[OTDev] OpenTox API extensions, documentation

Barry Hardy barry.hardy at douglasconnect.com
Wed Sep 1 09:07:51 CEST 2010


  Dear All:
- OpenTox API Development
Proposals for updated version 1.2 of the OpenTox API should be submitted 
in coming days for discussion and potential incorporation into the next 
OpenTox API specification (to be completed this month)
Draft pages are located at http://www.opentox.org/dev/apis/api-1.2 and 
require a login to the website to access and edit.

- API & Developer Documentation
Roman (cc'ed here)  is currently working on documenting "getting 
started" guidance for new service developers, which we should be 
starting to release on the OT web site this month. If you have run into 
an issue or solved it :), please let us know so it can be included.

Rajarshi has reviewed the current API documentation
http://www.opentox.org/dev/apis/api-1.1
and provides the following feedback:

Overall well documented API. The most obvious thing that jumps out is 
that there aren't examples for all URIs. Even simple URL's (for GET) or 
curl invocations (for POST) would be useful, if nothing else to look at 
the return values. (I see that some API pages such as the models page, 
have example URI's, but more would be nicer)

The inclusion of examples would be helpful, when explaining some of the 
specific REST services. For example, in the chemical compound service, 
the "Get the representation of a compound", it's not clear from the API 
docs how feature_uris[] should be specified. Where can I find a list of 
feature URI's? And will all feature URI's specified somewhere be 
available for any OpenTox service that provides this API?

Similarly, when I search for compounds, examples of what the search 
parameter could be would be useful. Similarly for the "sameas" parameter.

This becomes more useful for the Feature service - while I can 
understand what URL's to use to interact with the service I have no idea 
of what values I should be using for the parameters. Given that most of 
these services take RDF input, examples would be very useful, for a user 
who is not too familiar with RDF

In the Conformers section of the compound services, does this refer to 
pre-calculated conformers? What would happen if I call 
"compound/{id1}/conformer/" and there are no conformers available? Will 
it return the structure itself? Will it generate a set of conformers? 
Under what conditions will a 404 and 503 be returned?

@Developers - message is clear, we need to provide more concrete 
examples, linked but not scrambled with specs.

Thanks for your contribution Rajarshi!

Barry



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