USE CASE ARPHA

Context of use:

AWT 2.0 is an XML-based, WYSIWYG (What-You-See-Is-What-You-Get) authoring tool, which allows authors of scientific publications to conveniently and collaboratively work on their manuscripts and prepare them for submission to a journal. With AWT 2.0, users can take advantage of a variety of import and tagging features, to save technical time and effort, but also to ensure the machine-readability, semantic enrichment, and, thus, ontology-linked interoperability of their publications. AWT 2.0 offers features and workflows specially designed to cater to the biodiversity science community, e.g. direct import of GBIF data, automated tagging of taxa, biodiversity-specific article templates, and more. 

It provides an online collaborative environment where authors and collaborators (i.e. contributors other than co-authors, such as linguistic editors, proofreaders, or colleagues) can write, comment, edit, and prepare manuscripts for submission to a journal.

It uses a variety of predefined article templates and integrations with a set of import and tagging functionalities so that authors can save time on uploading datasets, formatting and creating reference lists, etc. Because of its XML-first design, semantic workflows and use of persistent identifiers (PIDs) for all entities of scientific value - many of which were originally developed specifically for the needs of the biodiversity community - AWT 2.0 also ensures the interoperability and re-use of data within the papers as soon as they are published.

Need:

The deluge of scattered biodiversity data, in addition to its natural evolution (e.g. synonymisations, redescriptions), makes it particularly challenging for biodiversity databases to identify and interlink data within published narratives, while also disambiguating different terms and entities. As a result, authors, as well as publication sources and databases are currently struggling to ensure that biodiversity data remains FAIR, linked, and efficient for the next generation of scientists. Post-publication text and data mining as well as literature exploration in general is a costly service that needs optimization and improved efficiency for researchers, publishers, and data aggregators.

Added Value:

AWT 2.0 makes it easier for authors to collaborate on and prepare their manuscripts in line with the WEB 2.0 demands, through semantic enhancements and use of PIDs, vocabularies, and ontologies. The most important benefits for the domain of biodiversity are the various biodiversity-specific data import and export features as well as bi-directional links with the World’s most important biodiversity data aggregators: GBIF, BOLD, INSDC, Catalogue of Life, ChecklistBank, TreatmentBank, BHL, Biodiversity Literature Repository (BLR), BiodiversityPMC (SiBILS), and many more.

Competitive Advantage:

While there are some other authoring tools on the market, AWT 2.0 supports features specially designed for the biodiversity community, including integration with major databases (e.g. GBIF, BOLD, see previous paragraph) and predefined article templates (e.g. Data paper, Software description, Species conservation profile, Catalogue, Checklist, Monitoring schema). In its AWT 2.0 version, the writing tool allows for manuscripts to be imported from and exported to JATS XML at any time so that they can be submitted to platforms and journals other than those hosted on the ARPHA publishing platform.

A qualitative upgrade on the current use of biodiversity data:

None of the existing authoring tools provides ontology-linked tagging of entities within the text. AWT 2.0 saves the effort of post-publication markup and semantic tagging so that it allows authors to personally check the semantic meaning and/or accuracy of the terms and taxon names in their manuscripts. It also provides the unique functionality of importing structured data from external resources, and semantic enhancement of literature citations (e.g. citation intent, according to the CiTO ontology: “(dis)agrees with” / “confirms” / “questions”). The export/import to/from JATS XML format ensures the interoperability of the content once published.

Exemplary Use of the Service:

Researchers can use AWT 2.0 as an extended and collaborative authoring environment, where they can discuss and edit manuscripts before submitting them to a journal.

For example, biodiversity researchers may easily import Darwin Core-compliant species occurrence data through web services or publish their biodiversity dataset (e.g. species occurrence dataset uploaded to GBIF) as a formal scientific publication. To do this, they will simply create a Data paper manuscript in AWT 2.0, upload their data directly from GBIF, and then add their narrative, to provide further context. Apart from the direct import, authors will also benefit from a list of predefined sections available in the data paper template and semantic enrichments, which will allow for each mentioned taxon to be mapped and linked to relevant databases.

Competencies and Skills that are needed to use the Service:

Any scientist should be able to work with the platform since it has been developed to be intuitive and user-friendly, while its interface and functionalities have been inspired by those of popular writing tools. The platform also offers a detailed and illustrated step-by-step user manual, a helpdesk, and a ticket feedback interface.

Challenges for the Users:

While the AWT 2.0 platform is developed to be optimally intuitive, users may need to consult the manual to better understand some of the more complex functionalities (e.g. data import). If they wish to make full use of the tool’s integration with third-party providers (e.g. GBIF), they might need to first familiarise themselves with their workflows and requirements.

Users Role in the Service Development