RESTful API usage for the NER service of miDatabase

Description

  • RESTful API URL: http://midb.quarkbiosciences.com:8080/rest4ner/[TypeOfConcept]/[Format]
  • [TypeOfConcept]:
    Concept to be identified Argument
    miRNA mirna
    Gene gene
    Expression expression
    Genetic genetic
    Pathologic status pathologicstatus
    Cohort cohort
    Ethnicity ethnicity
    Application application
    Sample type sampletype
    Drug drug
    Experimental design experimentaldesign
    Cancer cancer
    Non-Cancer noncancer
    Screening method/materials screeningmethod
    Validation validation
    Kit kit
    Statistics statistics
    Sample volume samplevolume
    ps. Multiple concepts are allowed and separated by a comma.
  • [Format]:
    text: returns tab-separated values of the type of the concept, the text of the concept, the position of the beginning of a concept, and the position of the end of the concept.
    json: returns JSON-formatted data of the type of the concept, the text of the concept, the position of the beginning of a concept, and the position of the end of the concept.
  • Data POSTing to the service: a JSON-formatted string with a key named "text" and the value of text to be processed.
    Example: {"text": "A kinetic model identifies phosphorylated estrogen receptor-a (ERa) as a critical regulator of ERa dynamics in breast cancer."}

Command-line usage

  • Submit a query for identifying miRNAs and returning a plain text result.

    $ curl -H "Content-Type: application/json" -d '{"text": "The three corresponding miRNAs (miR-205, miR-21, and miR-203) are all overexpressed in breast cancers."}' http://midb.quarkbiosciences.com:8080/rest4ner/mirna/text

    Result: mirna miR-205 32 39
    mirna miR-21 41 47 
    mirna miR-203 53 60

  • Submit a query for identifying Genes and returning a JSON-formatted result.

    $ curl -H "Content-Type: application/json" -d '{"text": "Emerling et al based their study on frequent co-occurrences of TP53 mutation and PIP4K2B gain in breast cancer."}' http://midb.quarkbiosciences.com:8080/rest4ner/gene/json

    Result: {"entities":[{"node":"TP53","concept":"gene","end":67,"begin":63},{"node":"PIP4K2B","concept":"gene","end":88,"begin":81}]}

  • Submit a query for identifying miRNAs, Genes, and Sample type and returning a plain text result.

    $ curl -H "Content-Type: application/json" -d '{"text": "We showed that PTEN and PDCD4 were repressed by miR-21 in genotoxic drug-treated breast cancer cells, which may contribute to decreased apoptosis and enhanced invasion."}' http://midb.quarkbiosciences.com:8080/rest4ner/mirna,gene,sampletype/text

    Result: mirna miR-21 48 54
    gene PDCD4 24 29
    gene PTEN 15 19
    sampletype breast cancer cells 81 100