edgeexpress.fcgi
server launched on: Fri Apr 19 09:58:37 2024 Tokyo time
uptime 0 hours 0.000 mins
Invocation number 0 PID 1962924
host : fantom45
dburl : mysql://localhost:3306/eeDB_fantom4
| 0 features in cache | 0 edges in cache |
| 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. |
| 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. |
| cgi parameter | description |
| mode=feature_sources | returns XML of all available Feature sources. types= filter is available |
| mode=edge_sources | returns XML of all available Edge sources. types= filter is available |
| mode=experiments | returns XML of all available Experiments. types= filter is available |
| mode=peers | returns 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=feature | returns feature(s) with metadata in XML, gff2, gff3, or bed fomats format |
| mode=genemodel | returns feature(s) with metadata in eeDB xml format, if node has 'transcript' or 'promoter' edges coming in, then these are also exported |
| mode=edges | works only with single feature access, returns all incoming and outgoing edges to the node in XML |
| mode=express | returns 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. |