Sunday, January 03, 2016

ELIXIR is setting up a Tools and Data Services Registry

ELIXIR is setting up a Tools and Data Services Registry. Recently, they organized a workshop in Amsterdam that I attended and where I learned how to add tools and services to their database. I played with the entry for WikiPathways, and one of the nice things is that it inherits from past European registry projects and allows the encoding if the input and output format, for tools and services alike. Here's what it gives for WikiPathways now:

The record editing facility is pretty straightforward and uses a number of tabs where you can add information.

A summary:

The publications:


Where documentation is found:

And information would is not really supplementary, such as the license terms:

Here, the collections are of particular interest. During the meeting, a few people from the Dutch Techcenter for Life Sciences decided to use a ELIXIR-NL group for all Dutch services that benefit the full ELIXIR network. Furthermore, the BIGCAT-UM collection was set up to indicate all services by our research group, which may eventually serve is a folder towards supporting the Dutch ZonMW Enabling Technologies Hotels calls.

Mind you, the registry can distinguish various services. The above entry is for the web interface, not for the web services. That entry in the registry is not that well populated yet, and that's for a reason. (Actually, more than one, one being that I did not create that entry and cannot change it).

But the WikiPathways Webservices are nicely exposed via a Swagger configuration file. Moreover, the registry supports JSON too, export and import. The format is pretty simply and we only need to create a Swagger 2.0 config file convertor. I just need to find a bit of time to finish my draft implementation.

Ison, J., Rapacki, K., Ménager, H., Kalaš, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G. D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Grüning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M. C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.-W., Licata, L., Mareuil, F., Mičetić, I., Friborg, R. M., Moretti, S., Morris, C., Möller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwämmle, V., Smith, C., Sperotto, M. M., Stockinger, H., Vařeková, R. S., Tosatto, S. C. E., de la Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Løngreen, P., Brunak, S., Jan. 2016. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research 44 (D1), D38-D47.