# HG changeset patch # User Mikel Egaña Aranguren # Date 1326881171 -3600 # Node ID fc4c8a9b3152202a72e06e020e7a4e979a5c63ff # Parent d3d6bdbcf3eadc2c969a405b6ca8692a183a194b# Parent 9dffd23fefcca24b9b786323cb76f1e91e4f9126 branch merge diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_annotator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/ncbo_annotator.xml Wed Jan 18 11:06:11 2012 +0100 @@ -0,0 +1,704 @@ + + Annotates biological texts with the terms of the bio-ontologies from BioPortal + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 + + + + \ No newline at end of file diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_annotator_galaxy.jar Binary file NCBO_services/ncbo_annotator_galaxy.jar has changed diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_recommender.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/ncbo_recommender.xml Wed Jan 18 11:06:11 2012 +0100 @@ -0,0 +1,286 @@ + + Provides a bio-ontology as a recommendation depending on the annotations from a biological text + java -jar ${__tool_data_path__}/shared/jars/ncbo_recommender_galaxy.jar $text $format $ontologyId $apikey > $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 + + + + \ No newline at end of file diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_recommender_galaxy.jar Binary file NCBO_services/ncbo_recommender_galaxy.jar has changed diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_resourceIndex.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/ncbo_resourceIndex.xml Wed Jan 18 11:06:11 2012 +0100 @@ -0,0 +1,320 @@ + + Search for resources matched up with terms in bio-ontologies depending on the given text + java -jar ${__tool_data_path__}/shared/jars/ncbo_resourceIndex_galaxy.jar $query $ontologyids $resourceId $mode $elementDetails $format $apikey > $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 + + + + \ No newline at end of file diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_resourceIndex_galaxy.jar Binary file NCBO_services/ncbo_resourceIndex_galaxy.jar has changed diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_search.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/ncbo_search.xml Wed Jan 18 11:06:11 2012 +0100 @@ -0,0 +1,281 @@ + + Search for terms in bio-ontologies depending on the text provided + java -jar ${__tool_data_path__}/shared/jars/ncbo_search_galaxy.jar $query $ontologyids $apikey > $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 + + + + \ No newline at end of file diff -r d3d6bdbcf3ea -r fc4c8a9b3152 NCBO_services/ncbo_search_galaxy.jar Binary file NCBO_services/ncbo_search_galaxy.jar has changed