The proposed e-BiodDiv can be defined like open biodiversity FAIR-ification services for
biospecimens stored in Swiss natural history museums. It will on the one hand provide a service for Swiss
biodiversity scientists to access and disseminate their research data about species in legacy and
prospective publications, provide access to data about their collections, scientists and specimens. It will
complement the recently funded SwissBioCollection program and genomic data. On the other hand, importing
treatments into the Swiss Institute of Bioinformatics Literature Services (SIBiLS) opens them for text and data
mining through SIBiLS dedicated tools, and by the life science community.
To a large extent, the eBioDiv service is based on existing services such as the Biodiversity
Literature Repository (BLR), Plazi TreatmentBank (TB), and Zenodo. The long term goal is to integrate this
service in the portfolio of SIBiLS linking the biodiversity research data infrastructure in Switzerland.
This project will complement and make use of the Horizon 2020 funded research
infrastructure (BiCIKL development by providing
the specific annotation services for the Swiss based scientists, and make a production level import of taxonomic
treatments into SIBiLS.
The Earth’s scholarly knowledge about species diversity (biodiversity) is included in a corpus of
several hundred million pages of publications spanning over 250 years , with an arbitrary starting point
of 1,753 for plants and 1,758 for animals. Each year an estimated 19,000 animal and plant species and a multiple
of augmentations of data are added to the already approximately known 1.9M species.
The data about each species are included in highly structured taxonomic treatments and figures.
Increasingly these treatments include implicit links to the data used to describe and augment it, such as omic
and digitized specimen data produced by SwissBioCollection. Because of its structure, this data can be extracted
automatically to a high degree, bidirectionally linked from the literature to the cited resources and vice
versa, made FAIR, and immediately reused by data aggregators such as GBIF and other researchers.
In addition to Patrick Ruch’s team at HES-SO and SIB (Swiss Institute of Bioinformatics) and Beat Esterman’s team at BFH, the project is built
on the direct contribution of Plazi and the Natural History Museum of
Bern (NMBE). The Swiss-based BLR and TB are the world’s leading
services of liberating biodiversity data imprisoned in PDFs (portable document format) and a major contributor
to the Global Biodiversity Information Facility (GBIF) where
the FAIR data is reused.