Web Services Wish List

Mar 26, 2013 at 4:43 AM
.NET Bio cannot be all things to all people, but it is designed to be extensible and to incorporate lots of additional capability via web services. So, given that I have a student who is dead keen to write lots of C#, what are the services that we don't already have that we really should have? From a good face to face discussion with Nigel, one really good candidate is some sort of hook into the pubmed literature search facility. Nice idea indeed. Any others that come to mind?
Mar 26, 2013 at 4:48 AM
See for example: http://www.ncbi.nlm.nih.gov/books/NBK25500/ which describes some of the e-utility calls.
Mar 28, 2013 at 4:53 PM

Was great meeting with you last week and I have a longer email about all of that which I am hoping to put together once time allows! Just wanted to quickly chime in on this as well though. I have been working a bit with Entrez this week, and I was using the Biopython libraries to access it. For the e-utils, they are a bit annoying as you can upload a query, and you get a ton of XML back. In biopython, they convert this XML into a bunch of dictionaries and key/value pairs (key being the name of the xml node, value being the node itself). This has the typical problems/annoyances of dynamic typing, but I am not sure how often they change the XML schema so it might be a reasonable approach.

In addition to grabbing data as an xml file from a url web request, NCBI also seems to support SOAP: http://www.ncbi.nlm.nih.gov/books/NBK55693/ which is pretty nice because it plays well with the VS add service reference, and then everything is returned as a statically typed object with appropriate fields. I haven't investigated it much, and am not sure how robust that would be to changes they make, but treating NCBI as a SOAP/web-service or a simple URL might be an early design decision to make.