EDIT WP5 Platform for Cybertaxonomy

For improving collaboration and integration of IST departments within EDIT, two institutional MoUs (approved by the BoD in January 2008) have been now developed and are available up to now. They are based on the same template, i.e. identical except for the understandings or agreements stated in Paragraph 4.

1) Content management system for websites with taxonomic data

2) Data transfer standard for collection unit data.

Import of specimen data in the EDIT Common Data Model database:

The EDIT Specimen Explorer for Taxonomists (http://search.biocase.org/edit/) provides users with fast and easy-to-use access to worldwide biodiversity data, and offers full control over query expansion. The portal accepts one or more Latin names, suggests related query terms for both zoological and botanical data, expands the query accordingly and offers complete BioCASE portal functionality for resulting specimen and observation data (from the GBIF index).

Objectives

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.

To ensure full compatibility of the EDIT Platform with other initiatives, as well as to foment its use as a tool for data integration and access, it was decided to develop a CDM interface for descriptive data. It was decided to use a unique already-existing public standard exchange format for descriptive data: the TDWG-SDD XML schema. This choice was made in accordance with the recent efforts of the developers of several existing tools (DiversityDescriptions [“DeltaAccess”], Xper², Lucid, FRIDA) to allow interoperability with SDD.

Closely related to the EDIT Common Data Model (CDM, http://cybertaxonomy.eu/blog/cdm) work package 5 implements an innovative taxonomic data input and editing tool, which will become the central tool for taxonomists working on their data held in CDM stores. The editor overcomes the traditional and time consuming form-based data entry procedures with state-of-the-art parsing technology allowing users to enter their data in free-text form which is then analyzed into its syntactic components without further user interaction.

The primary taxonomist’s interface to work with the EDIT platform for cybertaxonomy will be the taxonomic editor desktop application developed by work package 5. The software will be both a tool for capturing taxonomic data according to a specific taxonomic view and a tool for entering different taxonomic views for a particular taxon and the concept relations between views. The design of this software needs as much as possible User participation already in an early development stage.

As described in the C5.65 and C5.66 component reports, an online GIS webapplication for taxonomic visualisation of point occurrences and regional distribution has been developed by CSIC, in collaboration with BGBM and RMCA, with two major constituents: (i) An interactive online tool for taxonomists, to visualise their data and download the result in a host of image formats (png, jpg,...) in print quality for publication. See the EDIT WP5 C5.66 report. (ii) A REST webservice offering the same functions in an automated way by means of an Application Programming Interface (API).

Based on the M5.28 report (Report on Guidelines to produce publication ready maps), identifying the requirements for the service in terms of quality map printing, features for enhancing the MapViewer tool for publication-ready maps have been studied and implemented.

It should be noted that this implementation work is still ongoing, in close coordination with the map services API development and documentation (see C5.68 report).

The regional distribution map generation webservice within the EDIT WP5.4 GeoPlatform is now available.  It allows taxonomists to generate regional distribution maps from their own point data uploads. It can be used for map-making in everyday taxonomic work, much as you would use a GIS system, but without the steep learning curve and complex interface of the latter.

Symbolisation, zoom level, map positioning and background imagery can be adapted on-line, so users can adapt the maps exactly as they require for their daily work and their publications.

MNCN Madrid has been developing a web-application (EDIT MapViewer) that currently allows these actions: 

• The visualization of user point data in a specified map context
• Filtering and symbolization (colour, symbol and size) of the uploaded data
• The identification of user data through two different tools
• Add different WMS layers coming from the EDIT Web Map Server
• Make thematic searches in remote WMS servers
• Load and display layers from a pre-defined list of WMS Servers