Scratchpads

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Scratchpads

Scratchpads provide a virtual research environment that enables communities of researchers to manage, share and publish natural history data online (http://scratchpads.eu). Scientific data and content are automatically classified and grouped around a taxonomy chosen or supplied by the user. Scratchpads are built using the Drupal content management system and are actively maintained and developed by the Natural History Museum London (UK).

A scratchpad can be prepared with appropriate content types, such as photographs (pictures of species found many years back can be collected from legacy BHL literature), specimen identifications, DNA sequences, morphotype information using a standard vocabulary, soil characteristics, co-occurring species, habitat data, and so on.

AgriDrupal is a similar specialisation of the Drupal content management framework that is targeted at agricultural sciences and institutions rather than biodiversity science. The principal objective of AgriDrupal is to allow small agricultural institutions to manage their web presence together with their information resources, primarily through document repositories and directories of experts and organizations, ensuring that such repositories and directories are interoperable.

On the agINFRA project, FAO, the Natural History Museum and the Open University have worked together to integrate AgriDrupal and Scratchpads because this offers clear advantages to the users of both specialisations of the Drupal content management system. A combined AgriDrupal and Scratchpads solution offers greater functionality to both user groups, in addition to being able to attract a wider user base through the benefits to be gained from deploying an integrated AgriDrupal / Scratchpads solution.

Responsible bodies:

AgriDrupal-Scratchpads development

In order to demonstrate that it is possible to run AgriDrupal and Scratchpads in the same Drupal installion, the decision was take to develop the combined AgriDrupal-Scratchpads installation using a separate code branch of both AgriDrupal and Scratchpads. This was in order to have minimal impact on the continued development of both software systems. The eventual aim is for AgriDrupal and Scratchpads to work seamlessly together, without there being a separate specialisation of either system that is compatible with the other. However, until the development work had been done, the full ramifications of AgriDrupal and Scratchpads interoperating within the same Drupal instance were unknown.

At the time of writing, we have a combined AgriDrupal-Scratchpads installation running successfully at the Natural History Museum. The long term development aim is to continue development of AgriDrupal and Scratchpads, taking note of the requirements that each makes of Drupal and each other, in order that continued integration of the two systems into a combined AgriDrupal-Scratchpads installation is as seamless as possible from the software developers perspective.

Usage and deployment

Scratchpads are available at: http://scratchpads.eu

An example of a Scratchpad that is relevant to agricultural scientists is The GIASI Partnership Gateway (Global Invasive Alien Species Information Partnership) at http://giasipartnership.myspecies.info/

The combined AgriDrupal-Scratchpads Drupal installation is available as a hosted and supported installation on the Natural History Museum's Scratchpads network. Effectively this is a Software as a Service (SaaS) solution as users can request an AgriDrupal-Scratchpad from the main scratchpads.eu website. This will be set up and backed up by the Natural Hiistory Museum.

The NHM Scratchpads network does not work as a cloud service (creating discrete virtual machines for each instance), but it runs a single code base supporting multiple independent Scratchpad and now AgriDrupal-Scratchpad) sites. The combined platform can be deployed on request from http://get.scratchpads.eu/.

A demonstration of the combined AgriDrupal-Scratchpads installation is also available at: http://agridrupal.org/scratchpadsagri/

Example Usage Scenario

Sandy is an agronomist undertaking field research and recording and analysing the data she collects.

Before agINFRA

Sandy uses a notebook, camera, specimen jar and handbook to identify plants and record her findings. All her analysis and detailed recording will be done back at camp or on return to her laboratory. As an agronomist, Sandy is unaware of the existence and utility of Scratchpads, since until now they have only been designed and promoted to taxonomists in the biodiversity field:

agINFRA powered version

Using a Scratchpad, Sandy will be able to create a spreadsheet template against those data types which Sandy will use in the field, off-line, and imported into the Scratchpad when possible. Once back on-line the data can be enhanced with laboratory results (chemical analysis, DNA sequence etc.) linked through the specimen's identification tag. The results can be assembled and submitted for various analyses such as molecular, phylogenetic and ecological tools, depending on her immediate goal.

APIs

Following the integration of AgriDrupal and Scratchpads, the AgriDrupal SPARQL and OAI-PMH APIs are available within the combined AgriDrupal-Scratchpads installation.

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