The CDM format and storage includes all types of data needed for the taxonomist’s work. The taxonomic editor was developed to edit these data with the exception of descriptive data, because for these efficient tools are available for more than two decades (see www.bdtracker.net/softwareTracker/list/all/type/14). One of these tools (Xper2) is now able to run directly on the CDM classes and thus complements the Taxonomic Editor (EDITor). A user documentation describes how to edit and to use the descriptive data in the EDIT Platform for Cybertaxonomy.
The CDM library offers a lot of elements and functionalities in order to help taxonomists store their data. However, at least two elements were missing: the possibility to generate a clear and easy to read output of these data, either for publication or simply to have a readable preview of a part of or even an entire database; the possibility to automatically generate identification keys from these data, which is an essential goal of taxonomists, since taxonomy is the science of classification.
Several tools already exist to manage descriptive data or to use and to analyse these data(Xper², DiversityDescriptions, Linnaeus, or other tools). These tools have hence proven their interest and their accessibility for taxonomists even if they have little or no previous computer experience.
The present component details the collaboration between the activity 5.6 (description and keys) and an EDIT exemplar group (the Cichorieae exemplar group). For activity 5.6, the aim of this collaboration is the visibility of the integration of descriptive data into the EDIT Common Data Model (CDM). For the Cichorieae exemplar group of the WP6, this collaboration could help to get the best of their descriptive data and better fit the needs of the Cichorieae Dataportal website users.
Descriptive data are one of the most important categories of information produced by taxonomists when describing new species or performing taxonomic revisions. This is why the EDIT Common Data Model (CDM) is designed to include and store descriptive data. SDD is the current TDWG (Biodiversity Information Standards) standard for descriptive data. Most of the existing software managing descriptive data (e.g. Lucid, Xper², DiversityDescription) already support it, allowing their users to import or export descriptive datasets.
This report deals with the practical achievement of the inventory of identification keys and related descriptive datasets, with emphasis on the metadata fields selected and some issues raised by this inventory. Relevant metadata fields have been selected into a pre-existing metadata list defined in the KeyToNature project. The aim was to keep a short number of fields in order to keep a moderate-sized table for the display and facilitate the appropriation by the future participants.
One of the EDIT achievements is a cybertaxonomy-platform (http://dev.e-taxonomy.eu/platform/ ) providing a large range of computer tools for taxonomists (http://dev.e-taxonomy.eu/platform/, http://www.bdtracker.net/). These tools are designed to assist the taxonomist from fieldwork to publication of results, including the management of descriptive data, which have a key role in the taxonomic revision process.
This milestone corresponds to the delivery of demonstrator software, for further details see C5.118. It shows the successful import of SDD (Structured Descriptive Data) standard conformant data (which has been produced with an external tool) into an EDIT Common Data Model database, and the subsequent publication of the data in the CDM by means of a simple web page.
Taxon descriptions and other factual data are an essential component of taxonomic output. Up to now, the CDM programming library supports such data only in unstructured (textual) form. Structured descriptive data has to be integrated into the CDM and the library has to support its output. Creating an editor to input this type of data is not attempted within the EDIT project, largely because fully functional tools are available for this purpose. Instead, importing files following the international standard SDD (Structured Descriptive Data) format is made possible.
The cdmlib-model.description classes are designed to manage and store structured descriptive content. In order to display this content, different types of outputs need to be specified. As for today, the main use-case is the necessity to create output to the EDIT portals and potentially to the Taxonomic Editor. More generally, a flexible output for display on Web pages or in a format targeted to be read by another system would cover most use-cases.