Consider the following entries:
shared name name GeneID HEKScore JurkatScore protein Name Gene Symbol Gene Synonyms
O15258 O15258 11079 0.0 0.753 RER1_HUMAN Protein RER1 RER1 -
28872818 28872818 0.989 0.967 NP_057857 NefFull_HIV-1 - -
NEF NEF
The first row is a Uniprot ID, the second is a GI number, and the third is just a label. So I figured for illustrative purposes (since I can't map from GI to Uniprot) I would map from Uniprot to a new gene symbol column. If I use the web service (http://webservice.bridgedb.org/Human/attributes/S/O15258?attributeName=Symbol), I get:
Description Protein RER1
Synonyms O95322
Symbol RER1_HUMAN
Type Uniprot/SWISSPROT
OK, good. If I use the BridgeDB app, it tells me that no IDs were mapped. I also see lots of errors in the console:
org.bridgedb.IDMapperException: java.io.IOException: HTTP response: 404 - The server has not found anything matching the request URI
at org.bridgedb.webservice.bridgerest.BridgeRest.getAttributes(BridgeRest.java:466)
at org.bridgedb.IDMapperStack.getAttributes(IDMapperStack.java:338)
at org.bridgedb.cytoscape.internal.util.IDMapperWrapper.mapID(IDMapperWrapper.java:155)
at org.bridgedb.cytoscape.internal.AttributeBasedIDMappingImpl.map(AttributeBasedIDMappingImpl.java:111)
at org.bridgedb.cytoscape.internal.task.AttributeBasedIDMappingTask.run(AttributeBasedIDMappingTask.java:109)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Caused by: java.io.IOException: HTTP response: 404 - The server has not found anything matching the request URI
at org.bridgedb.webservice.bridgerest.BridgeRest$UrlBuilder.openReader(BridgeRest.java:273)
at org.bridgedb.webservice.bridgerest.BridgeRest$UrlBuilder.access$200(BridgeRest.java:197)
at org.bridgedb.webservice.bridgerest.BridgeRest.getAttributes(BridgeRest.java:454)
... 11 more
I assume that a lot of those are because of the non-matchable attributes (label and GI#), but it looks to me like every entry is getting that error. Any ideas?