EDIT Platform Web Services in the Biodiversity Infrastructure Landscape

Anton Güntsch; Andreas Kohlbecker; Andreas Müller; Walter Berendsohn; Katja Luther; Patrick Plitzner

doi:10.3897/tdwgproceedings.1.20363

Proceedings of TDWG : Conference Abstract

Conference Abstract

EDIT Platform Web Services in the Biodiversity Infrastructure Landscape

Anton Güntsch^‡, Andreas Kohlbecker^‡, Andreas Müller^‡, Walter G. Berendsohn^‡, Katja Luther^‡, Patrick Plitzner^‡

‡ Botanic Garden and Botanical Museum, Freie Universität, Berlin, Germany

Corresponding author: Anton Güntsch (a.guentsch@bgbm.org), Andreas Kohlbecker (a.kohlbecker@bgbm.org), Andreas Müller (a.mueller@bgbm.org)

Received: 16 Aug 2017 | Published: 16 Aug 2017

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.

Citation: Güntsch A, Kohlbecker A, Müller A, Berendsohn W, Luther K, Plitzner P (2017) EDIT Platform Web Services in the Biodiversity Infrastructure Landscape. Proceedings of TDWG 1: e20363. https://doi.org/10.3897/tdwgproceedings.1.20363

Abstract

The EDIT Platform for Cybertaxonomy is a standards based suite of software components supporting the taxonomic research workflow from field work to publication in journals and dynamic web portals (FUB, BGBM 2011). The underlying Common Data Model (CDM) covers the main biodiversity informatics foci such as names, classifications, descriptions, literature, multimedia, literature as well as specimens and observations and their derived objects. Today, more than 30 instances of the platform are serving data to the international biodiversity research communities.

An often overlooked feature of the platform is its well defined web service layer which provides capable functions for machine access and integration into the growing service-based biodiversity informatics landscape (FUB, BGBM 2010). All platform instances have a pre-installed and open service layer serving three different use cases: The CDM REST API provides a platform independent RESTful (read-only) interface to all resources represented in the CDM. In addition, a set of portal services have been designed to meet the special functional requirements of CDM data portals and their advanced navigation capabilities. While the "raw" REST API has already all functions for searching and browsing the entire information space spanned by the CDM, the integration of CDM services into external infrastructures and workflows requires an additional set of streamlined service endpoints with a special focus on documentation and version stability. To this end, the platform provides a set of "catalogue services" with optimized functions for (fuzzy) name, taxon, and occurrence data searches (FUB, BGBM 2013, FUB, BGBM 2014).

A good example for the integration of EDIT platform catalogue services into broader workflows is the "Taxonomic Data Refinement Workflow" implemented in the context of the EU 7th Framework Program Project BioVeL (Hardisty et al. 2016). The workflow uses the service layer of an EDIT Platform based instance of the Catalogue of Life (CoL) for resolving taxonomic discrepancies between specimen datasets (Mathew et al. 2014). The same service is also part of the Unified Taxonomic Information Service (UTIS) providing an easy-to-use interface for running simultaneous searches across multiple taxonomic checklists (FUB, BGBM 2016).

Keywords

EDIT Platform, Taxonomy, Web Service

Presenting author

Andreas Kohlbecker

Acknowledgements

Funding program

Grant title

Hosting institution

Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Germany

Ethics and security

Author contributions

Conflicts of interest

References

FUB, BGBM (2010)

EDIT Platform for Cybertaxonomy - REST API

. https://cybertaxonomy.eu/cdmlib/rest-api.html. Accessed on: 2012-8-04.

FUB, BGBM (2011)

EDIT Platform for Cybertaxonomy

. http://www.cybertaxonomy.org. Accessed on: 2017-8-04.

FUB, BGBM (2013)

EDIT Platform for Cybertaxonomy - Name Catalogue REST API

. https://cybertaxonomy.eu/cdmlib/rest-api-name-catalogue.html. Accessed on: 2017-8-04.

FUB, BGBM (2014)

EDIT Platform for Cybertaxonomy - Occurrence Catalogue REST API

. https://cybertaxonomy.eu/cdmlib/rest-api-occurrence-catalogue.html. Accessed on: 2017-8-04.

FUB, BGBM (2016)

EU BON taxonomic backbone

. https://cybertaxonomy.eu/eu-bon/utis/1.2/. Accessed on: 2017-8-14.

Hardisty AR, Bacall F, Beard N, Balcázar-Vargas M, Balech B, Barcza Z, Bourlat SJ, De Giovanni R, de Jong Y, De Leo F, Dobor L, Donvito G, Fellows D, Guerra AF, Ferreira N, Fetyukova Y, Fosso B, Giddy J, Goble C, Güntsch A, Haines R, Ernst VH, Hettling H, Hidy D, Horváth F, Ittzés D, Ittzés P, Jones A, Kottmann R, Kulawik R, Leidenberger S, Lyytikäinen-Saarenmaa P, Mathew C, Morrison N, Nenadic A, de la Hidalga AN, Obst M, Oostermeijer G, Paymal E, Pesole G, Pinto S, Poigné A, Fernandez FQ, Santamaria M, Saarenmaa H, Sipos G, Sylla K, Tähtinen M, Vicario S, Vos RA, Williams AR, Yilmaz P (2016)

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BMC ecology

(

. https://doi.org/10.1186/s12898-016-0103-y

Mathew C, Güntsch A, Obst M, Vicario S, Haines R, Williams AR, Jong Y, C. G (2014)

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

Biodiversity Data Journal

(

e4221

): . [In

English

]. https://doi.org/10.3897/BDJ.2.e4221

Supplementary material

Endnotes