Tip of the Week: BioCatalogue for finding web services
A couple of years back at a conference I was introduced to BioCatalogue. It seemed to me to be a really useful idea: locate bioinformatics tools and databases that are web-accessible, and that also have a mechanism to use the web service features to access the tool/server using strategies that don’t require the main web interface of the site. There are some introductions to the concept of web services out there–some of them are more for introduction, but most are aimed at programmers. Essentially it is kind of a back door into the tool, and lets you pull the information you need out in ways that you want–not constrained by the main user interface.
BioCatalogue is a curated collection of these web services. The creators of BioCatalogue provide the framework and perform some of the collection and annotation–but they also enable the user community to bring in web services and annotate them as well. This means that you can use BioCatalogue to find and learn more about the services, and you can feed back into the system as well if you join the community. If you are a software provider you can register your service there–so more people can locate you and learn about your project. Another really nice aspect of BioCatalogue is that they monitor the services. As we know at OpenHelix–plenty of times a tool you have accessed in the past is suddenly unavailable. Sometimes they are intermittent server problems, but sometimes they are longer-term issues. BioCatalogue is regularly checking the status of the tools so you can have confidence that the tool has been up and seems stable.
The Web Server issue (see the 2009 issue here) of Nucleic Acids Research provides a wealth of information about useful servers with bioinformatics tools. And there’s a paper for the 2010 Server issue about BioCatalogue that will offer more details on the background (linked below). In this week’s movie I can only briefly introduce the site and the features available. Check out the paper from the BioCatalogue team, and explore the documentation wiki to learn more about the features and functions that are provided.
Now, these web services are not for everyone. For many people the main user interface will still be the best mechanism to access a tool. But if you need more advanced or customized queries, or if you want to create inflows into your own tools, or if you want to use some of the cool work flow software that’s out there now (such as Galaxy or Taverna)–web services may be right for you.
Check out BioCatalogue (and remember the -ue spelling!) http://www.biocatalogue.org/
Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S., Lopez, R., & Goble, C. (2010). BioCatalogue: a universal catalogue of web services for the life sciences Nucleic Acids Research DOI: 10.1093/nar/gkq394