C5.91 CDM storage functionality [for specimen and observation data] implemented

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).

C5.83 Setup the initial CSSO security infrastructure for the platform


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.

C5.79 SDD Import/Export module for CDM v1 (software)

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.

C5.75 V1.0 of the CDM taxonomic editor available (software)

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.

C5.74 Specification of concept-related workflows to be supported by the taxonomic editor (wiki site)

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.

C5.68 API Documentation for map generation webservices available

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).

C5.67 Map generation web-services enhanced for publication ready maps

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).

C5.66 Regional distribution map generation webservice for online and print quality maps released and available on-line

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.

C5.65 Point occurrence map generation webservice for online and print quality maps released and online available

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

C5.64 Global background maps available in printing quality

The assessment of the needs of taxonomists in terms of Geospatial components and the e-conference previously held (see Component 5.32) indicated that there is a high interest in having access to camera ready maps for different publication means ( Websites, Presentations, scientific papers, large format maps, posters). The local post processing of maps for publication has been identified as being far from straightforward and often rather time consuming for non-specialists in GIS systems. The development of a freely available and easy-to-use tool able to produce maps for those taxonomists not experienced in the use of GIS programs is indeed an essential part of EDIT Work Package 5.4 (Geospatial Component).

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