ps. Multiple concepts are allowed and separated by a comma.
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
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.
Example: {"text": "A kinetic model identifies phosphorylated estrogen receptor-a (ERa) as a critical regulator of ERa dynamics in breast cancer."}
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