WP5.5 Taxonomic Core

C5.114 Refined CDM taxonomic editor available for Platform release 3

EDIT exemplar groups as well as several other initiatives have now started to use the CDM taxonomic editor as their primary software tool for data capture and maintenance of their community information stores. In the course of their work several demands on new features and refinements of existing functionalities were made. The feature requests were thoroughly analyzed and discussed with the WP5 developer group and led to a significantly revised Editor design and implementation, which will be part of the EDIT Platform version 3 to be released in September 2010.

C5.078 Fully functional version of CDM editor available (software)

The primary tool for taxonomists compiling and maintaining data in a Common Data Model (CDM) store is the Desktop Taxonomic Editor, which is now available in its version 2.0. The Editor has all necessary functions for creating taxonomic trees, organizing synonymies and name relations, and maintaining all kinds off factual data (now called "descriptions") such as distribution information and common names.

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M5.33 CDM Toolkit Bundle (data store, editor, conversion tools) available and documented to be used by EDIT partner institutions

The basic software equipment needed to carry out taxonomic work with the EDIT platform is a Common Data Model data store together with the desktop taxonomic editor and basic import and export functionalities, which can be used to set up the system with existing standardized data and export data, which have been finalized. We have bundled these functionalities within the CDM desktop taxonomic editor, which is available from http://dev.e-taxonomy.eu/trac/wiki/TaxonomicEditorDownload.

C5.113 CDM power user interface design study and pilot implementation

The power user of a taxonomic data storage model is a non-technical user responsible for the integrity of the data. While the normal user creates data – names, references, authors, etc. – as part of the workflow of editing a taxon, the power user can create, edit, and delete data outside of this workflow. Moreover, the normal user should be restricted from editing certain shared data.

M5.32 Three significant taxonomic initiatives setup as CDM projects

The implementation of a new electronic infrastructure for taxonomic data processing from the field to the printed publication should involve Users (Taxonomists) from the earliest possible stage of development. The EDIT Work Package 5 involved its User groups from the beginning by organising joint Developer/User-workshops, creating test-versions of important software components (e.g. data-portal, taxonomic editor), and publishing modelling decisions taken in the developers group on the relevant EDIT mailing lists.

C5.077 CDM data interface components available (software)

The Common Data Model (CDM) acts as the central “information broker” within EDIT’s platform for cybertaxonomy architecture. Apart from its role as an advanced storage facility for individual researcher and taxonomic communities it has to communicate with decoupled EDIT platform components such as data portals, (print) publication tools, fieldwork and mapping software, as well as collection databases and specimen information systems (see figure). Consequently, the implementation of CDM interfaces providing and accepting data according to established international biodiversity informatics data standards and quasi-standards is considered essential for the entire EDIT-based taxonomic information workflow.

C5.076 Taxonomic sample data available (data)

For the continued development, testing and assessment of the EDIT Common Data Model (CDM) as well as its related software products (e.g. data portal, taxonomic editor, import/export modules) the availability of real-world taxonomic data sets is essential. In collaboration with WP6 and other taxonomic initiatives, WP5 has organized the availability of eight significant taxonomic datasets and tested their compliance with the CDM model:

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.

M5.15 Taxonomic core components available for platform

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.

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