Data Publishing

Lyubomir Penev, Pavel Stoev & Teodor Georgiev


Data publishing framework for primary biodiversity data
Pensoft Data Publishing Policies and Guidelines for Biodiversity Data
Chavan, V., and L. Penev. "Data Paper: Mechanism to incentivise discovery of biodiversity data resources." BMC Bioinformatics 12(Suppl 15):S2 (2011).

ViBRANT partners were part of the GBIF task group that addressed the problem of encouraging data publication. The results were published in a special issue of BMC Bioinformatics and led directly to innovations by Pensoft described below.

In October 2011, ZooKeys launched its multiple-choice model for publishing biodiversity data that provides a non-exclusive choice of mechanisms for the publication of data of different kinds and complexity, in co-operation with specialised data repositories and data aggregators, based on the previously published Pensoft Data Publishing Policies and Guidelines for Biodiversity Data. One of the most important steps in this direction was the launch of an innovative route for publishing occurrence data and taxon checklists using an approved TDWG standard (Darwin Core), enriched metadata descriptions for published datasets, and the possibility of downloading both data and metadata in a machine-readable form, the Darwin Core Archive. This is supported by a specialised GBIF tool, the Integrated Publishing Toolkit (IPT) and Scratchpads. Use of this tool allows the production of “Data Paper” manuscripts that formally describe a dataset’s metadata as a peer-reviewed and citable scholarly publication[1].

    The GBIF - Pensoft workflow of data publishing  and automated generation of data paper manuscripts

A second important element of the multiple-choice data publishing model of Pensoft’s journals was the integration of its data publishing workflow with the Dryad Digital Repository, thus providing an option to its authors to archive data files of different kinds and complexity (e.g., phylogenetic, morphometric, ecological, environmental, etc.). The workflow of deposition of data in Dryad was illustrated by three exemplar papers [2],[3],[4].

Pensoft's latest innovation was announced on the 22nd of November 2011 with the launch of an automated export and indexing of identification keys metadata published in the journals in KeyCentral – a global database of keys and other identification resources for living organisms.