Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases

Abstract

This is a Research Presentation paper, one of the novel article formats developed for the Research Ideas and Outcomes (RIO) journal and aimed at representing brief research outcomes. In this paper we publish and discuss our webinar presentation for the Integrated Digitized Biocollections (iDigBio) audience on two novel publishing workflows for biodiversity data: (1) automatic import of specimen records into manuscripts, and (2) automatic generation of data paper manuscripts from Ecological Metadata Language (EML) metadata. Information on occurrences of species and information on the specimens that are evidence for these occurrences (specimen records) is stored in different biodiversity databases. These databases expose the information via public REST API's. We focused on the Global Biodiversity Information Facility (GBIF), Barcode of Life Data Systems (BOLD), iDigBio, and PlutoF, and utilized their API's to import occurrence or specimen records directly into a manuscript edited in the ARPHA Writing Tool (AWT). Furthermore, major ecological and biological databases around the world provide information about their datasets in the form of EML. A workflow was developed for creating data paper manuscripts in AWT from EML files. Such files could be downloaded, for example, from GBIF, DataONE, or the Long-Term Ecological Research Network (LTER Network).