EDIT WP5 Platform for Cybertaxonomy

On January 26th, a small rather informal meeting was held in Las Palmas de Gran Canaria, back-to-back with the EDIT ATBI+M manual workshop.

This was a good opportunity, as the lead developer for the CSIC mapViewer tool (Pere Roca Ristol) was there, and Anke Hoffmann for the management part. The partners not physically present have largely contributed via the (geo and dev) mailing lists, and their comments and suggestions were taken into account for the workplan and the outcomes of the workshop.

ViTaL, the Virtual Taxonomic Library is a component of the EDIT infrastructure, being created as part of WP5.3, which is concerned with the provision of Bibliographic tools for the taxonomic community. The services provided by ViTaL have been discussed in detail in previously published project documents. This report documents the completion of the milestone: M5.25 - Journal subscription information provided to the ViTaL team (NHML) by the initial set of actively collaborating institutions.

The general objective of the activity covers the design of a security infrastructure for the platform and the introduction of a secure Single Sign-On service (SSO) for the platform. The task to be achieved within the third JPA concerns the integration of a Community Single Sign-On (CSSO) security infrastructure within the platform.

The 3rd ISTC meeting was held on October 1-2, 2008 at the Department of Biodiversity Informatics and Laboratories at Botanic Garden and Botanical Museum in Berlin. The 3rd ISTC report and the presentations given at the meeting are available on the WP5 webpage http://cybertaxonomy.eu/blog/2007/04/04/istc.

This report has been compiled by Dominik Mikiewicz (MIZPAN) with contribution made by users of the wp5-geo-edit@mnhn.fr mailing list, especially Andreas Müller (BGBM), Pere Roca (CSIC) and Pablo Sastre Olmos (CSIC)

The ViTaL metasearch service uses the standard Z39.50 protocol to send queries to online public access catalogues (OPACs). ViTaL uses this facility to allow the querying of EDIT partner library resources, hence the need for these libraries to supply the relevant connection information to the ViTaL team.

To ensure the future compatibility of the platform with other initiatives in the world, it was decided to integrate the existing tools into the cybertaxonomy platform by using a unique already-existing public standard exchange format for descriptive data: the TDWG-SDD XML schema. This choice was made in accordance with the late efforts of several existing tools (DiversityDescriptions, Xper², Lucid, FRIDA) to allow interoperability with SDD.

The original EDIT platform for cybertaxonomy as planned in the initial description of work was designed as a set of loosely coupled independent biodiversity informatics applications communicating via well defined interfaces. This architecture has dramatically changed during the first project year towards a set of applications being built around a common data model (CDM) which is the basis for data processing in the entire platform (http://dev.e-taxonomy.eu/trac/wiki/CommonDataModel#CDMVersion1.0). This decision changed also the design of the “taxonomic core components” from an autonomous application and database system for capturing and maintaining taxonomic core data (names, taxa, synonymies, etc.) into an integrated part of the CDM-based platform.

Since 2001, the GBIF (Global biodiversity Information Facility) has been networking worldwide biodiversity data and making them freely available on the Internet. Currently, more than 150 million records (from simple occurrence data to highly structured specimen observation) are indexed by GBIF and accessible through several web portals. Almost all records available via these systems include the Latin name of the organism; which is used as a primary search term.

The Biodiversity Service & Application Tracker is a collection of links to software, tools and resources useful to taxonomists. All applications and services are categorised into an expandable and potentially hierarchical system covering major biodiversity topics. The site was developed and initially populated with the help of the EDIT WP5. EDIT also certifies software to be compatible with EDIT's Platform for Cybertaxonomy, a variety of tools known to work together to assist taxonomic work.