API Examples

Graphics

Gain/loss frequency chromosomal ideogram

http://progenetix.org/api?db=progenetix&collection=samples&api_out=ideogram&icdm_m=8144/3,8140/0

Gain/loss frequency histogram

http://arraymap.org/api/?db=arraymap&collection=samples&api_out=histogram&icdt_m=c18,c20&randno=100
histogram.png
Example histogram of cancer genome imbalances in 100 random colorectal carcinomas, directly generated from the API call shown
http://arraymap.org/api/?db=arraymap&collection=samples&api_out=histogram&icdm_m=0000&anysegmaxkb=10000&randno=1000&maxy=25&laby_m=0,7.5,15,22.5

Geographic map of publications

http://www.progenetix.org/api/?imgw=1024&api_out=pubmap&locscale=1&api_scope=publications&mapcaption=1

Data/Text

Called CNA segments from selected samples =api_out=segments=

http://progenetix.org/api/?db=progenetix&collection=samples&api_out=segments&text_m=metast&icdm_m=8500/3

Tab-delimited data table from selected samples =api_out=samples=

http://arraymap.org/api/?db=arraymap&api_out=samples&icdm_m=81&exportk_m=UID,DIAGNOSISTEXT,ICDMORPHOLOGY,ICDMORPHOLOGYCODE,ICDTOPOGRAPHY,ICDTOPOGRAPHYCODE,GRADE,TNM,DEATH,FOLLOWUP&randno=200

JSON data file from selected samples =api_out=samples&api_doctype=json=

http://progenetix.org/api/?db=progenetix&api_out=samples&api_doctype=json&icdm_m=817&randno=20

Sample count =api_out=count&api_doctype=json=

http://arraymap.org/api/?db=arraymap&api_out=count&genome=hg19&api_doctype=json&icdm_m=8,9&locus_m=17:7512444-7531593:-1
http://arraymap.org/api/?db=arraymap&api_out=count&genome=hg19&icdm_m=8,9&locus_m=17:7512444-7531593:-1

ICD morphology list =api_out=icdmlist&text_m=breast=

This example uses a text match to list all ICD morphologies having samples with a match in any annotation field.

http://arraymap.org/api/?project=progenetix&genome=hg18&db=progenetix&text_m=breast&api_out=icdmlist

Looking up all ICD morphologies with samples in colon or rectum (C189 and C20):

http://progenetix.org/api/?api_out=icdmlist&icdt_m=189,20&db=arraymap

Looking up all publications for sample numbers and geographic data:

http://progenetix.org/qmongo/?db=progenetix&collection=publications&all=multvalues&afqfield=PMID&querytext=...&exportk_m=PMID,NO_ACGH,NO_WES,NO_WGS,CITY,COUNTRY&sortby=COUNTRY&counter=y

Michael, 2018-07-20