Wednesday, February 06, 2008

Simple, Open Bug Track System: social bookmarking

Jim replied to the request by Anthony in my blog for a bug track system for CrystalEye (in beta), after a discussion on the CIF processing pipeline (see here, here, here and here).

Instead of setting up a BTS at SourceForge, locally with Buzilla, or at LaunchPad, he suggested to use Connotea:
    To report a problem in CrystalEye, simply bookmark an example of the problem with the tag “crystaleyeproblem”, using the Description field to describe the problem. All the problems will appear on the tag feed.

    When we fix the problem we’ll add the tag “crystaleyefixed” to the same bookmark. If you subscribe to this feed, you’ll know to remove the crystaleyeproblem tag.

    In the fullness of time, we’re planning to use connotea tags to annotate structures where full processing hasn’t been possible (uncalculatable bond orders, charges etc).
Now, Connotea is advertised as a [f]ree online reference management for all researchers, clinicians and scientists, and I have never really been happy with any HTML page ending up in the system, I would counter the suggestion by using social bookmarking websites for any HTML page (not just publications), such as (see their list of CrystalEye bookmarks).

Anyway, it does not really matter, and Connotea has an open API to query the database. This will allow Jim to write a simple userscript to enhance each CrystalEye page with a list of bug reports. That will allow every CrystalEye visitor to see what others are commenting on it. In that respect, many other things can be envisioned... Getting comments on the paper behind the crystal structure from Chemical blogspace and Postgenomic, ...


  1. I did consider - it does currently have better functionality for this than Connotea. For example, we could use for: tags to target alerts when we'd fixed problems.

    The main reason for using Connotea is that the automatic tagging we want to do is against the terms of service. We've spoken to the relevant person at Connotea (Ian Mulvany) and have permission to start automatically tagging (as long as we warn him and limit the scale initially!).

    I take your point about the scope of Connotea; I suppose in that respect it would be ideal to have a special service for data checking. There's a tension, though between having a separate service for data checking, and needing yet another bookmarklet in your browser.

    We're looking forward to mashing all this data back in to CrystalEye too!

  2. Don't worry about it. Connotea uses a special DC:IDENTIFIER tag when it can get a doi or pmid id. That was how I got Connotea to spit out this stuff: