Posted by lwalley on November 13, 2009 at 12:32pm
Drupal's modular framework makes it an ideal candidate for collaborative development. Is there enough interest from developers in biodiversity informatics to build a set of common extensible base content types which comply to the TDWG standards? What level of compatibility can we achieve with EDIT's CDM framework, whilst still benefiting from Drupal contributed modules?
Comments
Thanks Lisa, Some building
Thanks Lisa,
Some building blocks:
Literature - Pretty much covered by http://drupal.org/project/biblio with modifications
Specimens - Scratchpads darwincore a start http://home.scratchpads.eu/node/17
Names - Lifedesk / Scratchpads classification module (link?)
RDF drupal modules (http://drupal.org/project/rdf, http://drupal.org/project/rdfcck)
Science Collaboration Framework - http://sciencecollaboration.org/
But I think we need to start a Wiki page in this group to cover these kind of links
Wiki page of resources
Cheers Kehan, I started a wiki page of project listings with links to any module downloads here: http://groups.drupal.org/node/30444 but a new page with module reviews for different aspects of biodiversity informatics would be good. I started one up: http://groups.drupal.org/node/38098
The cdm_dataportal module
The cdm_dataportal module is a set of Drupal modules which mostly cover the requirements pointed out by you Lisa.
The cdm_dataportal module allows publishing data from a CDM Server directly to the web. A CDM Server exposes the data stored in the CDM Store the data model Common Data Model covers all areas of information which are important for taxonomy: Names, taxa, synonyms, specimens, collections, descriptions, distribution, media, ...
Since the underlying Common Data Model (CDM) is based on standards like SDD, TCS, ABCD and other TDWG schema it is possible to import and export data completely without or with only a very limited loss of data or data granularity.
One of the aims of the CDM DataPortal module is to allow integration/coupling with other Drupal modules. For example it should be possible to use the comments module to allow users to comment a taxon or a media item. Since CDM objects are not stored in the data base which is used by Drupal some linkage between CDM objects and Drupal nodes has to be established. In order to accomplish this, for each CDM item an according Drupal node would have to be created which then links to the according CDM object. Although implementing this is not a big task, this feature unfortunately is not jet available.
Further To-Do’s are: The modules are only available for Drupal 5 by now. Currently it is only a publishing tool, so there is no form based editor to add, update, delete entities in the CDM Store and no import function for data is available. Well, for all these tasks we have created the Taxonomic Editor.
Despite of these current limitations I believe that the cdm_dataportal module is a promising candidate for using Drupal and many of its contributed modules as a biodiversity informatics framework. So the to answer Lisa’s question "What level of compatibility can we achieve with EDIT's CDM framework, whilst still benefiting from Drupal contributed modules?" is the following: If the cdm_dataportal module would be used as the core of a whole set of biodiversity related modules to create something like a "BioDrupal", this system would not only be fully compatible with the CDM 'framework' it would also benefit from all this functionality already implemented in the CDM Library.
Taking Drupal offline? Or bringing Taxonomic Editor online?
Andreas, once CDM is mapped to Drupal nodes are there any plans to allow editing of nodes and thus synchronisation between 'BioDrupal' and the Taxonomic Editor? Essentially what I believe is ultimately needed is a Web enabled desktop application, ideally a single package to handle multiple data types e.g. and dare I say it, a Microsoft Office for biodiversity informatics. Drupal offers many benefits in terms of extensibility, and the nature of our distributed funding and consequently our distributed development efforts lends itself to this.
There are opportunities with the likes of Google Gears, Firefox support for offline apps and of course Adobe Air to really make this happen, but I think only if development efforts are stretched across multiple projects. CDM also lends itself to this.
Could BioDrupal work offline too? Can we build usable interfaces in Drupal that are comparable to for example Microsoft Word, i.e. like the Taxonomic Editor? Or would we be trying to fit a square peg into a round hole?
Application that Runs on Online and Offline mode
There are applications like TinyMCE which can be plugged in Drupal for formatting. It is also possible to build a custom application that can run online and could be switched to offline mode when necessary. However, most applications are either client or server centric.