Biodiversity Information Science and Standards : Conference Abstract
Conference Abstract
PlutoF: Biodiversity data management platform for the complete data lifecycle
expand article infoUrmas Kõljalg, Kessy Abarenkov§, Allan Zirk§, Veljo Runnel, Timo Piirmann, Raivo Pöhönen, Filipp Ivanov
‡ University of Tartu, Tartu, Estonia
§ University of Tartu, Natural History Museum, Tartu, Estonia
Open Access


PlutoF online platform ( is built for the management of biodiversity data. The concept is to provide a common workbench where the full data lifecycle can be managed and support seamless data sharing between single users, workgroups and institutions. Today, large and sophisticated biodiversity datasets are increasingly developed and managed by international workgroups. PlutoF's ambition is to serve such collaborative projects as well as to provide data management services to single users, museum or private collections and research institutions.

Data management in PlutoF follows a logical order of the data lifecycle Fig. 1. At first, project metadata is uploaded including the project description, data management plan, participants, sampling areas, etc. Data upload and management activities then follow which is often linked to the internal data sharing. Some data analyses can be performed directly in the workbench or data can be exported in standard formats. PlutoF includes also data publishing module. Users can publish their data, generating a citable DOI without datasets leaving PlutoF workbench. PlutoF is part of the DataCite collaboration ( and so far released more than 600 000 DOIs. Another option is to publish observation or collection datasets via the GBIF (Global Biodiversity Information Facility) portal. A. new feature implemented in 2019 allows users to publish High Throughput Sequencing data as taxon occurrences in GBIF. There is an additional option to send specific datasets directly to the Pensoft online journals. Ultimately, PlutoF works as a data archive which completes the data life cycle.

Figure 1.

Full data lifecycle with PlutoF platform. PlutoF follows standards, which ensure that users data are FAIR (Findable, Accessible, Interoperable, Reusable) throughout every phase of the data lifecycle.

In PlutoF users can manage different data types. Most common types include specimen and living specimen data, nucleotide sequences, human observations, material samples, taxonomic backbones and ecological data. Another important feature is that these data types can be managed as a single datasets or projects.

PlutoF follows several biodiversity standards. Examples include Darwin Core, GGBN (Global Genome Biodiversity Network), EML (Ecological Metadata Language), MCL (Microbiological Common Language), and MIxS (Minimum Information about any (x) Sequence).


data management, biodiversity data, FAIR Data, data lifecycle

Presenting author

Allan Zirk

Presented at

Biodiversity_Next 2019

Funding program

PlutoF is funded by Estonian research infrastructure roadmap object NATARC ( Future funding will be probably provided by the Est-DiSSCo which is listed in the new national roadmap. New business model will be created in 2020 which allows other institutions and countries to take part in the development of PlutoF.