Retrieve literature associated to a variant

http://candy.hesge.ch/Variomes/api/rankLit.jsp

Parameters

Parameter nameDescriptionExampleDefault value
genvarsOne or several genes and mutationsBRAF (V600E)
BRAF (V600E) AND BRAF (V600K)
BRCA1 (C61G) OR BRCA1 (M18V)
no default valueMandatory
diseaseAny disease termUveal melanomano default valueOptional
genderThe gender of the patientmale or femalenoneOptional
ageThe age of the patient (in year)25noneOptional
minDateLimit the search to publications published from the indicated year (included)19801900Optional
maxDateLimit the search to publications published until the indicated year (included)20102021Optional
collectionCollection to search inmedline,pmc (separated by a comma)medline,pmcOptional
ctRetrieval of clinical trials*true or falsefalseOptional
mustDiseaseIndicate if the disease must be mentioned in the publicationtrue or falsetrueOptional
mustGeneIndicate if the gene must be mentioned in the publicationtrue or falsetrueOptional
mustVariantIndicate if the variant must be mentioned in the publicationtrue or falsetrueOptional
keywordsPositiveA list of terms that should be mentioned in the publicationsurviv;treat (separated by semi-colons)Optional
keywordsNegativeA list of terms that should not be mentioned in the publicationsequencing;immuno;detect (separated by semi-colons)Optional

* If you want to retrieve only clinical trials, use the API http://candy.hesge.ch/CT/CTSVIP/rankCT.js described below.

Examples

http://candy.hesge.ch/Variomes/api/rankLit.jsp?genvars=CDK4 (amplification)

http://candy.hesge.ch/Variomes/api/rankLit.jsp?genvars=EGFR (L858R)&disease=melanoma

http://candy.hesge.ch/Variomes/api/rankLit.jsp?genvars=EGFR (L858R)&gender=male&age=14&minDate=1990&ct=true

http://candy.hesge.ch/Variomes/api/rankLit.jsp?genvars=EGFR (L858R)&disease=adenocarcinoma&collection=medline,pmc

http://candy.hesge.ch/Variomes/api/rankLit.jsp?genvars=BRCA1 (C61G) OR NRAS (Q61R)&collection=pmc&ct=true&minDate=2010

http://candy.hesge.ch/Variomes/api/rankLit.jsp?genvars=BRAF(V600E AND BRAF(V600K)&gender=female&age=12&disease=melanoma&mustDisease=false

Retrieve detailed information about a publication

http://candy.hesge.ch/Variomes/api/fetchLit.jsp

Parameters

Parameter nameDescriptionExampleDefault value
idsAny list of publications identifier (medline or pmc)27145535;31647501no default valueMandatory
genvarsOne or several genes and mutationsBRAF (V600E)
BRAF (V600E) AND BRAF (V600K)
BRCA1 (C61G) OR BRCA1 (M18V)
no default valueMandatory
diseaseAny disease termsUveal melanomano default valueOptional
genderThe gender of the patientmale or femalenoneOptional
ageThe age of the patient (in year)25noneOptional

Examples

http://candy.hesge.ch/Variomes/api/fetchLit.jsp?ids=27145535;31671409

http://candy.hesge.ch/Variomes/api/fetchLit.jsp?ids=27145535;31671409&genvars=NRAS (Q61R)

http://candy.hesge.ch/Variomes/api/fetchLit.jsp?ids=27145535;31671409;31647501&genvars=NRAS (Q61R)&disease=Juvenile%20Myelomonocytic%20Leukemia&age=2&gender=male

Retrieve detailed information about a clinical trial associated or not to a variant

http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp

Parameters

Parameter nameDescriptionExampleDefault value
genvarsOne or several genes and mutationsBRAF (V600E)
NX_P15056(V600E)
BRAF (V600E) AND BRAF (V600K)
BRCA1 (C61G) OR BRCA1 (M18V))
no default valueMandatory
diseaseCode or name included in the NCI Thesaurus terminologyC3224
tatata
no default valueOptional
genderThe gender of the patientmale or femalenoneOptional
ageThe age of the patient (in year)25noneOptional
mustVIndicates if the variant must be mentioned in the clinical trialtrue or falsetrueOptional

Examples

http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp?genvars=BRAF(V600K)

http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp?genvars=BRAF(V600K)%20OR%20BRAF(V600E)

http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp?genvars=BRAF(V600K)%20AND%20BRAF(V600E)&gender=Male

http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp?genvars=BRAF(V600E)%20AND%20BRAF(V600K)%20&gender=Female%20&age=20

http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp?genvars=BRAF(V600E)%20&gender=Female%20&age=20%20&disease=C4035%20&mustV=true

http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp?genvars=BRAF(V600E)%20AND%20BRAF(V600K)%20&gender=Female%20&age=12%20&disease=melanoma%20&mustV=true

SIBiLS (Swiss Institute of Bioinformatics Literature Services)

Fetch APIs and search APIs of SIBiLS are described on this page:

http://candy.hesge.ch/SIBiLS/

Retrieve synonyms for variant

The synvar service is described on this page:

http://goldorak.hesge.ch/synvar/resources/info.html