The simplest way to get started with FuncNet is to submit a job via the web interface. You will need a text file containing a list of human proteins, represented by UniProt primary accessions, one per line. You can also either supply a second list of reference proteins involved in the system you are investigating, or you can choose a GO term to provide reference proteins automatically.
For an explanation of how the scores are calculated in the Results screen of the web interface, see this post.
Advanced usage
The entire FuncNet pipeline is based around web services using the SOAP protocol. It is optimized for automated bulk querying from any scripts or programs supporting SOAP (‘SOAP clients’) so it can be easily integrated into your data analysis workflow.
FuncNet queries can be submitted from any SOAP client which supports the ‘document/literal wrapped’ style. All modern SOAP toolkits support this model. The interface is intentionally very simple, so databinding (mapping between XML messages and in-memory objects) shouldn’t be a problem, regardless of what programming language you use, and of course you can ‘roll your own’ XML if you prefer.
We’ve provided some libraries and scripts to help get you started, so you don’t have to develop a client from scratch, and will be adding more examples in different languages over time. Feel free to send us your own in any language.
We also provide a simple interactive web interface where you can submit new jobs, check on their progress, and retrieve the results when you’re done, although you will get better performance and more flexibility if you use the web services directly.
In addition, FuncNet now supports the EnCORE protocol developed for the ENFIN network. Details of this method are available here. You can submit FuncNet jobs via the EnVision 2 interface at the EBI.
If you want to try out the FuncNet web services directly without even seeing any code, download soapUI. This is a very handy Java tool for testing web services. Choose ‘New WSDL Project’ from the File menu, paste in the URL of a FuncNet WSDL, and it’ll generate the appropriate request templates for you. Then you can insert some UniProt primary accessions in the <p> fields (see examples), fill in any other details required, submit the query by pressing the green ‘play’ button, and wait for a response.
If you’re querying a predictor directly, it all happens sychronously, that is, soapUI will wait for the results to come directly from the predictor. If you send a request to the entire pipeline, via the SubmitTwoProteinSets operation of the front-end service, a job ID will be returned immediately. You can use this to monitor your job’s status, cancel it, or — when ready — retrieve its results, using the other methods. This mode of operation is known as asynchronous.
See the example queries page for more detailed information on message formats and how to interpret the responses. Remember to check the status page for up-to-date information on availability, performance, maintenance issues etc.
NB FuncNet only understands UniProt primary accessions, and is currently limited to human proteins. Some predictors will reject requests with less than three proteins in each set.
If you have a list of identifiers in another format, you can convert them to UniProt accessions via UniProt’s ID mapping service.
