Fast CGI object server (perl)

edgeexpress.fcgi

server launched on: Wed Oct 29 21:33:02 2014 Tokyo time
uptime 28 hours 5.939 mins
Invocation number 27 PID 17361
host : fantom45.gsc.riken.jp
dburl : mysql://fantom40.gsc.riken.jp:3306/eeDB_fantom4


3001 features in cache5169 edges in cache

Object access methods

cgi parameter description
id=[number]directly access a 'feature' by it's internal id. useful for linking between subsystems
eid=[number]directly access an 'edge' by it's internal id. useful for linking between subsystems
entrezID=[number]directly access an Entrez Gene feature using the unique entrezID
name=[string]does search on feature's primary name, returns first occurance. since primary name is not required to be unique in database, this method is only useful for debugging and is not guaranteed to be rebust or reproducible for data modes.
search=[name]does a metadata search for all matching features and returns compact list in XML
types=[source,source,...]used in combination with name=, search=, and loc= access methods to restrict search. Both single or multiple type lists are available.

Output formats

cgi parameter description
format=[xml,gff2,gff3,bed,tsv]changes the output format of the result. XML is an EdgeExpress defined XML format, while GFF2, GFF3, and BED are common formats. XML is supported in all access modes, but GFF2, GFF3, and BED are only available in direct feauture access modes. TSV (tab-separated-values) is only available in a few modes. Default format is XML.

Output modes

cgi parameter description
mode=feature_sourcesreturns XML of all available Feature sources. types= filter is available
mode=edge_sourcesreturns XML of all available Edge sources. types= filter is available
mode=experimentsreturns XML of all available Experiments. types= filter is available
mode=peersreturns XML of all connected peers in the peer-peer database federation
mode=fantom4[default] returns center feature with FANTOM4 edge information. XML format only.
mode=featurereturns feature(s) with metadata in XML, gff2, gff3, or bed fomats format
mode=genemodelreturns feature(s) with metadata in eeDB xml format, if node has 'transcript' or 'promoter' edges coming in, then these are also exported
mode=edgesworks only with single feature access, returns all incoming and outgoing edges to the node in XML
mode=expressreturns feature/expression data in either XML or TSV formats. Works either with 'probe' features or other features linked by single edge to a 'probe' feature.