy Ontology (SAO)</option> - <option value="e-1087">Ontology of Geographical Region</option> - <option value="e-1094">Pathogen transmission</option> - <option value="e-1131">MGED Ontology</option> - <option value="e-1106">Gene Regulation Ontology</option> - <option value="e-1054">Amino Acid</option> - <option value="e-1056">Basic Vertebrate Anatomy</option> - <option value="e-1083">NanoParticle Ontology</option> - <option value="e-1053">Foundational Model of Anatomy</option> - <option value="e-1092">Infectious disease</option> - <option value="e-1393">Information Artifact Ontology</option> - <option value="e-1395">MDSS Mo</option> - <option value="e-1397">Gazetteer</option> - <option value="e-1398">Ontology of Language Disorder in Autism</option> - <option value="e-1399">Pilot Ontology</option> - <option value="e-1406">linkingkin2pep</option> - <option value="e-1409">PKO_Re</option> - <option value="e-1410">Kinetic Simulation Algorithm Ontology</option> - <option value="e-1415">Common Terminology Criteria for Adverse Events</option> - <option value="e-1418">TOK_Ontology</option> - <option value="e-1419">Taxonomic rank vocabulary</option> - <option value="e-1422">MedDRA</option> - <option value="e-1424">National Drug Data File</option> - <option value="e-1425">ICD-10-PCS</option> - <option value="e-1426">Master Drug Data Base</option> - <option value="e-1429">ICPC-2 PLUS</option> - <option value="e-1430">AIR</option> - <option value="e-1438">Breast tissue cell lines</option> - <option value="e-1439">General Formal Ontology</option> - <option value="e-1440">General Formal Ontology: Biology</option> - <option value="e-1343">Health Level Seven</option> - <option value="e-1484">International Classification of External Causes of Injuries</option> - <option value="e-1487">Body System</option> - <option value="e-1490">Platynereis stage ontology</option> - <option value="e-1491">IMGT-ONTOLOGY</option> - <option value="e-1494">Tissue Microarray Ontology</option> - <option value="e-1497">PMA 2010</option> - <option value="e-1500">RNA ontology</option> - <option value="e-1501">Neomark Oral Cancer-Centred Ontology</option> - <option value="e-1504">Current Procedural Terminology</option> - <option value="e-1505">Ontology for MicroRNA Target Prediction</option> - <option value="e-1506">Gene Ontology Extension</option> - <option value="e-1507">Cell Cycle Ontology</option> - <option value="e-1509">ICPS Network</option> - <option value="e-1510">Metathesaurus CPT Hierarchical Terms</option> - <option value="e-1515">Interaction Network Ontology</option> - <option value="e-1516">ICD10</option> - <option value="e-1521">Neural Motor Recovery Ontology</option> - <option value="e-1522">BioPAX</option> - <option value="e-1523">OBOE SBC</option> - <option value="e-1524">OBOE</option> - <option value="e-1526">CRISP Thesaurus, 2006</option> - <option value="e-1527">VANDF</option> - <option value="e-1528">HUGO</option> - <option value="e-1529">HCPCS</option> - <option value="e-1530">Animal natural history and life history</option> - <option value="e-1534">apollo-akesios</option> - <option value="e-1537">Brucellosis Ontology</option> - <option value="e-1538">Role Ontology</option> - <option value="e-1539">Neural-Immune Gene Ontology</option> - <option value="e-1540">Ontology for Drug Discovery Investigations</option> - <option value="e-1541">Cell line ontology</option> - <option value="e-1545">Wheat trait </option> - <option value="e-1547">BRENDA tissue / enzyme source</option> - <option value="e-1552">Reproductive traits ontology</option> - <option value="e-1553">ICD10CM</option> - <option value="e-1560">Cognitive Paradigm Ontology</option> - <option value="e-1423">RxNORM</option> - <option value="e-1517">Human developmental anatomy, abstract version, v2</option> - <option value="e-1016">Drosophila development</option> - <option value="e-1062">PRotein Ontology (PRO)</option> - <option value="e-1000">Mouse adult gross anatomy</option> - <option value="e-1065">Tick gross anatomy</option> - <option value="e-1123">Ontology for Biomedical Investigations</option> - <option value="e-1078">Spatial Ontology</option> - <option value="e-1007">Chemical entities of biological interest</option> - <option value="e-1049">C. elegans development</option> - <option value="e-1070">Gene Ontology</option> - <option value="e-1136">Experimental Factor Ontology</option> - <option value="e-1141">Ontology of Physics for Biology</option> - <option value="e-1005">BRENDA tissue / enzyme source</option> - <option value="e-1321">Neural ElectroMagnetic Ontologies</option> - <option value="e-1043">Physico-chemical process</option> - <option value="e-1064">Fly taxonomy</option> - <option value="e-1076">Ontology of Clinical Research (OCRe)</option> - <option value="e-1110">Teleost Anatomy Ontology</option> - <option value="e-1362">Hymenoptera Anatomy Ontology</option> - <option value="e-1030">Mosquito gross anatomy</option> - <option value="e-1029">Molecule role (INOH Protein name/family name ontology)</option> - <option value="e-1144">Dendritic cell</option> - <option value="e-1125">Human Phenotype Ontology</option> - <option value="e-1023">Biological imaging methods</option> - <option value="e-1021">Human developmental anatomy, abstract version</option> - <option value="e-1046">Systems Biology</option> - <option value="e-1051">Zebrafish anatomy and development</option> - <option value="e-1037">Cereal plant trait</option> - <option value="e-1107">Phenotypic quality</option> - <option value="e-1081">Teleost taxonomy</option> - <option value="e-1048">C. elegans gross anatomy</option> - <option value="e-1050">Maize gross anatomy</option> - <option value="e-1036">Plant environmental conditions</option> - <option value="e-1109">Sequence types and features</option> - <option value="e-1022">Human developmental anatomy, timed version</option> - <option value="e-1095">Xenopus anatomy and development</option> - <option value="e-1027">Medaka fish anatomy and development</option> - <option value="e-1011">Event (INOH pathway ontology)</option> - <option value="e-1010">Mouse gross anatomy and development</option> - <option value="e-1015">Drosophila gross anatomy</option> - <option value="e-1090">Amphibian gross anatomy</option> - <option value="e-1019">Fungal gross anatomy</option> - <option value="e-1067">C. elegans phenotype</option> - <option value="e-1069">Environment Ontology</option> - <option value="e-1112">Units of measurement</option> - <option value="e-1091">Spider Ontology</option> - <option value="e-1017">FlyBase Controlled Vocabulary</option> - <option value="e-1348">Online Mendelian Inheritance in Man</option> - <option value="e-1172">Vaccine Ontology</option> - <option value="e-1222">Ascomycete phenotype ontology</option> - <option value="e-1105">Mass spectrometry</option> - <option value="e-1237">Situation-Based Access Control</option> - <option value="e-1008">Dictyostelium discoideum anatomy</option> - <option value="e-1150">Rat Strain Ontology</option> - <option value="e-1101">International Classification of Diseases</option> - <option value="e-1314">Cell Line Ontology</option> - <option value="e-1009">Human disease</option> - <option value="e-1084">NIFSTD</option> - <option value="e-1025">Mammalian phenotype</option> - <option value="e-1035">Pathway ontology</option> - <option value="e-1012">Evidence codes</option> - <option value="e-1115">Yeast phenotypes</option> - <option value="e-1001">Cereal plant gross anatomy</option> - <option value="e-1006">Cell type</option> - <option value="e-1077">Mosquito insecticide resistance</option> - <option value="e-1085">Ontology of Glucose Metabolism Disorder</option> - <option value="e-1057">RadLex</option> - <option value="e-1031">Mouse pathology</option> - <option value="e-1032">NCI Thesaurus</option> - <option value="e-1381">NIF Dysfunction</option> - <option value="e-1401">International Classification for Nursing Practice</option> - <option value="e-1402">NIF Cell</option> - <option value="e-1404">Uber anatomy ontology</option> - <option value="e-1407">Terminology for the Description of Dynamics</option> - <option value="e-1411">International Classification of Functioning, Disability and Health (ICF)</option> - <option value="e-1413">Software Ontology</option> - <option value="e-1414">Ontology for General Medical Science</option> - <option value="e-1444">Chemical Information Ontology</option> - <option value="e-1461">Translational Medicine Ontology</option> - <option value="e-1488">SysMO-JERM</option> - <option value="e-1489">Adverse Event Ontology</option> - <option value="e-1498">EDAM</option> - <option value="e-1532">SemanticScience Integrated Ontology</option> - <option value="e-1550">PHARE</option> - <option value="e-1555">Vertebrate Anatomy Ontology</option> - <option value="e-1565">Ontology of Medically Related Social Entities</option> - <option value="e-1567">Pharmacovigilance Ontology</option> - <option value="e-1568">Anatomical Entity Ontology</option> - <option value="e-1569">Host Pathogen Interactions Ontology</option> - <option value="e-1570">Traditional Medicine Constitution Value Set</option> - <option value="e-1571">Traditional Medicine Other Factors Value Set</option> - <option value="e-1572">Traditional Medicine Signs and Symptoms Value Set</option> - <option value="e-1573">Traditional Medicine Meridian Value Sets</option> - <option value="e-1574">vertebrate Homologous Organ Groups</option> - <option value="e-1575">ExO</option> - <option value="e-1576">FDA Medical Devices (2010)</option> - <option value="e-1578">HOM_ElixhauserScores</option> - <option value="e-1580">Adverse Event Reporting ontology</option> - <option value="e-1581">HEALTH_INDICATORS</option> - <option value="e-1582">COA</option> - <option value="e-1583">Clinical Measurement Ontology</option> - <option value="e-1584">Measurement Method Ontology</option> - <option value="e-1585">Experimental Conditions Ontology</option> - <option value="e-1587">Plant Ontology</option> - <option value="e-1588">Ontology of General Purpose Datatypes</option> - <option value="e-1596">MajDxCatgrs-DxRltdGrps</option> - <option value="e-1613">Bone Dysplasia Ontology</option> - <option value="e-1614">IxnO</option> - <option value="e-1615">Systems Chemical Biology/Chemogenomics </option> - <option value="e-1616">Phylogenetic Ontology</option> - <option value="e-1621">Neuro Behavior Ontology</option> - </param> - <param name="ontologiesToKeepInResult" type="select" multiple="true" label="Indicates the list of ontologies to keep in the result of the annotation process"> - <option value="k-all" selected="true">ALL</option> - <option value="k-1394">Syndromic Surveillance Ontology</option> - <option value="k-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> - <option value="k-1158">Cell Behavior Ontology</option> - <option value="k-1033">NMR-instrument specific component of metabolomics investigations</option> - <option value="k-1351">Medical Subject Headings</option> - <option value="k-1146">Electrocardiography Ontology</option> - <option value="k-1041">Protein modification</option> - <option value="k-1058">SNP-Ontology</option> - <option value="k-1099">African Traditional Medicine</option> - <option value="k-1134">BioTop</option> - <option value="k-1247">GeoSpecies Ontology</option> - <option value="k-1024">Loggerhead nesting</option> - <option value="k-1257">MeGO</option> - <option value="k-1135">Pseudogene</option> - <option value="k-1126">Family Health History Ontology</option> - <option value="k-1108">Plant structure</option> - <option value="k-1114">Bilateria anatomy</option> - <option value="k-1100">Ontology for Genetic Interval</option> - <option value="k-1044">Sample processing and separation techniques</option> - <option value="k-1347">MedlinePlus Health Topics</option> - <option value="k-1152">Minimal anatomical terminology</option> - <option value="k-1063">Common Anatomy Reference Ontology</option> - <option value="k-1089">BIRNLex</option> - <option value="k-1116">Bleeding History Phenotype</option> - <option value="k-1104">Biomedical Resource Ontology</option> - <option value="k-1350">Logical Observation Identifier Names and Codes</option> - <option value="k-1082">Gene Regulation Ontology</option> - <option value="k-1047">Cereal plant development</option> - <option value="k-1349">Physician Data Query</option> - <option value="k-1190">Parasite Life Cycle</option> - <option value="k-1192">Proteomics Pipeline Infrastructure for CPTAC</option> - <option value="k-1352">National Drug File</option> - <option value="k-1059">Computer-based Patient Record Ontology</option> - <option value="k-1052">Protein Ontology</option> - <option value="k-1341">COSTART</option> - <option value="k-1344">International Classification of Primary Care</option> - <option value="k-1061">Suggested Ontology for Pharmacogenomics</option> - <option value="k-1353">SNOMED Clinical Terms</option> - <option value="k-1224">Symptom Ontology</option> - <option value="k-1013">eVOC (Expressed Sequence Annotation for Humans)</option> - <option value="k-1149">DermLex: The Dermatology Lexicon</option> - <option value="k-1311">Malaria Ontology</option> - <option value="k-1335">Parasite Experiment Ontology</option> - <option value="k-1370">Amphibian taxonomy</option> - <option value="k-1354">WHO Adverse Reaction Terminology</option> - <option value="k-1148">BioPortal Metadata</option> - <option value="k-1038">Plant growth and developmental stage</option> - <option value="k-1132">NCBI organismal classification</option> - <option value="k-1328">Ontology of homology and related concepts in biology</option> - <option value="k-1290">ABA Adult Mouse Brain</option> - <option value="k-1055">Galen</option> - <option value="k-1332">Basic Formal Ontology</option> - <option value="k-1183">Lipid Ontology</option> - <option value="k-1026">Multiple alignment</option> - <option value="k-1130">Cancer Research and Management ACGT Master Ontology</option> - <option value="k-1060">Epoch Clinical Trial Ontologies</option> - <option value="k-1369">PhysicalFields</option> - <option value="k-1086">Ontology for disease genetic investigation</option> - <option value="k-1122">Skin Physiology Ontology</option> - <option value="k-1142">Cardiac Electrophysiology Ontology</option> - <option value="k-1128">Comparative Data Analysis Ontology</option> - <option value="k-1088">MaHCO - An MHC Ontology</option> - <option value="k-1249">Smoking Behavior Risk Ontology</option> - <option value="k-1039">Proteomics data and process provenance</option> - <option value="k-1040">Protein-protein interaction</option> - <option value="k-1068">Subcellular Anatomy Ontology (SAO)</option> - <option value="k-1087">Ontology of Geographical Region</option> - <option value="k-1094">Pathogen transmission</option> - <option value="k-1131">MGED Ontology</option> - <option value="k-1106">Gene Regulation Ontology</option> - <option value="k-1054">Amino Acid</option> - <option value="k-1056">Basic Vertebrate Anatomy</option> - <option value="k-1083">NanoParticle Ontology</option> - <option value="k-1053">Foundational Model of Anatomy</option> - <option value="k-1092">Infectious disease</option> - <option value="k-1393">Information Artifact Ontology</option> - <option value="k-1395">MDSS Mo</option> - <option value="k-1397">Gazetteer</option> - <option value="k-1398">Ontology of Language Disorder in Autism</option> - <option value="k-1399">Pilot Ontology</option> - <option value="k-1406">linkingkin2pep</option> - <option value="k-1409">PKO_Re</option> - <option value="k-1410">Kinetic Simulation Algorithm Ontology</option> - <option value="k-1415">Common Terminology Criteria for Adverse Events</option> - <option value="k-1418">TOK_Ontology</option> - <option value="k-1419">Taxonomic rank vocabulary</option> - <option value="k-1422">MedDRA</option> - <option value="k-1424">National Drug Data File</option> - <option value="k-1425">ICD-10-PCS</option> - <option value="k-1426">Master Drug Data Base</option> - <option value="k-1429">ICPC-2 PLUS</option> - <option value="k-1430">AIR</option> - <option value="k-1438">Breast tissue cell lines</option> - <option value="k-1439">General Formal Ontology</option> - <option value="k-1440">General Formal Ontology: Biology</option> - <option value="k-1343">Health Level Seven</option> - <option value="k-1484">International Classification of External Causes of Injuries</option> - <option value="k-1487">Body System</option> - <option value="k-1490">Platynereis stage ontology</option> - <option value="k-1491">IMGT-ONTOLOGY</option> - <option value="k-1494">Tissue Microarray Ontology</option> - <option value="k-1497">PMA 2010</option> - <option value="k-1500">RNA ontology</option> - <option value="k-1501">Neomark Oral Cancer-Centred Ontology</option> - <option value="k-1504">Current Procedural Terminology</option> - <option value="k-1505">Ontology for MicroRNA Target Prediction</option> - <option value="k-1506">Gene Ontology Extension</option> - <option value="k-1507">Cell Cycle Ontology</option> - <option value="k-1509">ICPS Network</option> - <option value="k-1510">Metathesaurus CPT Hierarchical Terms</option> - <option value="k-1515">Interaction Network Ontology</option> - <option value="k-1516">ICD10</option> - <option value="k-1521">Neural Motor Recovery Ontology</option> - <option value="k-1522">BioPAX</option> - <option value="k-1523">OBOE SBC</option> - <option value="k-1524">OBOE</option> - <option value="k-1526">CRISP Thesaurus, 2006</option> - <option value="k-1527">VANDF</option> - <option value="k-1528">HUGO</option> - <option value="k-1529">HCPCS</option> - <option value="k-1530">Animal natural history and life history</option> - <option value="k-1534">apollo-akesios</option> - <option value="k-1537">Brucellosis Ontology</option> - <option value="k-1538">Role Ontology</option> - <option value="k-1539">Neural-Immune Gene Ontology</option> - <option value="k-1540">Ontology for Drug Discovery Investigations</option> - <option value="k-1541">Cell line ontology</option> - <option value="k-1545">Wheat trait </option> - <option value="k-1547">BRENDA tissue / enzyme source</option> - <option value="k-1552">Reproductive traits ontology</option> - <option value="k-1553">ICD10CM</option> - <option value="k-1560">Cognitive Paradigm Ontology</option> - <option value="k-1423">RxNORM</option> - <option value="k-1517">Human developmental anatomy, abstract version, v2</option> - <option value="k-1016">Drosophila development</option> - <option value="k-1062">PRotein Ontology (PRO)</option> - <option value="k-1000">Mouse adult gross anatomy</option> - <option value="k-1065">Tick gross anatomy</option> - <option value="k-1123">Ontology for Biomedical Investigations</option> - <option value="k-1078">Spatial Ontology</option> - <option value="k-1007">Chemical entities of biological interest</option> - <option value="k-1049">C. elegans development</option> - <option value="k-1070">Gene Ontology</option> - <option value="k-1136">Experimental Factor Ontology</option> - <option value="k-1141">Ontology of Physics for Biology</option> - <option value="k-1005">BRENDA tissue / enzyme source</option> - <option value="k-1321">Neural ElectroMagnetic Ontologies</option> - <option value="k-1043">Physico-chemical process</option> - <option value="k-1064">Fly taxonomy</option> - <option value="k-1076">Ontology of Clinical Research (OCRe)</option> - <option value="k-1110">Teleost Anatomy Ontology</option> - <option value="k-1362">Hymenoptera Anatomy Ontology</option> - <option value="k-1030">Mosquito gross anatomy</option> - <option value="k-1029">Molecule role (INOH Protein name/family name ontology)</option> - <option value="k-1144">Dendritic cell</option> - <option value="k-1125">Human Phenotype Ontology</option> - <option value="k-1023">Biological imaging methods</option> - <option value="k-1021">Human developmental anatomy, abstract version</option> - <option value="k-1046">Systems Biology</option> - <option value="k-1051">Zebrafish anatomy and development</option> - <option value="k-1037">Cereal plant trait</option> - <option value="k-1107">Phenotypic quality</option> - <option value="k-1081">Teleost taxonomy</option> - <option value="k-1048">C. elegans gross anatomy</option> - <option value="k-1050">Maize gross anatomy</option> - <option value="k-1036">Plant environmental conditions</option> - <option value="k-1109">Sequence types and features</option> - <option value="k-1022">Human developmental anatomy, timed version</option> - <option value="k-1095">Xenopus anatomy and development</option> - <option value="k-1027">Medaka fish anatomy and development</option> - <option value="k-1011">Event (INOH pathway ontology)</option> - <option value="k-1010">Mouse gross anatomy and development</option> - <option value="k-1015">Drosophila gross anatomy</option> - <option value="k-1090">Amphibian gross anatomy</option> - <option value="k-1019">Fungal gross anatomy</option> - <option value="k-1067">C. elegans phenotype</option> - <option value="k-1069">Environment Ontology</option> - <option value="k-1112">Units of measurement</option> - <option value="k-1091">Spider Ontology</option> - <option value="k-1017">FlyBase Controlled Vocabulary</option> - <option value="k-1348">Online Mendelian Inheritance in Man</option> - <option value="k-1172">Vaccine Ontology</option> - <option value="k-1222">Ascomycete phenotype ontology</option> - <option value="k-1105">Mass spectrometry</option> - <option value="k-1237">Situation-Based Access Control</option> - <option value="k-1008">Dictyostelium discoideum anatomy</option> - <option value="k-1150">Rat Strain Ontology</option> - <option value="k-1101">International Classification of Diseases</option> - <option value="k-1314">Cell Line Ontology</option> - <option value="k-1009">Human disease</option> - <option value="k-1084">NIFSTD</option> - <option value="k-1025">Mammalian phenotype</option> - <option value="k-1035">Pathway ontology</option> - <option value="k-1012">Evidence codes</option> - <option value="k-1115">Yeast phenotypes</option> - <option value="k-1001">Cereal plant gross anatomy</option> - <option value="k-1006">Cell type</option> - <option value="k-1077">Mosquito insecticide resistance</option> - <option value="k-1085">Ontology of Glucose Metabolism Disorder</option> - <option value="k-1057">RadLex</option> - <option value="k-1031">Mouse pathology</option> - <option value="k-1032">NCI Thesaurus</option> - <option value="k-1381">NIF Dysfunction</option> - <option value="k-1401">International Classification for Nursing Practice</option> - <option value="k-1402">NIF Cell</option> - <option value="k-1404">Uber anatomy ontology</option> - <option value="k-1407">Terminology for the Description of Dynamics</option> - <option value="k-1411">International Classification of Functioning, Disability and Health (ICF)</option> - <option value="k-1413">Software Ontology</option> - <option value="k-1414">Ontology for General Medical Science</option> - <option value="k-1444">Chemical Information Ontology</option> - <option value="k-1461">Translational Medicine Ontology</option> - <option value="k-1488">SysMO-JERM</option> - <option value="k-1489">Adverse Event Ontology</option> - <option value="k-1498">EDAM</option> - <option value="k-1532">SemanticScience Integrated Ontology</option> - <option value="k-1550">PHARE</option> - <option value="k-1555">Vertebrate Anatomy Ontology</option> - <option value="k-1565">Ontology of Medically Related Social Entities</option> - <option value="k-1567">Pharmacovigilance Ontology</option> - <option value="k-1568">Anatomical Entity Ontology</option> - <option value="k-1569">Host Pathogen Interactions Ontology</option> - <option value="k-1570">Traditional Medicine Constitution Value Set</option> - <option value="k-1571">Traditional Medicine Other Factors Value Set</option> - <option value="k-1572">Traditional Medicine Signs and Symptoms Value Set</option> - <option value="k-1573">Traditional Medicine Meridian Value Sets</option> - <option value="k-1574">vertebrate Homologous Organ Groups</option> - <option value="k-1575">ExO</option> - <option value="k-1576">FDA Medical Devices (2010)</option> - <option value="k-1578">HOM_ElixhauserScores</option> - <option value="k-1580">Adverse Event Reporting ontology</option> - <option value="k-1581">HEALTH_INDICATORS</option> - <option value="k-1582">COA</option> - <option value="k-1583">Clinical Measurement Ontology</option> - <option value="k-1584">Measurement Method Ontology</option> - <option value="k-1585">Experimental Conditions Ontology</option> - <option value="k-1587">Plant Ontology</option> - <option value="k-1588">Ontology of General Purpose Datatypes</option> - <option value="k-1596">MajDxCatgrs-DxRltdGrps</option> - <option value="k-1613">Bone Dysplasia Ontology</option> - <option value="k-1614">IxnO</option> - <option value="k-1615">Systems Chemical Biology/Chemogenomics </option> - <option value="k-1616">Phylogenetic Ontology</option> - <option value="k-1621">Neuro Behavior Ontology</option> - </param> - <param name="semanticTypes" type="select" multiple="true" label="Indicates the list of semantic types to use in the annotation process"> - <option value="T-all" selected="true">ALL</option> - <option value="T000">UMLS concept</option> - <option value="T998">Jax Mouse/Human Gene dictionary concept</option> - <option value="T999">NCBO BioPortal concept</option> - <option value="T116">Amino Acid, Peptide, or Protein</option> - <option value="T121">Pharmacologic Substance</option> - <option value="T130">Indicator, Reagent, or Diagnostic Aid</option> - <option value="T119">Lipid</option> - <option value="T126">Enzyme</option> - <option value="T123">Biologically Active Substance</option> - <option value="T109">Organic Chemical</option> - <option value="T131">Hazardous or Poisonous Substance</option> - <option value="T110">Steroid</option> - <option value="T125">Hormone</option> - <option value="T114">Nucleic Acid, Nucleoside, or Nucleotide</option> - <option value="T111">Eicosanoid</option> - <option value="T118">Carbohydrate</option> - <option value="T124">Neuroreactive Substance or Biogenic Amine</option> - <option value="T127">Vitamin</option> - <option value="T195">Antibiotic</option> - <option value="T129">Immunologic Factor</option> - <option value="T024">Tissue</option> - <option value="T115">Organophosphorus Compound</option> - <option value="T073">Manufactured Object</option> - <option value="T081">Quantitative Concept</option> - <option value="T170">Intellectual Product</option> - <option value="T029">Body Location or Region</option> - <option value="T184">Sign or Symptom</option> - <option value="T033">Finding</option> - <option value="T037">Injury or Poisoning</option> - <option value="T191">Neoplastic Process</option> - <option value="T023">Body Part, Organ, or Organ Component</option> - <option value="T005">Virus</option> - <option value="T047">Disease or Syndrome</option> - <option value="T019">Congenital Abnormality</option> - <option value="T169">Functional Concept</option> - <option value="T190">Anatomical Abnormality</option> - <option value="T022">Body System</option> - <option value="T018">Embryonic Structure</option> - <option value="T101">Patient or Disabled Group</option> - <option value="T093">Health Care Related Organization</option> - <option value="T089">Regulation or Law</option> - <option value="T061">Therapeutic or Preventive Procedure</option> - <option value="T062">Research Activity</option> - <option value="T046">Pathologic Function</option> - <option value="T041">Mental Process</option> - <option value="T055">Individual Behavior</option> - <option value="T004">Fungus</option> - <option value="T060">Diagnostic Procedure</option> - <option value="T070">Natural Phenomenon or Process</option> - <option value="T197">Inorganic Chemical</option> - <option value="T057">Occupational Activity</option> - <option value="T083">Geographic Area</option> - <option value="T074">Medical Device</option> - <option value="T002">Plant</option> - <option value="T065">Educational Activity</option> - <option value="T092">Organization</option> - <option value="T009">Invertebrate</option> - <option value="T025">Cell</option> - <option value="T196">Element, Ion, or Isotope</option> - <option value="T067">Phenomenon or Process</option> - <option value="T080">Qualitative Concept</option> - <option value="T102">Group Attribute</option> - <option value="T098">Population Group</option> - <option value="T040">Organism Function</option> - <option value="T034">Laboratory or Test Result</option> - <option value="T201">Clinical Attribute</option> - <option value="T097">Professional or Occupational Group</option> - <option value="T064">Governmental or Regulatory Activity</option> - <option value="T054">Social Behavior</option> - <option value="T003">Alga</option> - <option value="T007">Bacterium</option> - <option value="T044">Molecular Function</option> - <option value="T053">Behavior</option> - <option value="T069">Environmental Effect of Humans</option> - <option value="T042">Organ or Tissue Function</option> - <option value="T103">Chemical</option> - <option value="T122">Biomedical or Dental Material</option> - <option value="T015">Mammal</option> - <option value="T020">Acquired Abnormality</option> - <option value="T030">Body Space or Junction</option> - <option value="T026">Cell Component</option> - <option value="T043">Cell Function</option> - <option value="T059">Laboratory Procedure</option> - <option value="T052">Activity</option> - <option value="T056">Daily or Recreational Activity</option> - <option value="T079">Temporal Concept</option> - <option value="T091">Biomedical Occupation or Discipline</option> - <option value="T192">Receptor</option> - <option value="T031">Body Substance</option> - <option value="T048">Mental or Behavioral Dysfunction</option> - <option value="T058">Health Care Activity</option> - <option value="T120">Chemical Viewed Functionally</option> - <option value="T100">Age Group</option> - <option value="T104">Chemical Viewed Structurally</option> - <option value="T171">Language</option> - <option value="T032">Organism Attribute</option> - <option value="T095">Self-help or Relief Organization</option> - <option value="T078">Idea or Concept</option> - <option value="T090">Occupation or Discipline</option> - <option value="T167">Substance</option> - <option value="T068">Human-caused Phenomenon or Process</option> - <option value="T168">Food</option> - <option value="T028">Gene or Genome</option> - <option value="T014">Reptile</option> - <option value="T050">Experimental Model of Disease</option> - <option value="T045">Genetic Function</option> - <option value="T011">Amphibian</option> - <option value="T013">Fish</option> - <option value="T094">Professional Society</option> - <option value="T087">Amino Acid Sequence</option> - <option value="T066">Machine Activity</option> - <option value="T185">Classification</option> - <option value="T006">Rickettsia or Chlamydia</option> - <option value="T049">Cell or Molecular Dysfunction</option> - <option value="T008">Animal</option> - <option value="T051">Event</option> - <option value="T038">Biologic Function</option> - <option value="T194">Archaeon</option> - <option value="T086">Nucleotide Sequence</option> - <option value="T039">Physiologic Function</option> - <option value="T012">Bird</option> - <option value="T063">Molecular Biology Research Technique</option> - <option value="T017">Anatomical Structure</option> - <option value="T082">Spatial Concept</option> - <option value="T088">Carbohydrate Sequence</option> - <option value="T099">Family Group</option> - <option value="T001">Organism</option> - <option value="T075">Research Device</option> - <option value="T096">Group</option> - <option value="T016">Human</option> - <option value="T072">Physical Object</option> - <option value="T071">Entity</option> - <option value="T200">Clinical Drug</option> - <option value="T085">Molecular Sequence</option> - <option value="T077">Conceptual Entity</option> - <option value="T010">Vertebrate</option> - <option value="T203">Drug Delivery Device</option> - <option value="T021">Fully Formed Anatomical Structure</option> - <option value="T204">Eukaryote</option> - </param> - <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"/> - <param name="mappingTypes" type="select" multiple="true" label="the list of mapping type to use during the mapping expansion step"> - <option value="m-all" selected="true">ALL</option> - <option value="m-null">None</option> - <option value="m-Automatic">Automatic</option> - <option value="m-Manual">Manual</option> - </param> - <param name="textToAnnotate" type="text" size="100" value="" label="Text to annotate"/> - <param name="format" type="select" label="File output format"> - <option value="xml" selected="true">XML</option> - <option value="text">Text</option> - <option value="tabDelimited">Tab Delimited</option> - </param> - <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> - </inputs> - <outputs> - <data format="text" name="output" /> - </outputs> - <tests> - <test> - <param name="longestOnly"/> - <param name="wholeWordOnly"/> - <param name="filterNumber"/> - <param name="stopWords"/> - <param name="withDefaultStopWords"/> - <param name="isTopWordsCaseSensitive"/> - <param name="mintermSize"/> - <param name="scored"/> - <param name="withSynonyms"/> - <param name="ontologiesToExpand"/> - <param name="ontologiesToKeepInResult"/> - <param name="semanticTypes"/> - <param name="levelMax"/> - <param name="mappingTypes"/> - <param name="textToAnnotate"/> - <param name="format"/> - <param name="apikey"/> - </test> - </tests> - <help> - -**Usage** - Enter bioportal API key, a text to annotate and specify the parameters, and the annotations will be retrieved. - -**Contact** - - Please send any request or comment to jose.minyarro@um.es - -**More information** - - http://bioportal.bioontology.org - - </help> - -</tool> \ No newline at end of file
--- a/NCBO_services/ncbo_recommender.xml Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,286 +0,0 @@ -<tool id="ncbo_recommender" name="Recommends a bio-ontology depending on annotations of a text" version="1.0.1"> - <description>Provides a bio-ontology as a recommendation depending on the annotations from a biological text</description> - <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_recommender_galaxy.jar $text $format $ontologyId $apikey > $output </command> - <inputs> - <param name="text" type="text" size="100" value="" label="Text to provide a recommendation of the most suitable bio-ontology"/> - <param name="format" type="select" label="File output format"> - <option value="xml" selected="true">XML</option> - <option value="text">Text</option> - <option value="simpleText">Simple Text</option> - </param> - <param name="ontologyId" type="select" multiple="true" label="Indicates the list of ontologies to search for the recommendation process"> - <option value="all" selected="true">ALL</option> - <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> - <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> - </inputs> - <outputs> - <data format="text" name="output" /> - </outputs> - <tests> - <test> - <param name="text"/> - <param name="format"/> - <param name="ontologyId"/> - <param name="apikey"/> - </test> - </tests> - <help> - -**Usage** - Enter bioportal API key, a text, the output format and a list of bioontolgies Ids and the recommender retrieves the bioontology with the best annotations. - -**Contact** - - Please send any request or comment to jose.minyarro@um.es - -**More information** - - http://bioportal.bioontology.org - - </help> - -</tool> \ No newline at end of file
--- a/NCBO_services/ncbo_resourceIndex.xml Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,320 +0,0 @@ -<tool id="ncbo_resourceIndex" name="Search for resources matched up with terms in bio-ontologies depending on the given text" version="1.0.1"> - <description>Search for resources matched up with terms in bio-ontologies depending on the given text</description> - <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_resourceIndex_galaxy.jar $query $ontologyids $resourceId $mode $elementDetails $format $apikey > $output</command> - <inputs> - <param name="query" type="text" size="100" value="" label="Text to search for terms in the selected bio-ontologys"/> - <param name="ontologyids" type="select" multiple="true" label="Indicates the list of ontologies to search for during the search process"> - <option value="all" selected="true">ALL</option> - <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> - <param name="resourceId" type="select" multiple="true" label="Indicates the list of resources Ids to search for during the Resource Index search process"> - <option value="all" selected="true">ALL</option> - <option value="PGGE">PharmGKB [Gene]</option> - <option value="BSM">Biositemaps</option> - <option value="CDD">Conserved Domain Database (CDD)</option> - <option value="CT">ClinicalTrials.gov</option> - <option value="GM">ARRS GoldMiner</option> - <option value="PC">Pathway Commons</option> - <option value="DBK">DrugBank</option> - <option value="AERS">Adverse Event Reporting System Data</option> - <option value="PM">PubMed</option> - <option value="MICAD">MICAD</option> - <option value="OMIM">Online Mendelian Inheritance in Man</option> - <option value="GAP">Database of Genotypes and Phenotypes</option> - <option value="PCM">PubChem</option> - <option value="PGDI">PharmGKB [Disease]</option> - <option value="WP">WikiPathways</option> - <option value="SMD">Stanford Microarray Database</option> - <option value="AE">ArrayExpress</option> - <option value="RXRD">ResearchCrossroads</option> - <option value="GEO">Gene Expression Omnibus DataSets</option> - <option value="REAC">Reactome</option> - <option value="UPKB">UniProt KB</option> - <option value="CANANO">caNanoLab</option> - <option value="PGDR">PharmGKB [Drug]</option> - </param> - <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 "> - <option value="unioin" selected="true">Union</option> - <option value="intersection">Intersection</option> - </param> - <param name="elementDetails" type="boolean" value="true" label="Tick the box whether the returned resource elements should be detailled or not"/> - <param name="format" type="select" label="Gets the results in a particular format"> - <option value="xml" selected="true">XML</option> - <option value="text">Text</option> - <option value="tabDelimited">Tab Delimited</option> - <option value="rdf">RDF</option> - <option value="owl">OWL</option> - </param> - <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> - </inputs> - <outputs> - <data format="text" name="output"/> - </outputs> - <tests> - <test> - <param name="query"/> - <param name="ontologyids"/> - <param name="resourceId"/> - <param name="apikey"/> - </test> - </tests> - <help> - -**Usage** - 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. - Example of search text: Melanoma - -**Contact** - - Please send any request or comment to jose.minyarro@um.es - -**More information** - - http://bioportal.bioontology.org - - </help> - -</tool> \ No newline at end of file
--- a/NCBO_services/ncbo_search.xml Mon Mar 19 08:25:59 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,281 +0,0 @@ -<tool id="ncbo_search" name="Search for terms in bio-ontologies depending on the text provided" version="1.0.1"> - <description>Search for terms in bio-ontologies depending on the text provided</description> - <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_search_galaxy.jar $query $ontologyids $apikey > $output</command> - <inputs> - <param name="query" type="text" size="100" value="" label="Text to search for terms in the selected bio-ontologys"/> - <param name="ontologyids" type="select" multiple="true" label="Indicates the list of ontologies to search for during the search process"> - <option value="all" selected="true">ALL</option> - <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> - <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> - </inputs> - <outputs> - <data format="text" name="output" /> - </outputs> - <tests> - <test> - <param name="query"/> - <param name="ontologyids"/> - <param name="apikey"/> - </test> - </tests> - <help> - -**Usage** - Enter bioportal API key, a text, and the list of bioontolgies Ids to search for and the search interface retrieves the bioontology terms associated with the text provided. - Example of search text: Breast cancer - -**Contact** - - Please send any request or comment to jose.minyarro@um.es - -**More information** - - http://bioportal.bioontology.org - - </help> - -</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,82 @@ + + + + ============= + NCBO Services + ============= + + + +INSTALLATION +============ + +1.- Stop Galaxy. + +2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/ + +3.- Create directory /galaxy-dist/tools/NCBO_services/ + +4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/ + +5.- Add the following lines to /galaxy-dist/tool_conf.xml: + + <section name="NCBO services" id="NCBO_services"> + <tool file="NCBO_services/get_ontology.xml"/> + <tool file="NCBO_services/extract.xml"/> + <tool file="NCBO_services/get_ontology_view.xml"/> + <tool file="NCBO_services/ncbo_annotator.xml"/> + <tool file="NCBO_services/ncbo_recommender.xml"/> + <tool file="NCBO_services/ncbo_search.xml"/> + <tool file="NCBO_services/ncbo_resourceIndex.xml"/> + </section> + +6.- Start Galaxy. + + + +USAGE +===== + +Each tool has a different functionality, but all of them need a +bioportal API key. The API key can be obtained by creating an account at +bioportal (http://bioportal.bioontology.org/). + + + +CONTACT +======= + +Please send any request or comment to mikel.egana.aranguren@gmail.com or +jose.minya@gmail.com. + + + +ACKNOWLEDGEMENTS +================ + +The work on get_ontology, extract and get_ontology_view is funded by the +Marie Curie Cofund program of the EU, FP7. + + + +COPYRIGHT AND LICENSE +===================== + +get_ontology, extract and get_ontology_view are copyright of Mikel +Egaña Aranguren (2012), and they are distributed under a GPL 3 license +(http://www.gnu.org/licenses/) + + + + + + + + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract.java Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,65 @@ +package es.upm.fi.dia.oeg.ncbo.galaxy; + +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; + +import org.apache.http.HttpEntity; +import org.apache.http.HttpResponse; +import org.apache.http.client.ClientProtocolException; +import org.apache.http.client.HttpClient; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.DefaultHttpClient; + +public class extract { + + /** + * @param args + * @throws IOException + * @throws ClientProtocolException + */ + public static void main(String[] args) throws ClientProtocolException, IOException { + +// http://www.bioontology.org/wiki/index.php/View_Extraction +// ./viewextractor/{ontology version id}[?{args}]&apikey={YourAPIKey} + + String api_key = args [0]; + String ontologyversionid = args [1]; // 35686 + String conceptid = args [2]; // E800-E999.9 + String filterrelations = args [3]; // PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass,[R]SIB,SI + String ontologyname = args [4]; // http://who.int/icd9 + + HttpClient client = new DefaultHttpClient(); + +// HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/35686/" + +// "?conceptid=E800-E999.9&filterrelations=PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass," + +// "[R]SIB,SIB&existontology=true&ontologyname=http://who.int/icd9&apikey=74c12fc6-9423-455a-a619-b94f47d1951b"); + + HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/" + ontologyversionid + + "/?conceptid="+ conceptid +"&filterrelations=" + filterrelations + + "&existontology=true&ontologyname="+ ontologyname + "&apikey=" + api_key); + + HttpResponse response = client.execute(get); + HttpEntity entity = response.getEntity(); + if (entity != null) { + InputStream instream = entity.getContent(); + InputStreamReader is=new InputStreamReader(instream); + BufferedReader br=new BufferedReader(is); + String read=br.readLine(); + BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out)); + while(read!=null){ +// System.out.println(read); + bw.write(read); + bw.newLine(); + read=br.readLine(); + } + bw.close(); + instream.close(); + } + + } + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract.xml Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,46 @@ +<tool id="extract" name="Extract a branch from an ontology" version="1.0.1"> + <description>Retrieves a subtree from an ontology using a root concept</description> + <command>java -jar ${__tool_data_path__}/shared/jars/extract.jar $api_key $ontologyversionid $conceptid $filterrelations $ontologyname > $output </command> + + <inputs> + <param name="api_key" type="text" size="100" label="BioPortal API key" /> + <param name="ontologyversionid" type="text" size="100" label="Ontology version ID" /> + <param name="conceptid" type="text" size="100" label="Concept id" /> + <param name="filterrelations" type="text" value="None" size="100" label="Filter relations" /> + <param name="ontologyname" type="text" size="100" label="Ontology name" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="api_key"/> + </test> + </tests> + <help> + +**What it does** + +It extracts a subtree from an ontology contained in BioPortal, and retrieves such subtree as an OWL ontology. + +**Parameters** + +* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. +* Ontology version ID: it can be obtained from BioPortal, in the Ontology page, on the versions column, by looking at the version URL. For example, it is 46754 for the Gene Ontology. +* Concept ID: the root term. For example, GO:0051179. +* Filter relations: for example "is_a,part_of". +* Ontology name: the URI for the new ontology. For example http://go_redux_is_a.owl. + +**Contact** + +Please send any request or comment to mikel.egana.aranguren@gmail.com. + +**More information** + +http://bioportal.bioontology.org + +http://www.bioontology.org/wiki/index.php/BioPortal_REST_services + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_ontology.java Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,49 @@ +package es.upm.fi.dia.oeg.ncbo.galaxy; + +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; + +import org.apache.http.HttpEntity; +import org.apache.http.HttpResponse; +import org.apache.http.client.ClientProtocolException; +import org.apache.http.client.HttpClient; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.client.methods.HttpPost; +import org.apache.http.impl.client.DefaultHttpClient; + +public class get_ontology { + + /** + * @param args + * @throws IOException + * @throws ClientProtocolException + */ + public static void main(String[] args) throws ClientProtocolException, IOException { + String api_key = args [0]; + String ontology_id = args [1]; // 1522 + HttpClient client = new DefaultHttpClient(); + + HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/virtual/download/" + ontology_id + "?apikey=" +api_key); + HttpResponse response = client.execute(get); + HttpEntity entity = response.getEntity(); + if (entity != null) { + InputStream instream = entity.getContent(); + InputStreamReader is=new InputStreamReader(instream); + BufferedReader br=new BufferedReader(is); + String read=br.readLine(); + BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out)); + while(read!=null){ +// System.out.println(read); + bw.write(read); + bw.newLine(); + read=br.readLine(); + } + bw.close(); + instream.close(); + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_ontology.xml Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,384 @@ +<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> + #if $id_opts.id_opts_menu=="id_by_hand" #java -jar ${__tool_data_path__}/shared/jars/get_ontology.jar $api_key $id_opts.ontology_id > $output + #else #java -jar ${__tool_data_path__}/shared/jars/get_ontology.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="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"> + <!-- Automatically generated with http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey --> + <param name="ontology_id" type="select" multiple="false" label="Choose ontology from this list"> + <option value="1158">Cell Behavior Ontology</option> + <option value="1016">Drosophila development</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="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="1058">SNP-Ontology</option> + <option value="1099">African Traditional Medicine</option> + <option value="1134">BioTop</option> + <option value="1078">Spatial Ontology</option> + <option value="1247">GeoSpecies Ontology</option> + <option value="1007">Chemical entities of biological interest</option> + <option value="1024">Loggerhead nesting</option> + <option value="1257">MeGO</option> + <option value="1135">Pseudogene</option> + <option value="1049">C. elegans development</option> + <option value="1070">Gene Ontology</option> + <option value="1126">Family Health History Ontology</option> + <option value="1108">Plant Anatomy</option> + <option value="1114">Bilateria anatomy</option> + <option value="1100">Ontology for Genetic Interval</option> + <option value="1136">Experimental Factor Ontology</option> + <option value="1141">Ontology of Physics for Biology</option> + <option value="1044">Sample processing and separation techniques</option> + <option value="1347">MedlinePlus Health Topics</option> + <option value="1005">BRENDA tissue / enzyme source</option> + <option value="1152">Minimal anatomical terminology</option> + <option value="1063">Common Anatomy Reference Ontology</option> + <option value="1321">Neural ElectroMagnetic Ontologies</option> + <option value="1043">Physico-chemical process</option> + <option value="1064">Fly taxonomy</option> + <option value="1089">BIRNLex</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="1116">Bleeding History Phenotype</option> + <option value="1104">Biomedical Resource 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">Plant Trait Ontology</option> + <option value="1350">Logical Observation Identifier Names and Codes</option> + <option value="1082">Gene Regulation Ontology</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="1047">Cereal Plant Development</option> + <option value="1349">Physician Data Query</option> + <option value="1190">Ontology for Parasite LifeCycle</option> + <option value="1036">Plant environmental conditions</option> + <option value="1109">Sequence types and features</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="1304">Breast Cancer Grading Ontology</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="1022">Human developmental anatomy, timed version</option> + <option value="1014">Physico-chemical methods and properties</option> + <option value="1224">Symptom Ontology</option> + <option value="1095">Xenopus anatomy and development</option> + <option value="1042">OBO relationship types</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="1027">Medaka fish anatomy and development</option> + <option value="1354">WHO Adverse Reaction Terminology</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="1020">Habronattus courtship</option> + <option value="1148">BioPortal Metadata</option> + <option value="1038">Plant Growth and Development Stage</option> + <option value="1132">NCBI organismal classification</option> + <option value="1328">Ontology of homology and related concepts in biology</option> + <option value="1019">Fungal gross anatomy</option> + <option value="1290">ABA Adult Mouse Brain</option> + <option value="1067">C. elegans phenotype</option> + <option value="1069">Environment Ontology</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="1112">Units of measurement</option> + <option value="1369">PhysicalFields</option> + <option value="1086">Ontology for disease genetic investigation</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="1122">Skin Physiology Ontology</option> + <option value="1142">Cardiac Electrophysiology Ontology</option> + <option value="1128">Comparative Data Analysis Ontology</option> + <option value="1172">Vaccine Ontology</option> + <option value="1088">MaHCO - An MHC Ontology</option> + <option value="1245">Cell line ontology</option> + <option value="1222">Ascomycete phenotype ontology</option> + <option value="1249">Smoking Behavior Risk Ontology</option> + <option value="1039">Proteomics data and process provenance</option> + <option value="1105">Mass spectrometry</option> + <option value="1040">Protein-protein interaction</option> + <option value="1237">Situation-Based Access Control</option> + <option value="1008">Dictyostelium discoideum anatomy</option> + <option value="1068">Subcellular Anatomy Ontology (SAO)</option> + <option value="1087">Ontology of Geographical Region</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 ontology</option> + <option value="1094">Pathogen transmission</option> + <option value="1084">NIFSTD</option> + <option value="1025">Mammalian phenotype</option> + <option value="1131">MGED Ontology</option> + <option value="1035">Pathway ontology</option> + <option value="1106">Gene Regulation Ontology</option> + <option value="1054">Amino Acid</option> + <option value="1056">Basic Vertebrate Anatomy</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="1083">NanoParticle Ontology</option> + <option value="1053">Foundational Model of Anatomy</option> + <option value="1031">Mouse pathology</option> + <option value="1092">Infectious Disease Ontology</option> + <option value="1032">NCI Thesaurus</option> + <option value="1381">NIF Dysfunction</option> + <option value="1393">Information Artifact Ontology</option> + <option value="1394">Syndromic Surveillance 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="1401">International Classification for Nursing Practice</option> + <option value="1402">NIF Cell</option> + <option value="1404">Uber anatomy ontology</option> + <option value="1406">linkingkin2pep</option> + <option value="1407">Terminology for the Description of Dynamics</option> + <option value="1409">PKO_Re</option> + <option value="1410">Kinetic Simulation Algorithm Ontology</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="1415">Common Terminology Criteria for Adverse Events</option> + <option value="1417">Influenza Ontology</option> + <option value="1418">TOK_Ontology</option> + <option value="1419">Taxonomic rank vocabulary</option> + <option value="1422">MedDRA</option> + <option value="1423">RxNORM</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="1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> + <option value="1428">Nursing Interventions Classification (NIC)</option> + <option value="1429">ICPC-2 PLUS</option> + <option value="1430">AI/RHEUM</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="1444">Chemical Information Ontology</option> + <option value="1343">Health Level Seven</option> + <option value="1461">Translational Medicine Ontology</option> + <option value="1484">International Classification of External Causes of Injuries</option> + <option value="1487">Body System</option> + <option value="1488">SysMO-JERM</option> + <option value="1489">Ontology of Adverse Events (OAE)</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="1498">Bioinformatics operations, types of data, data formats and topics</option> + <option value="1499">NCI Metathesaurus</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="1517">Human developmental anatomy, abstract version, v2</option> + <option value="1520">Leukocyte Surface Markers</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="1532">SemanticScience Integrated Ontology</option> + <option value="1533">BioAssay Ontology</option> + <option value="1534">apollo-akesios</option> + <option value="1535">Terminology of Anatomy of Human Histology</option> + <option value="1536">Terminology of Anatomy of Human Embryology</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="1544">Crop Ontology</option> + <option value="1545">Wheat trait </option> + <option value="1550">PHARE</option> + <option value="1552">Reproductive trait and phenotype ontology</option> + <option value="1553">ICD10CM</option> + <option value="1555">Vertebrate Anatomy Ontology</option> + <option value="1560">Cognitive Paradigm 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">CAO</option> + <option value="1583">Clinical Measurement Ontology</option> + <option value="1584">Measurement Method Ontology</option> + <option value="1585">Experimental Conditions Ontology</option> + <option value="1586">Orphanet Ontology of Rare Diseases</option> + <option value="1587">Plant Ontology</option> + <option value="1588">Ontology of General Purpose Datatypes</option> + <option value="1596">HOM_MDCs-DRGS</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> + <option value="1625">HOM-ICD9CM_PROCEDURES</option> + <option value="1626">Enzyme Mechanism Ontology</option> + <option value="1627">HOMERUN Ontology</option> + <option value="1629">HOM-UCARE</option> + <option value="1630">HOM-EPIC</option> + <option value="1631">HOM-HARVARD</option> + <option value="1632">Web-Service Interaction Ontology</option> + <option value="1633">Cognitive Atlas</option> + <option value="1638">Ontology of Data Mining</option> + <option value="1639">Epilepsy</option> + <option value="1640">Pediatric Terminology</option> + <option value="1641">HOM-ICD9CM-ECODES</option> + <option value="1642">HOM-DXPROCS_MDCDRG</option> + <option value="1643">HOM-ICD9_PROCS_OSHPD</option> + <option value="1645">HOM-MDCDRG_OSHPD</option> + <option value="1647">HOM-ICD9_DXandVCODES_OSHPD</option> + <option value="1648">HOM-DATASOURCE_OSHPD</option> + <option value="1649">HOM-OSHPD</option> + <option value="1650">Units Ontology</option> + <option value="1651">Sleep Domain Ontology</option> + <option value="1652">HOM-OSHPD_UseCase</option> + <option value="1653">HOM-PROCS2_OSHPD</option> + <option value="1654">HOM-DXVCODES2_OSHPD</option> + <option value="1655">PharmGKB-in-OWL</option> + <option value="1656">PhenomeBLAST ontology</option> + <option value="1657">Quadrupedal Gait</option> + <option value="1658">Hewan Invertebrata</option> + <option value="1659">Vertebrate Trait Ontology</option> + <option value="1660">HOM-DATASOURCE_EPIC</option> + <option value="1661">HOM-Transplant Ontology</option> + <option value="1665">Student Health Record</option> + <option value="1666">Emotion Ontology</option> + <option value="1667">HOM-DATASOURCE_OSHPDSC</option> + <option value="1668">HOM-OSHPD-SC</option> + <option value="1670">ICD_Oncology-3</option> + <option value="1671">Quantitative Imaging Biomarker Ontology</option> + <option value="1672">DIKB-Evidence-Ontology</option> + <option value="1675">CEEROntology</option> + <option value="1676">Randomized Controlled Trials (RCT) Ontology</option> + <option value="1679">JADNI test ontology2</option> + <option value="1680">BioActivity Ontology3</option> + <option value="1681">JADNI test ontology</option> + <option value="1682">Human disease in Bioactivity</option> + <option value="1683">BioActivity Ontology</option> + <option value="1684">BioActivity Ontology2</option> + <option value="1686">Neomark Oral Cancer Ontology</option> + <option value="1688">UniprotCoreBH</option> + <option value="1689">Fission Yeast Phenotype Ontology</option> + <option value="1691">yipd_test</option> + <option value="1692">test-purl</option> + <option value="1693">ICD9-ICD10-PCS (partial)</option> + <option value="1694">HOM-CPT</option> + <option value="1696">Synapse Ontology</option> + <option value="1697">HOM-ORTHO</option> + <option value="1698">HOM-DATASRC-ORTHO</option> + <option value="1699">VIVO</option> + <option value="1700">Test Pradip PURL</option> + <option value="1701">HOM-ORTHOSURGERY</option> + <option value="1702">Eurofut</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="api_key"/> + <param name="id_opts.ontology_id"/> + </test> + </tests> + <help> + +**What it does** + +It retrieves an ontology from BioPortal. + +**Parameters** + +* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. +* Ontology ID: provide it by hand (e.g. 1522 for BioPAX), or select from list. + +**Contact** + +Please send any request or comment to mikel.egana.aranguren@gmail.com. + +**More information** + +http://bioportal.bioontology.org + +http://www.bioontology.org/wiki/index.php/BioPortal_REST_services + + + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_ontology_view.java Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,54 @@ +package es.upm.fi.dia.oeg.ncbo.galaxy; + +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; + +import org.apache.http.HttpEntity; +import org.apache.http.HttpResponse; +import org.apache.http.client.ClientProtocolException; +import org.apache.http.client.HttpClient; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.client.methods.HttpPost; +import org.apache.http.impl.client.DefaultHttpClient; + +public class get_ontology_view { + + /** + * @param args + * @throws IOException + * @throws ClientProtocolException + */ + public static void main(String[] args) throws ClientProtocolException, IOException { +// http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Download_a_specific_ontology_view_based_on_the_ontology_view_version_id +// Download a specific ontology view based on the ontology view version id + + String api_key = args [0]; + String ontology_view_id = args [1]; + + HttpClient client = new DefaultHttpClient(); +// http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey + HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/ontologies/download/" + ontology_view_id + "?apikey=" + api_key); + + HttpResponse response = client.execute(get); + HttpEntity entity = response.getEntity(); + if (entity != null) { + InputStream instream = entity.getContent(); + InputStreamReader is=new InputStreamReader(instream); + BufferedReader br=new BufferedReader(is); + String read=br.readLine(); + BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out)); + while(read!=null){ +// System.out.println(read); + bw.write(read); + bw.newLine(); + read=br.readLine(); + } + bw.close(); + instream.close(); + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_ontology_view.xml Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,40 @@ +<tool id="get_ontology_view" name="Get a concrete view of an ontology" version="1.0.1"> + <description>Retrieves a view of an ontology using the view id</description> + <command>java -jar ${__tool_data_path__}/shared/jars/get_ontology_view.jar $api_key $ontologyviewid > $output </command> + + <inputs> + <param name="api_key" type="text" size="100" label="BioPortal API key" /> + <param name="ontologyviewid" type="text" size="100" label="Ontology view ID" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="api_key"/> + </test> + </tests> + <help> + +**What it does** + +It retrieves a view from an ontology contained in BioPortal. + +**Parameters** + +* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. +* Ontology view ID: it can be obtained from BioPortal, in the Ontology page, on the views section, by looking at the view URL. For example, it is 41014 for the generic Gene Ontology slim. + +**Contact** + +Please send any request or comment to mikel.egana.aranguren@gmail.com. + +**More information** + +http://bioportal.bioontology.org + +http://www.bioontology.org/wiki/index.php/BioPortal_REST_services + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ncbo_annotator.xml Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,704 @@ +<tool id="ncbo_annotator" name="Annotates a text with bio-ontology terms" version="1.0.1"> + <description>Annotates biological texts with the terms of the bio-ontologies from BioPortal</description> + <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> + <inputs> + <param name="longestOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only the longest word"/> + <param name="wholeWordOnly" type="boolean" value="true" label="Tick the box if the Annotator should annotate only whole words"/> + <param name="filterNumber" type="boolean" value="true" label="Tick the box if the Annotator should filter numbers before annotating the text"/> + <param name="stopWords" type="text" value="" size="100" label="List the words that the Annotator should omit from the text"/> + <param name="withDefaultStopWords" type="boolean" value="true" label="Tick the box if the Annotator should use the default list of stop words"/> + <param name="isTopWordsCaseSensitive" type="boolean" value="false" label="Tick the box whether the stop words are case sensitive or not"/> + <param name="mintermSize" type="integer" value="3" min="0" max="100" label="Indicates the minimum length for the terms to annotate"/> + <param name="scored" type="boolean" value="true" label="Tick the box whether the Annotator should assign a numeric accuracy to each annotation or not"/> + <param name="withSynonyms" type="boolean" value="true" label="Tick the box if the Annotator should use synonyms in the direct annotation"/> + <param name="ontologiesToExpand" type="select" multiple="true" label="Indicates the list of ontologies to use with the mapping semantic expansion component"> + <option value="e-all" selected="true">ALL</option> + <option value="e-1394">Syndromic Surveillance Ontology</option> + <option value="e-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> + <option value="e-1158">Cell Behavior Ontology</option> + <option value="e-1033">NMR-instrument specific component of metabolomics investigations</option> + <option value="e-1351">Medical Subject Headings</option> + <option value="e-1146">Electrocardiography Ontology</option> + <option value="e-1041">Protein modification</option> + <option value="e-1058">SNP-Ontology</option> + <option value="e-1099">African Traditional Medicine</option> + <option value="e-1134">BioTop</option> + <option value="e-1247">GeoSpecies Ontology</option> + <option value="e-1024">Loggerhead nesting</option> + <option value="e-1257">MeGO</option> + <option value="e-1135">Pseudogene</option> + <option value="e-1126">Family Health History Ontology</option> + <option value="e-1108">Plant structure</option> + <option value="e-1114">Bilateria anatomy</option> + <option value="e-1100">Ontology for Genetic Interval</option> + <option value="e-1044">Sample processing and separation techniques</option> + <option value="e-1347">MedlinePlus Health Topics</option> + <option value="e-1152">Minimal anatomical terminology</option> + <option value="e-1063">Common Anatomy Reference Ontology</option> + <option value="e-1089">BIRNLex</option> + <option value="e-1116">Bleeding History Phenotype</option> + <option value="e-1104">Biomedical Resource Ontology</option> + <option value="e-1350">Logical Observation Identifier Names and Codes</option> + <option value="e-1082">Gene Regulation Ontology</option> + <option value="e-1047">Cereal plant development</option> + <option value="e-1349">Physician Data Query</option> + <option value="e-1190">Parasite Life Cycle</option> + <option value="e-1192">Proteomics Pipeline Infrastructure for CPTAC</option> + <option value="e-1352">National Drug File</option> + <option value="e-1059">Computer-based Patient Record Ontology</option> + <option value="e-1052">Protein Ontology</option> + <option value="e-1341">COSTART</option> + <option value="e-1344">International Classification of Primary Care</option> + <option value="e-1061">Suggested Ontology for Pharmacogenomics</option> + <option value="e-1353">SNOMED Clinical Terms</option> + <option value="e-1224">Symptom Ontology</option> + <option value="e-1013">eVOC (Expressed Sequence Annotation for Humans)</option> + <option value="e-1149">DermLex: The Dermatology Lexicon</option> + <option value="e-1311">Malaria Ontology</option> + <option value="e-1335">Parasite Experiment Ontology</option> + <option value="e-1370">Amphibian taxonomy</option> + <option value="e-1354">WHO Adverse Reaction Terminology</option> + <option value="e-1148">BioPortal Metadata</option> + <option value="e-1038">Plant growth and developmental stage</option> + <option value="e-1132">NCBI organismal classification</option> + <option value="e-1328">Ontology of homology and related concepts in biology</option> + <option value="e-1290">ABA Adult Mouse Brain</option> + <option value="e-1055">Galen</option> + <option value="e-1332">Basic Formal Ontology</option> + <option value="e-1183">Lipid Ontology</option> + <option value="e-1026">Multiple alignment</option> + <option value="e-1130">Cancer Research and Management ACGT Master Ontology</option> + <option value="e-1060">Epoch Clinical Trial Ontologies</option> + <option value="e-1369">PhysicalFields</option> + <option value="e-1086">Ontology for disease genetic investigation</option> + <option value="e-1122">Skin Physiology Ontology</option> + <option value="e-1142">Cardiac Electrophysiology Ontology</option> + <option value="e-1128">Comparative Data Analysis Ontology</option> + <option value="e-1088">MaHCO - An MHC Ontology</option> + <option value="e-1249">Smoking Behavior Risk Ontology</option> + <option value="e-1039">Proteomics data and process provenance</option> + <option value="e-1040">Protein-protein interaction</option> + <option value="e-1068">Subcellular Anatomy Ontology (SAO)</option> + <option value="e-1087">Ontology of Geographical Region</option> + <option value="e-1094">Pathogen transmission</option> + <option value="e-1131">MGED Ontology</option> + <option value="e-1106">Gene Regulation Ontology</option> + <option value="e-1054">Amino Acid</option> + <option value="e-1056">Basic Vertebrate Anatomy</option> + <option value="e-1083">NanoParticle Ontology</option> + <option value="e-1053">Foundational Model of Anatomy</option> + <option value="e-1092">Infectious disease</option> + <option value="e-1393">Information Artifact Ontology</option> + <option value="e-1395">MDSS Mo</option> + <option value="e-1397">Gazetteer</option> + <option value="e-1398">Ontology of Language Disorder in Autism</option> + <option value="e-1399">Pilot Ontology</option> + <option value="e-1406">linkingkin2pep</option> + <option value="e-1409">PKO_Re</option> + <option value="e-1410">Kinetic Simulation Algorithm Ontology</option> + <option value="e-1415">Common Terminology Criteria for Adverse Events</option> + <option value="e-1418">TOK_Ontology</option> + <option value="e-1419">Taxonomic rank vocabulary</option> + <option value="e-1422">MedDRA</option> + <option value="e-1424">National Drug Data File</option> + <option value="e-1425">ICD-10-PCS</option> + <option value="e-1426">Master Drug Data Base</option> + <option value="e-1429">ICPC-2 PLUS</option> + <option value="e-1430">AIR</option> + <option value="e-1438">Breast tissue cell lines</option> + <option value="e-1439">General Formal Ontology</option> + <option value="e-1440">General Formal Ontology: Biology</option> + <option value="e-1343">Health Level Seven</option> + <option value="e-1484">International Classification of External Causes of Injuries</option> + <option value="e-1487">Body System</option> + <option value="e-1490">Platynereis stage ontology</option> + <option value="e-1491">IMGT-ONTOLOGY</option> + <option value="e-1494">Tissue Microarray Ontology</option> + <option value="e-1497">PMA 2010</option> + <option value="e-1500">RNA ontology</option> + <option value="e-1501">Neomark Oral Cancer-Centred Ontology</option> + <option value="e-1504">Current Procedural Terminology</option> + <option value="e-1505">Ontology for MicroRNA Target Prediction</option> + <option value="e-1506">Gene Ontology Extension</option> + <option value="e-1507">Cell Cycle Ontology</option> + <option value="e-1509">ICPS Network</option> + <option value="e-1510">Metathesaurus CPT Hierarchical Terms</option> + <option value="e-1515">Interaction Network Ontology</option> + <option value="e-1516">ICD10</option> + <option value="e-1521">Neural Motor Recovery Ontology</option> + <option value="e-1522">BioPAX</option> + <option value="e-1523">OBOE SBC</option> + <option value="e-1524">OBOE</option> + <option value="e-1526">CRISP Thesaurus, 2006</option> + <option value="e-1527">VANDF</option> + <option value="e-1528">HUGO</option> + <option value="e-1529">HCPCS</option> + <option value="e-1530">Animal natural history and life history</option> + <option value="e-1534">apollo-akesios</option> + <option value="e-1537">Brucellosis Ontology</option> + <option value="e-1538">Role Ontology</option> + <option value="e-1539">Neural-Immune Gene Ontology</option> + <option value="e-1540">Ontology for Drug Discovery Investigations</option> + <option value="e-1541">Cell line ontology</option> + <option value="e-1545">Wheat trait </option> + <option value="e-1547">BRENDA tissue / enzyme source</option> + <option value="e-1552">Reproductive traits ontology</option> + <option value="e-1553">ICD10CM</option> + <option value="e-1560">Cognitive Paradigm Ontology</option> + <option value="e-1423">RxNORM</option> + <option value="e-1517">Human developmental anatomy, abstract version, v2</option> + <option value="e-1016">Drosophila development</option> + <option value="e-1062">PRotein Ontology (PRO)</option> + <option value="e-1000">Mouse adult gross anatomy</option> + <option value="e-1065">Tick gross anatomy</option> + <option value="e-1123">Ontology for Biomedical Investigations</option> + <option value="e-1078">Spatial Ontology</option> + <option value="e-1007">Chemical entities of biological interest</option> + <option value="e-1049">C. elegans development</option> + <option value="e-1070">Gene Ontology</option> + <option value="e-1136">Experimental Factor Ontology</option> + <option value="e-1141">Ontology of Physics for Biology</option> + <option value="e-1005">BRENDA tissue / enzyme source</option> + <option value="e-1321">Neural ElectroMagnetic Ontologies</option> + <option value="e-1043">Physico-chemical process</option> + <option value="e-1064">Fly taxonomy</option> + <option value="e-1076">Ontology of Clinical Research (OCRe)</option> + <option value="e-1110">Teleost Anatomy Ontology</option> + <option value="e-1362">Hymenoptera Anatomy Ontology</option> + <option value="e-1030">Mosquito gross anatomy</option> + <option value="e-1029">Molecule role (INOH Protein name/family name ontology)</option> + <option value="e-1144">Dendritic cell</option> + <option value="e-1125">Human Phenotype Ontology</option> + <option value="e-1023">Biological imaging methods</option> + <option value="e-1021">Human developmental anatomy, abstract version</option> + <option value="e-1046">Systems Biology</option> + <option value="e-1051">Zebrafish anatomy and development</option> + <option value="e-1037">Cereal plant trait</option> + <option value="e-1107">Phenotypic quality</option> + <option value="e-1081">Teleost taxonomy</option> + <option value="e-1048">C. elegans gross anatomy</option> + <option value="e-1050">Maize gross anatomy</option> + <option value="e-1036">Plant environmental conditions</option> + <option value="e-1109">Sequence types and features</option> + <option value="e-1022">Human developmental anatomy, timed version</option> + <option value="e-1095">Xenopus anatomy and development</option> + <option value="e-1027">Medaka fish anatomy and development</option> + <option value="e-1011">Event (INOH pathway ontology)</option> + <option value="e-1010">Mouse gross anatomy and development</option> + <option value="e-1015">Drosophila gross anatomy</option> + <option value="e-1090">Amphibian gross anatomy</option> + <option value="e-1019">Fungal gross anatomy</option> + <option value="e-1067">C. elegans phenotype</option> + <option value="e-1069">Environment Ontology</option> + <option value="e-1112">Units of measurement</option> + <option value="e-1091">Spider Ontology</option> + <option value="e-1017">FlyBase Controlled Vocabulary</option> + <option value="e-1348">Online Mendelian Inheritance in Man</option> + <option value="e-1172">Vaccine Ontology</option> + <option value="e-1222">Ascomycete phenotype ontology</option> + <option value="e-1105">Mass spectrometry</option> + <option value="e-1237">Situation-Based Access Control</option> + <option value="e-1008">Dictyostelium discoideum anatomy</option> + <option value="e-1150">Rat Strain Ontology</option> + <option value="e-1101">International Classification of Diseases</option> + <option value="e-1314">Cell Line Ontology</option> + <option value="e-1009">Human disease</option> + <option value="e-1084">NIFSTD</option> + <option value="e-1025">Mammalian phenotype</option> + <option value="e-1035">Pathway ontology</option> + <option value="e-1012">Evidence codes</option> + <option value="e-1115">Yeast phenotypes</option> + <option value="e-1001">Cereal plant gross anatomy</option> + <option value="e-1006">Cell type</option> + <option value="e-1077">Mosquito insecticide resistance</option> + <option value="e-1085">Ontology of Glucose Metabolism Disorder</option> + <option value="e-1057">RadLex</option> + <option value="e-1031">Mouse pathology</option> + <option value="e-1032">NCI Thesaurus</option> + <option value="e-1381">NIF Dysfunction</option> + <option value="e-1401">International Classification for Nursing Practice</option> + <option value="e-1402">NIF Cell</option> + <option value="e-1404">Uber anatomy ontology</option> + <option value="e-1407">Terminology for the Description of Dynamics</option> + <option value="e-1411">International Classification of Functioning, Disability and Health (ICF)</option> + <option value="e-1413">Software Ontology</option> + <option value="e-1414">Ontology for General Medical Science</option> + <option value="e-1444">Chemical Information Ontology</option> + <option value="e-1461">Translational Medicine Ontology</option> + <option value="e-1488">SysMO-JERM</option> + <option value="e-1489">Adverse Event Ontology</option> + <option value="e-1498">EDAM</option> + <option value="e-1532">SemanticScience Integrated Ontology</option> + <option value="e-1550">PHARE</option> + <option value="e-1555">Vertebrate Anatomy Ontology</option> + <option value="e-1565">Ontology of Medically Related Social Entities</option> + <option value="e-1567">Pharmacovigilance Ontology</option> + <option value="e-1568">Anatomical Entity Ontology</option> + <option value="e-1569">Host Pathogen Interactions Ontology</option> + <option value="e-1570">Traditional Medicine Constitution Value Set</option> + <option value="e-1571">Traditional Medicine Other Factors Value Set</option> + <option value="e-1572">Traditional Medicine Signs and Symptoms Value Set</option> + <option value="e-1573">Traditional Medicine Meridian Value Sets</option> + <option value="e-1574">vertebrate Homologous Organ Groups</option> + <option value="e-1575">ExO</option> + <option value="e-1576">FDA Medical Devices (2010)</option> + <option value="e-1578">HOM_ElixhauserScores</option> + <option value="e-1580">Adverse Event Reporting ontology</option> + <option value="e-1581">HEALTH_INDICATORS</option> + <option value="e-1582">COA</option> + <option value="e-1583">Clinical Measurement Ontology</option> + <option value="e-1584">Measurement Method Ontology</option> + <option value="e-1585">Experimental Conditions Ontology</option> + <option value="e-1587">Plant Ontology</option> + <option value="e-1588">Ontology of General Purpose Datatypes</option> + <option value="e-1596">MajDxCatgrs-DxRltdGrps</option> + <option value="e-1613">Bone Dysplasia Ontology</option> + <option value="e-1614">IxnO</option> + <option value="e-1615">Systems Chemical Biology/Chemogenomics </option> + <option value="e-1616">Phylogenetic Ontology</option> + <option value="e-1621">Neuro Behavior Ontology</option> + </param> + <param name="ontologiesToKeepInResult" type="select" multiple="true" label="Indicates the list of ontologies to keep in the result of the annotation process"> + <option value="k-all" selected="true">ALL</option> + <option value="k-1394">Syndromic Surveillance Ontology</option> + <option value="k-1427">Read Codes, Clinical Terms Version 3 (CTV3) </option> + <option value="k-1158">Cell Behavior Ontology</option> + <option value="k-1033">NMR-instrument specific component of metabolomics investigations</option> + <option value="k-1351">Medical Subject Headings</option> + <option value="k-1146">Electrocardiography Ontology</option> + <option value="k-1041">Protein modification</option> + <option value="k-1058">SNP-Ontology</option> + <option value="k-1099">African Traditional Medicine</option> + <option value="k-1134">BioTop</option> + <option value="k-1247">GeoSpecies Ontology</option> + <option value="k-1024">Loggerhead nesting</option> + <option value="k-1257">MeGO</option> + <option value="k-1135">Pseudogene</option> + <option value="k-1126">Family Health History Ontology</option> + <option value="k-1108">Plant structure</option> + <option value="k-1114">Bilateria anatomy</option> + <option value="k-1100">Ontology for Genetic Interval</option> + <option value="k-1044">Sample processing and separation techniques</option> + <option value="k-1347">MedlinePlus Health Topics</option> + <option value="k-1152">Minimal anatomical terminology</option> + <option value="k-1063">Common Anatomy Reference Ontology</option> + <option value="k-1089">BIRNLex</option> + <option value="k-1116">Bleeding History Phenotype</option> + <option value="k-1104">Biomedical Resource Ontology</option> + <option value="k-1350">Logical Observation Identifier Names and Codes</option> + <option value="k-1082">Gene Regulation Ontology</option> + <option value="k-1047">Cereal plant development</option> + <option value="k-1349">Physician Data Query</option> + <option value="k-1190">Parasite Life Cycle</option> + <option value="k-1192">Proteomics Pipeline Infrastructure for CPTAC</option> + <option value="k-1352">National Drug File</option> + <option value="k-1059">Computer-based Patient Record Ontology</option> + <option value="k-1052">Protein Ontology</option> + <option value="k-1341">COSTART</option> + <option value="k-1344">International Classification of Primary Care</option> + <option value="k-1061">Suggested Ontology for Pharmacogenomics</option> + <option value="k-1353">SNOMED Clinical Terms</option> + <option value="k-1224">Symptom Ontology</option> + <option value="k-1013">eVOC (Expressed Sequence Annotation for Humans)</option> + <option value="k-1149">DermLex: The Dermatology Lexicon</option> + <option value="k-1311">Malaria Ontology</option> + <option value="k-1335">Parasite Experiment Ontology</option> + <option value="k-1370">Amphibian taxonomy</option> + <option value="k-1354">WHO Adverse Reaction Terminology</option> + <option value="k-1148">BioPortal Metadata</option> + <option value="k-1038">Plant growth and developmental stage</option> + <option value="k-1132">NCBI organismal classification</option> + <option value="k-1328">Ontology of homology and related concepts in biology</option> + <option value="k-1290">ABA Adult Mouse Brain</option> + <option value="k-1055">Galen</option> + <option value="k-1332">Basic Formal Ontology</option> + <option value="k-1183">Lipid Ontology</option> + <option value="k-1026">Multiple alignment</option> + <option value="k-1130">Cancer Research and Management ACGT Master Ontology</option> + <option value="k-1060">Epoch Clinical Trial Ontologies</option> + <option value="k-1369">PhysicalFields</option> + <option value="k-1086">Ontology for disease genetic investigation</option> + <option value="k-1122">Skin Physiology Ontology</option> + <option value="k-1142">Cardiac Electrophysiology Ontology</option> + <option value="k-1128">Comparative Data Analysis Ontology</option> + <option value="k-1088">MaHCO - An MHC Ontology</option> + <option value="k-1249">Smoking Behavior Risk Ontology</option> + <option value="k-1039">Proteomics data and process provenance</option> + <option value="k-1040">Protein-protein interaction</option> + <option value="k-1068">Subcellular Anatomy Ontology (SAO)</option> + <option value="k-1087">Ontology of Geographical Region</option> + <option value="k-1094">Pathogen transmission</option> + <option value="k-1131">MGED Ontology</option> + <option value="k-1106">Gene Regulation Ontology</option> + <option value="k-1054">Amino Acid</option> + <option value="k-1056">Basic Vertebrate Anatomy</option> + <option value="k-1083">NanoParticle Ontology</option> + <option value="k-1053">Foundational Model of Anatomy</option> + <option value="k-1092">Infectious disease</option> + <option value="k-1393">Information Artifact Ontology</option> + <option value="k-1395">MDSS Mo</option> + <option value="k-1397">Gazetteer</option> + <option value="k-1398">Ontology of Language Disorder in Autism</option> + <option value="k-1399">Pilot Ontology</option> + <option value="k-1406">linkingkin2pep</option> + <option value="k-1409">PKO_Re</option> + <option value="k-1410">Kinetic Simulation Algorithm Ontology</option> + <option value="k-1415">Common Terminology Criteria for Adverse Events</option> + <option value="k-1418">TOK_Ontology</option> + <option value="k-1419">Taxonomic rank vocabulary</option> + <option value="k-1422">MedDRA</option> + <option value="k-1424">National Drug Data File</option> + <option value="k-1425">ICD-10-PCS</option> + <option value="k-1426">Master Drug Data Base</option> + <option value="k-1429">ICPC-2 PLUS</option> + <option value="k-1430">AIR</option> + <option value="k-1438">Breast tissue cell lines</option> + <option value="k-1439">General Formal Ontology</option> + <option value="k-1440">General Formal Ontology: Biology</option> + <option value="k-1343">Health Level Seven</option> + <option value="k-1484">International Classification of External Causes of Injuries</option> + <option value="k-1487">Body System</option> + <option value="k-1490">Platynereis stage ontology</option> + <option value="k-1491">IMGT-ONTOLOGY</option> + <option value="k-1494">Tissue Microarray Ontology</option> + <option value="k-1497">PMA 2010</option> + <option value="k-1500">RNA ontology</option> + <option value="k-1501">Neomark Oral Cancer-Centred Ontology</option> + <option value="k-1504">Current Procedural Terminology</option> + <option value="k-1505">Ontology for MicroRNA Target Prediction</option> + <option value="k-1506">Gene Ontology Extension</option> + <option value="k-1507">Cell Cycle Ontology</option> + <option value="k-1509">ICPS Network</option> + <option value="k-1510">Metathesaurus CPT Hierarchical Terms</option> + <option value="k-1515">Interaction Network Ontology</option> + <option value="k-1516">ICD10</option> + <option value="k-1521">Neural Motor Recovery Ontology</option> + <option value="k-1522">BioPAX</option> + <option value="k-1523">OBOE SBC</option> + <option value="k-1524">OBOE</option> + <option value="k-1526">CRISP Thesaurus, 2006</option> + <option value="k-1527">VANDF</option> + <option value="k-1528">HUGO</option> + <option value="k-1529">HCPCS</option> + <option value="k-1530">Animal natural history and life history</option> + <option value="k-1534">apollo-akesios</option> + <option value="k-1537">Brucellosis Ontology</option> + <option value="k-1538">Role Ontology</option> + <option value="k-1539">Neural-Immune Gene Ontology</option> + <option value="k-1540">Ontology for Drug Discovery Investigations</option> + <option value="k-1541">Cell line ontology</option> + <option value="k-1545">Wheat trait </option> + <option value="k-1547">BRENDA tissue / enzyme source</option> + <option value="k-1552">Reproductive traits ontology</option> + <option value="k-1553">ICD10CM</option> + <option value="k-1560">Cognitive Paradigm Ontology</option> + <option value="k-1423">RxNORM</option> + <option value="k-1517">Human developmental anatomy, abstract version, v2</option> + <option value="k-1016">Drosophila development</option> + <option value="k-1062">PRotein Ontology (PRO)</option> + <option value="k-1000">Mouse adult gross anatomy</option> + <option value="k-1065">Tick gross anatomy</option> + <option value="k-1123">Ontology for Biomedical Investigations</option> + <option value="k-1078">Spatial Ontology</option> + <option value="k-1007">Chemical entities of biological interest</option> + <option value="k-1049">C. elegans development</option> + <option value="k-1070">Gene Ontology</option> + <option value="k-1136">Experimental Factor Ontology</option> + <option value="k-1141">Ontology of Physics for Biology</option> + <option value="k-1005">BRENDA tissue / enzyme source</option> + <option value="k-1321">Neural ElectroMagnetic Ontologies</option> + <option value="k-1043">Physico-chemical process</option> + <option value="k-1064">Fly taxonomy</option> + <option value="k-1076">Ontology of Clinical Research (OCRe)</option> + <option value="k-1110">Teleost Anatomy Ontology</option> + <option value="k-1362">Hymenoptera Anatomy Ontology</option> + <option value="k-1030">Mosquito gross anatomy</option> + <option value="k-1029">Molecule role (INOH Protein name/family name ontology)</option> + <option value="k-1144">Dendritic cell</option> + <option value="k-1125">Human Phenotype Ontology</option> + <option value="k-1023">Biological imaging methods</option> + <option value="k-1021">Human developmental anatomy, abstract version</option> + <option value="k-1046">Systems Biology</option> + <option value="k-1051">Zebrafish anatomy and development</option> + <option value="k-1037">Cereal plant trait</option> + <option value="k-1107">Phenotypic quality</option> + <option value="k-1081">Teleost taxonomy</option> + <option value="k-1048">C. elegans gross anatomy</option> + <option value="k-1050">Maize gross anatomy</option> + <option value="k-1036">Plant environmental conditions</option> + <option value="k-1109">Sequence types and features</option> + <option value="k-1022">Human developmental anatomy, timed version</option> + <option value="k-1095">Xenopus anatomy and development</option> + <option value="k-1027">Medaka fish anatomy and development</option> + <option value="k-1011">Event (INOH pathway ontology)</option> + <option value="k-1010">Mouse gross anatomy and development</option> + <option value="k-1015">Drosophila gross anatomy</option> + <option value="k-1090">Amphibian gross anatomy</option> + <option value="k-1019">Fungal gross anatomy</option> + <option value="k-1067">C. elegans phenotype</option> + <option value="k-1069">Environment Ontology</option> + <option value="k-1112">Units of measurement</option> + <option value="k-1091">Spider Ontology</option> + <option value="k-1017">FlyBase Controlled Vocabulary</option> + <option value="k-1348">Online Mendelian Inheritance in Man</option> + <option value="k-1172">Vaccine Ontology</option> + <option value="k-1222">Ascomycete phenotype ontology</option> + <option value="k-1105">Mass spectrometry</option> + <option value="k-1237">Situation-Based Access Control</option> + <option value="k-1008">Dictyostelium discoideum anatomy</option> + <option value="k-1150">Rat Strain Ontology</option> + <option value="k-1101">International Classification of Diseases</option> + <option value="k-1314">Cell Line Ontology</option> + <option value="k-1009">Human disease</option> + <option value="k-1084">NIFSTD</option> + <option value="k-1025">Mammalian phenotype</option> + <option value="k-1035">Pathway ontology</option> + <option value="k-1012">Evidence codes</option> + <option value="k-1115">Yeast phenotypes</option> + <option value="k-1001">Cereal plant gross anatomy</option> + <option value="k-1006">Cell type</option> + <option value="k-1077">Mosquito insecticide resistance</option> + <option value="k-1085">Ontology of Glucose Metabolism Disorder</option> + <option value="k-1057">RadLex</option> + <option value="k-1031">Mouse pathology</option> + <option value="k-1032">NCI Thesaurus</option> + <option value="k-1381">NIF Dysfunction</option> + <option value="k-1401">International Classification for Nursing Practice</option> + <option value="k-1402">NIF Cell</option> + <option value="k-1404">Uber anatomy ontology</option> + <option value="k-1407">Terminology for the Description of Dynamics</option> + <option value="k-1411">International Classification of Functioning, Disability and Health (ICF)</option> + <option value="k-1413">Software Ontology</option> + <option value="k-1414">Ontology for General Medical Science</option> + <option value="k-1444">Chemical Information Ontology</option> + <option value="k-1461">Translational Medicine Ontology</option> + <option value="k-1488">SysMO-JERM</option> + <option value="k-1489">Adverse Event Ontology</option> + <option value="k-1498">EDAM</option> + <option value="k-1532">SemanticScience Integrated Ontology</option> + <option value="k-1550">PHARE</option> + <option value="k-1555">Vertebrate Anatomy Ontology</option> + <option value="k-1565">Ontology of Medically Related Social Entities</option> + <option value="k-1567">Pharmacovigilance Ontology</option> + <option value="k-1568">Anatomical Entity Ontology</option> + <option value="k-1569">Host Pathogen Interactions Ontology</option> + <option value="k-1570">Traditional Medicine Constitution Value Set</option> + <option value="k-1571">Traditional Medicine Other Factors Value Set</option> + <option value="k-1572">Traditional Medicine Signs and Symptoms Value Set</option> + <option value="k-1573">Traditional Medicine Meridian Value Sets</option> + <option value="k-1574">vertebrate Homologous Organ Groups</option> + <option value="k-1575">ExO</option> + <option value="k-1576">FDA Medical Devices (2010)</option> + <option value="k-1578">HOM_ElixhauserScores</option> + <option value="k-1580">Adverse Event Reporting ontology</option> + <option value="k-1581">HEALTH_INDICATORS</option> + <option value="k-1582">COA</option> + <option value="k-1583">Clinical Measurement Ontology</option> + <option value="k-1584">Measurement Method Ontology</option> + <option value="k-1585">Experimental Conditions Ontology</option> + <option value="k-1587">Plant Ontology</option> + <option value="k-1588">Ontology of General Purpose Datatypes</option> + <option value="k-1596">MajDxCatgrs-DxRltdGrps</option> + <option value="k-1613">Bone Dysplasia Ontology</option> + <option value="k-1614">IxnO</option> + <option value="k-1615">Systems Chemical Biology/Chemogenomics </option> + <option value="k-1616">Phylogenetic Ontology</option> + <option value="k-1621">Neuro Behavior Ontology</option> + </param> + <param name="semanticTypes" type="select" multiple="true" label="Indicates the list of semantic types to use in the annotation process"> + <option value="T-all" selected="true">ALL</option> + <option value="T000">UMLS concept</option> + <option value="T998">Jax Mouse/Human Gene dictionary concept</option> + <option value="T999">NCBO BioPortal concept</option> + <option value="T116">Amino Acid, Peptide, or Protein</option> + <option value="T121">Pharmacologic Substance</option> + <option value="T130">Indicator, Reagent, or Diagnostic Aid</option> + <option value="T119">Lipid</option> + <option value="T126">Enzyme</option> + <option value="T123">Biologically Active Substance</option> + <option value="T109">Organic Chemical</option> + <option value="T131">Hazardous or Poisonous Substance</option> + <option value="T110">Steroid</option> + <option value="T125">Hormone</option> + <option value="T114">Nucleic Acid, Nucleoside, or Nucleotide</option> + <option value="T111">Eicosanoid</option> + <option value="T118">Carbohydrate</option> + <option value="T124">Neuroreactive Substance or Biogenic Amine</option> + <option value="T127">Vitamin</option> + <option value="T195">Antibiotic</option> + <option value="T129">Immunologic Factor</option> + <option value="T024">Tissue</option> + <option value="T115">Organophosphorus Compound</option> + <option value="T073">Manufactured Object</option> + <option value="T081">Quantitative Concept</option> + <option value="T170">Intellectual Product</option> + <option value="T029">Body Location or Region</option> + <option value="T184">Sign or Symptom</option> + <option value="T033">Finding</option> + <option value="T037">Injury or Poisoning</option> + <option value="T191">Neoplastic Process</option> + <option value="T023">Body Part, Organ, or Organ Component</option> + <option value="T005">Virus</option> + <option value="T047">Disease or Syndrome</option> + <option value="T019">Congenital Abnormality</option> + <option value="T169">Functional Concept</option> + <option value="T190">Anatomical Abnormality</option> + <option value="T022">Body System</option> + <option value="T018">Embryonic Structure</option> + <option value="T101">Patient or Disabled Group</option> + <option value="T093">Health Care Related Organization</option> + <option value="T089">Regulation or Law</option> + <option value="T061">Therapeutic or Preventive Procedure</option> + <option value="T062">Research Activity</option> + <option value="T046">Pathologic Function</option> + <option value="T041">Mental Process</option> + <option value="T055">Individual Behavior</option> + <option value="T004">Fungus</option> + <option value="T060">Diagnostic Procedure</option> + <option value="T070">Natural Phenomenon or Process</option> + <option value="T197">Inorganic Chemical</option> + <option value="T057">Occupational Activity</option> + <option value="T083">Geographic Area</option> + <option value="T074">Medical Device</option> + <option value="T002">Plant</option> + <option value="T065">Educational Activity</option> + <option value="T092">Organization</option> + <option value="T009">Invertebrate</option> + <option value="T025">Cell</option> + <option value="T196">Element, Ion, or Isotope</option> + <option value="T067">Phenomenon or Process</option> + <option value="T080">Qualitative Concept</option> + <option value="T102">Group Attribute</option> + <option value="T098">Population Group</option> + <option value="T040">Organism Function</option> + <option value="T034">Laboratory or Test Result</option> + <option value="T201">Clinical Attribute</option> + <option value="T097">Professional or Occupational Group</option> + <option value="T064">Governmental or Regulatory Activity</option> + <option value="T054">Social Behavior</option> + <option value="T003">Alga</option> + <option value="T007">Bacterium</option> + <option value="T044">Molecular Function</option> + <option value="T053">Behavior</option> + <option value="T069">Environmental Effect of Humans</option> + <option value="T042">Organ or Tissue Function</option> + <option value="T103">Chemical</option> + <option value="T122">Biomedical or Dental Material</option> + <option value="T015">Mammal</option> + <option value="T020">Acquired Abnormality</option> + <option value="T030">Body Space or Junction</option> + <option value="T026">Cell Component</option> + <option value="T043">Cell Function</option> + <option value="T059">Laboratory Procedure</option> + <option value="T052">Activity</option> + <option value="T056">Daily or Recreational Activity</option> + <option value="T079">Temporal Concept</option> + <option value="T091">Biomedical Occupation or Discipline</option> + <option value="T192">Receptor</option> + <option value="T031">Body Substance</option> + <option value="T048">Mental or Behavioral Dysfunction</option> + <option value="T058">Health Care Activity</option> + <option value="T120">Chemical Viewed Functionally</option> + <option value="T100">Age Group</option> + <option value="T104">Chemical Viewed Structurally</option> + <option value="T171">Language</option> + <option value="T032">Organism Attribute</option> + <option value="T095">Self-help or Relief Organization</option> + <option value="T078">Idea or Concept</option> + <option value="T090">Occupation or Discipline</option> + <option value="T167">Substance</option> + <option value="T068">Human-caused Phenomenon or Process</option> + <option value="T168">Food</option> + <option value="T028">Gene or Genome</option> + <option value="T014">Reptile</option> + <option value="T050">Experimental Model of Disease</option> + <option value="T045">Genetic Function</option> + <option value="T011">Amphibian</option> + <option value="T013">Fish</option> + <option value="T094">Professional Society</option> + <option value="T087">Amino Acid Sequence</option> + <option value="T066">Machine Activity</option> + <option value="T185">Classification</option> + <option value="T006">Rickettsia or Chlamydia</option> + <option value="T049">Cell or Molecular Dysfunction</option> + <option value="T008">Animal</option> + <option value="T051">Event</option> + <option value="T038">Biologic Function</option> + <option value="T194">Archaeon</option> + <option value="T086">Nucleotide Sequence</option> + <option value="T039">Physiologic Function</option> + <option value="T012">Bird</option> + <option value="T063">Molecular Biology Research Technique</option> + <option value="T017">Anatomical Structure</option> + <option value="T082">Spatial Concept</option> + <option value="T088">Carbohydrate Sequence</option> + <option value="T099">Family Group</option> + <option value="T001">Organism</option> + <option value="T075">Research Device</option> + <option value="T096">Group</option> + <option value="T016">Human</option> + <option value="T072">Physical Object</option> + <option value="T071">Entity</option> + <option value="T200">Clinical Drug</option> + <option value="T085">Molecular Sequence</option> + <option value="T077">Conceptual Entity</option> + <option value="T010">Vertebrate</option> + <option value="T203">Drug Delivery Device</option> + <option value="T021">Fully Formed Anatomical Structure</option> + <option value="T204">Eukaryote</option> + </param> + <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"/> + <param name="mappingTypes" type="select" multiple="true" label="the list of mapping type to use during the mapping expansion step"> + <option value="m-all" selected="true">ALL</option> + <option value="m-null">None</option> + <option value="m-Automatic">Automatic</option> + <option value="m-Manual">Manual</option> + </param> + <param name="textToAnnotate" type="text" size="100" value="" label="Text to annotate"/> + <param name="format" type="select" label="File output format"> + <option value="xml" selected="true">XML</option> + <option value="text">Text</option> + <option value="tabDelimited">Tab Delimited</option> + </param> + <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="longestOnly"/> + <param name="wholeWordOnly"/> + <param name="filterNumber"/> + <param name="stopWords"/> + <param name="withDefaultStopWords"/> + <param name="isTopWordsCaseSensitive"/> + <param name="mintermSize"/> + <param name="scored"/> + <param name="withSynonyms"/> + <param name="ontologiesToExpand"/> + <param name="ontologiesToKeepInResult"/> + <param name="semanticTypes"/> + <param name="levelMax"/> + <param name="mappingTypes"/> + <param name="textToAnnotate"/> + <param name="format"/> + <param name="apikey"/> + </test> + </tests> + <help> + +**Usage** + Enter bioportal API key, a text to annotate and specify the parameters, and the annotations will be retrieved. + +**Contact** + + Please send any request or comment to jose.minyarro@um.es + +**More information** + + http://bioportal.bioontology.org + + </help> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ncbo_recommender.xml Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,286 @@ +<tool id="ncbo_recommender" name="Recommends a bio-ontology depending on annotations of a text" version="1.0.1"> + <description>Provides a bio-ontology as a recommendation depending on the annotations from a biological text</description> + <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_recommender_galaxy.jar $text $format $ontologyId $apikey > $output </command> + <inputs> + <param name="text" type="text" size="100" value="" label="Text to provide a recommendation of the most suitable bio-ontology"/> + <param name="format" type="select" label="File output format"> + <option value="xml" selected="true">XML</option> + <option value="text">Text</option> + <option value="simpleText">Simple Text</option> + </param> + <param name="ontologyId" type="select" multiple="true" label="Indicates the list of ontologies to search for the recommendation process"> + <option value="all" selected="true">ALL</option> + <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> + <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="text"/> + <param name="format"/> + <param name="ontologyId"/> + <param name="apikey"/> + </test> + </tests> + <help> + +**Usage** + Enter bioportal API key, a text, the output format and a list of bioontolgies Ids and the recommender retrieves the bioontology with the best annotations. + +**Contact** + + Please send any request or comment to jose.minyarro@um.es + +**More information** + + http://bioportal.bioontology.org + + </help> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ncbo_resourceIndex.xml Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,320 @@ +<tool id="ncbo_resourceIndex" name="Search for resources matched up with terms in bio-ontologies depending on the given text" version="1.0.1"> + <description>Search for resources matched up with terms in bio-ontologies depending on the given text</description> + <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_resourceIndex_galaxy.jar $query $ontologyids $resourceId $mode $elementDetails $format $apikey > $output</command> + <inputs> + <param name="query" type="text" size="100" value="" label="Text to search for terms in the selected bio-ontologys"/> + <param name="ontologyids" type="select" multiple="true" label="Indicates the list of ontologies to search for during the search process"> + <option value="all" selected="true">ALL</option> + <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> + <param name="resourceId" type="select" multiple="true" label="Indicates the list of resources Ids to search for during the Resource Index search process"> + <option value="all" selected="true">ALL</option> + <option value="PGGE">PharmGKB [Gene]</option> + <option value="BSM">Biositemaps</option> + <option value="CDD">Conserved Domain Database (CDD)</option> + <option value="CT">ClinicalTrials.gov</option> + <option value="GM">ARRS GoldMiner</option> + <option value="PC">Pathway Commons</option> + <option value="DBK">DrugBank</option> + <option value="AERS">Adverse Event Reporting System Data</option> + <option value="PM">PubMed</option> + <option value="MICAD">MICAD</option> + <option value="OMIM">Online Mendelian Inheritance in Man</option> + <option value="GAP">Database of Genotypes and Phenotypes</option> + <option value="PCM">PubChem</option> + <option value="PGDI">PharmGKB [Disease]</option> + <option value="WP">WikiPathways</option> + <option value="SMD">Stanford Microarray Database</option> + <option value="AE">ArrayExpress</option> + <option value="RXRD">ResearchCrossroads</option> + <option value="GEO">Gene Expression Omnibus DataSets</option> + <option value="REAC">Reactome</option> + <option value="UPKB">UniProt KB</option> + <option value="CANANO">caNanoLab</option> + <option value="PGDR">PharmGKB [Drug]</option> + </param> + <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 "> + <option value="unioin" selected="true">Union</option> + <option value="intersection">Intersection</option> + </param> + <param name="elementDetails" type="boolean" value="true" label="Tick the box whether the returned resource elements should be detailled or not"/> + <param name="format" type="select" label="Gets the results in a particular format"> + <option value="xml" selected="true">XML</option> + <option value="text">Text</option> + <option value="tabDelimited">Tab Delimited</option> + <option value="rdf">RDF</option> + <option value="owl">OWL</option> + </param> + <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> + </inputs> + <outputs> + <data format="text" name="output"/> + </outputs> + <tests> + <test> + <param name="query"/> + <param name="ontologyids"/> + <param name="resourceId"/> + <param name="apikey"/> + </test> + </tests> + <help> + +**Usage** + 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. + Example of search text: Melanoma + +**Contact** + + Please send any request or comment to jose.minyarro@um.es + +**More information** + + http://bioportal.bioontology.org + + </help> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ncbo_search.xml Mon Oct 08 14:25:04 2012 +0200 @@ -0,0 +1,281 @@ +<tool id="ncbo_search" name="Search for terms in bio-ontologies depending on the text provided" version="1.0.1"> + <description>Search for terms in bio-ontologies depending on the text provided</description> + <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_search_galaxy.jar $query $ontologyids $apikey > $output</command> + <inputs> + <param name="query" type="text" size="100" value="" label="Text to search for terms in the selected bio-ontologys"/> + <param name="ontologyids" type="select" multiple="true" label="Indicates the list of ontologies to search for during the search process"> + <option value="all" selected="true">ALL</option> + <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> + <param name="apikey" type="text" size="100" value="" label="BioPortal API key"/> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="query"/> + <param name="ontologyids"/> + <param name="apikey"/> + </test> + </tests> + <help> + +**Usage** + Enter bioportal API key, a text, and the list of bioontolgies Ids to search for and the search interface retrieves the bioontology terms associated with the text provided. + Example of search text: Breast cancer + +**Contact** + + Please send any request or comment to jose.minyarro@um.es + +**More information** + + http://bioportal.bioontology.org + + </help> + +</tool> \ No newline at end of file