Application

Search for herbs associated with a disease

Provide a new search tool allowing one to search for herb information for a given disease (such as Alzheimer or Parkinson). This tool returns:

• herbs associated with the input disease, as reported by TCMGeneDIT. The returned results are ordered by the statistics confidence of the association. Only herbs with higher than 95% association confidence are returned.

The link to each herb brings one to the information page about this herb, which assembles information about:

• descriptions about this herb from DBpedia
• putative effects of this herb from TCMGeneDIT
• clinical trials relating to this herb from LinkedCT
• genes associated with this herb reported in TCMGeneDIT and other diseases reported with these genes from Diseasome

Search for aTags of a herb

Provided another new search tool that allows one to search for aTags for a given herb: http://www.open-biomed.org.uk/admed/admedapps/searchForAtags. These aTags provide additional knowledge about a query herb, retrieved from aTags for TCM

Example SPARQL queries for challenging questions

TCM genes associated with a disease

PREFIX tcm: <http://purl.org/net/tcm/tcm.lifescience.ntu.edu.tw/>
SELECT DISTINCT ?gene ?genename ?externalgene
WHERE {
?disease rdfs:label ?diseasename . filter regex(?diseasename, "^Alzheimer", "i") .
?association tcm:contextAssociation ?disease ; 
             tcm:contextAssociation ?herb ; 
             tcm:contextAssociation ?gene .
?gene rdf:type tcm:Gene ; rdfs:label ?genename .
optional {?externalgene owl:sameAs ?gene } .
}limit 300 

Search for diseases associated with TCM genes from Diseasome

PREFIX dis: <http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/> 
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

SELECT DISTINCT ?gene ?disease ?diseasename ?superdisease ?supername ?subdisease ?subname WHERE { 
{
 {
    ?gene rdf:type dis:genes . 
    filter regex(str(?gene), "http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/APP").
    ?disease dis:associatedGene ?gene .
 }
 union 
 {
    ?gene rdf:type dis:genes . 
    filter regex(str(?gene), "http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/TTR").
    ?disease dis:associatedGene ?gene .
 }
 union 
 {
    ?gene rdf:type dis:genes . 
    filter regex(str(?gene), "http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/ACHE").
    ?disease dis:associatedGene ?gene .
 }
 union 
 {
    ?gene rdf:type dis:genes . 
    filter regex(str(?gene), "http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/APOE").
    ?disease dis:associatedGene ?gene .
 }
}
{
    ?disease dis:name ?diseasename . 
    optional {?disease dis:diseaseSubtypeOf ?superdisease .?superdisease dis:name ?supername .}
    optional {?subdisease dis:diseaseSubtypeOf ?disease . ?subdisease dis:name ?subname .}
}
}

Search for side-effects of TCM herbs

TCM -----------> DailyMed (via ingredient) DailyMed ------> SIDER (via drug)

Search for ingredients of TCM herbs

PREFIX tcm:      <http://purl.org/net/tcm/tcm.lifescience.ntu.edu.tw/>
select distinct ?ingredient ?dailymedIngredient
where { 
<http://purl.org/net/tcm/tcm.lifescience.ntu.edu.tw/id/medicine/Ginkgo_biloba>      tcm:ingredient ?ingredient . 
?dailymedIngredient owl:sameAs ?ingredient .

Search for drugs from Dailymed

PREFIX dailymed:  <http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select distinct ?drug ?drugname
where {     
    ?drug dailymed:activeIngredient <http://www4.wiwiss.fu-berlin.de/dailymed/resource/ingredient/Histidine> ;
         dailymed:name ?drugname ; dailymed:representedOrganization ?organization .
}

Search for side effects of drugs from SIDER

PREFIX sider:      <http://www4.wiwiss.fu-berlin.de/sider/resource/sider/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select distinct ?effect ?effectname
where {
    ?drug rdfs:label ?drugname . filter regex(?drugname, "folic acid", "i")  .
    ?drug sider:sideEffect ?effect .
   ?effect rdfs:label ?effectname .
}LIMIT 100 

Data Source

• A third release of the RDF TCM dataset was released and available at Open-BiomMed
• A set of linksets linking the TCM datasets with other drug datasets available as RDF are also produced. These linksets include;
• gene name URI mappings from TCM to Entrez Gene, DBpedia, Diseasome, and Drugbank. The first set of mapping was produced by SPARQL queries to the Entrez gene SPARQL endpoint at DERI (http;//hcls.deri.org:8080/sparql) and the others were automatically generated using Silk by Anja Jentzsch.
• disease URI mappings from tCM to DBpedia, Diseasome, and Sider, generated using Silk by Anja.
• drug name URI mappings from TCM to Drugbank, generated using Silk by Anja.
• herb name URI mappings from TCM to DBpedia, generated using Silk by Anja.
• Ingredient name URI mappings from TCM to Dailymed, generated using Silk by Anja.

Data Service

All the above datasets will be available as RDF dump once the mapping generation is completed. Currently, these datasets are accessible through a SPARQL endpoint at http://www.open-biomed.org.uk/sparql/