A comprehensive reference model for biological collections and surveys

Abstract

Summary Berendsohn, W. G., Anagnostopoulos, A., Hagedorn, G., Jakupovic, J., Nimis, P. L., Valdés, B., Güntsch, A., Pankhurst, R. J. & White, R. J.: A comprehensive reference model for biological collections and surveys. – Taxon 48: 511‐562. 1999. ISSN 0040‐0262. The article describes an extended entity‐relationship model covering biological collections, i.e. natural history collections of biotic origin; data collections used in floristic or faunistic mapping, survey, and monitoring projects; live collections such as botanical or zoological gardens, seed banks, microbial strain collections and gene banks; as well as novel collection kinds such as of secondary metabolites or DNA samples. The central element in the model is the unit, which stands for any object containing, being or being part of a living, fossilised, or conserved organism. The unit may be gathered (observed or collected) in the field and derived units may recursively emerge from it through specimen processing, breeding or cultivation. In addition, units may form associations (e.g. host/parasite), ensembles (lichen on a rock with fossils), and assemblages (herd, artificial grouping). Gathering events, specimen management (acquisition, accession, storage, preservation, exchange, ownership), and taxonomic or other identifications relate to the unit and are treated in detail. Geographic and geo‐ecological data have not been fully modelled; taxonomic (name) data and descriptive information are treated by reference to other published models.

VegetWeb – the national online-repository of vegetation plots from Germany

“…VegetWeb's architecture was developed based on http://planto.de, MoreTax (Berendsohn 2003) and http://vegbank.org and allows applying concept taxonomy to plant names (Berendsohn et al 1999). VegetWeb serves as a repository with fast query interface.…”

Delivering a name-server for biodiversity information

“…These may confirm or change a previous determination, or result in multiple determinations (according to different experts). Berendsohn, Anagnostopoulos, Hagedorn, Jakupovic, Nimis, Valdés, et al (1999) list nine types of identification event, including a negative determination (the specimen does not belong to a particular taxon) and similarly, for observational data, where a species was not found during a survey. These last two identification types would need to be properly distinguished in search results; something that is possible within a single database, but more difficult when integrating results from dispersed databases.…”

The CDM Applied: Unit-Derivation, from Field Observations to DNA Sequences

“…Each derivation step also produces meta data storing who, when and how the derivation was done. The Platform's Common Data Model (CDM) and the applications build on the CDM library thus represent the first comprehensive implementation of the largely theoretical models developed in the late 1990ies (Berendsohn et al 1999)…”

“…Each derivation step also produces meta data storing who, when and how the derivation was done. The Platform's Common Data Model (CDM) and the applications build on the CDM library thus represent the first comprehensive implementation of the largely theoretical models developed in the late 1990ies (Berendsohn et al 1999)This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. …”