Biodiversity Data Journal and ARPHA publishing platform

[ Tool description | Examples of use of BDJ and AWT | Standards used ]


Tool description:

The Biodiversity Data Journal (BDJ) and associated ARPHA publishing platform represent together a next-generation, narrative (text) and data integrated publishing workflow, launched to mobilise, review, publish, store, disseminate, make interoperable, collate and re-use data through the act of scholarly publishing. All these processes are realised for the first time within a single, authoring, peer-review and publishing, online collaborative platform.

The Biodiversity Data Journal is a novel, community peer-reviewed, open-access journal, launched to accelerate mobilisation, dissemination and sharing of biodiversity-related data of any kind. All structural elements of the articles – text, descriptions, species occurrences, data tables, etc. – are treated, stored and downloaded as DATA in both human and machine-readable formats. The journal will publish papers on any taxon of any geological age from any part of the world with no lower or upper limit to manuscript size, for example:

  • new taxa and nomenclatural acts

  • data papers describing biodiversity-related databases;

  • local or regional checklists and inventories;

  • ecological and biological observations of species and  communities;

  • identification keys, from conventional dichotomous to multi-access interactive online keys;

  • descriptions of biodiversity-related software tools.

ARPHA stands for  Authoring, Reviewing, Publishing, Hosting and Archiving, all in one place. It is a is an innovative publishing solution developed by Pensoft that supports the full life cycle of a manuscript, from authoring and reviewing to publishing and dissemination. ARPHA consists of two interconnected workflows. A journal can use either of the two or a combination of both: 1) ARPHA-XML web-based authoring, peer-review and publishing, and 2) ARPHA-DOC - Document-based peer-review and publishing. The XML-based workflow is currently used by three journals of Pensoft - Biodiversity Data Journal, Research Ideas and Outcomes and One Ecosystem. The second, file-based submission workflow, is currently used by 12 journals published by Pensoft.

The data publishing strategy in ARPHA aims at increasing the proportion of structured text and data within the article content, so as to allow for both human use and machine readability to the maximum possible extent. ARPHA was successfully prototyped in 2013 by the Biodiversity Data Journal and the associated Pensoft Writing Tool. The latter, together with the document-based Pensoft Journal System (PJS), has since been upgraded, refactored and re-branded into a generic ARPHA authoring, editorial and publishing platform. The core of this novel workflow is a collaborative online manuscript authoring module called ARPHA Writing Tool (AWT). AWT's innovative features allow for upfront markup, "atomization" and structuralization of the free-text content already during the authoring process, import/download of structured data into/from human-readable text, automated export and dissemination of small data, on-the-fly layout of composite figures, and import of literature and data references from trusted online resources into the manuscript. ARPHA is also probably the world's first publishing system that allows for submission of complex manuscripts via an API.

The AWT provides:

  • Full life cycle of a manuscript, from writing through submission, revisions and re-submission within a single online collaborative platform;

  • Conversion of Darwin Core and other data files into text and vice versa, from text to data;

  • Automated import of data-structured manuscripts generated in various platforms (Scratchpads, GBIF Integrated Publishing Toolkit (IPT), DataOne data base, authors’ databases);

  • Automated import of occurrence data from BOLD, iDigBio and GBIF platforms;

  • A set of pre-defined, but flexible, Biological Codes and Darwin Core compliant, article templates;

  • Easy online collaborative editing by co-authors and peers;

  • A novel, community-based and public, pre-submission, pre-publication and post-publication peer-review processes.


Examples of use of BDJ and AWT:

During the first two months after its launch on 16th of September 2013, BDJ published some 50 articles (taxonomic, data papers, software descriptions, general research articles), including the landmark Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal and Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data.  The journal has already ca. 1500 users and this number increases daily. As of today (15th of January 2016), the journal has published altogether 250 articles, of which 34 data papers and 10 software descriptions.

Darwin Core Archives are generated automatically for all occurrence data and taxon treatments in each separate published paper. The DwC-A formats follow the standards used for harvesting by GBIF and Encyclopedia of Life (EOL).

The journal accepts manuscripts generated by the Scratchpads Publication Module in XML format through the AWT, at the “click of a button”.


Standards used:

Darwin Core, Darwin Core Archive, Ecological Metadata Language.

Additional resources: