PlutoF platform


About the PlutoF

The PlutoF platform provides online service to create, manage, share, analyze, and mobilize biodiversity data. Data types cover ecology, taxonomy, metagenomics, nature conservation, natural history collections, etc. PlutoF is developed by the IT team of Natural History Museum, part of the University of Tartu, Estonia. Such a common platform aims to gurantee that the databases are managed within a professional, sustainable and stable architecture. It provides synergies by sharing common modules across the system. The common taxonomy module is based on standard sources such as the Fauna Europeana (de Jong et al. 2014) and Index Fungorum and may be developed collectively further by the users.
PlutoF platform also provides data curation and third party annotations to the data from external resources, such as DNA sequence data from GenBank.

Curated datasets hosted by PlutoF platform can be made available through public web portals. Examples include the GBIF, the UNITE community who curate DNA-based fungal species concepts and provide open access to their datasets through the UNITE portal or the eBiodiversity portal that includes taxonomic, ecological and genetic information on species found in Estonia.

The PlutoF API provides a structured system that eases the implementation of citizen science based mobile app reporting schema, thus facilitating community-based tools for data sharing. Using the PlutoF citizen science module you will be able to  engage citizen scientists,  teachers  and children  in  your biodiversity project.



What type of data can be published using the PlutoF?

  • Observation data
  • Natural history collections
  • Ecological/environmental data
  • DNA data
  • Images and sounds
  • Citizen science data
  • Habitats
  • Interacting taxa
  • Traits


In what format should be the data?

The recommended way of adding the new data is to create first a template (.csv file) using "Import" function and then merge the template with your data file. It will allow you to upload the data in a bulk. You can also add observations directly via the project page or using the apps. It's also possible to add an observation by uploading the image file with sound recording.


PlutoF workflow:

To be able to share your data you have to register fist at PlutoF platform.

Example workflows for different type of data:

Getting started: 1) Register/Login,  2) Create/Import Taxon Occurrences, 3) Search/Manage/Share/Publish

Specimen Based Projects: 1) Create Project, 2) Create Sampling Areas,  3) Create/Import Specimens, 4) Search/Manage/Share/Publish

Analyses: 1) Upload Data,  2) Start Analysis (seriateBLAST, ITSx, ATOSH),  3) View and Store Results

Collections: 1) Create/Import Specimen Records,  2) Search/Manage/Share/Publish,  3) Collection Transactions (loans, borrows, assessments, treatments), 4) Label printing and Reports

Collection Projects: 1) Create Project,  2) Create Sampling Areas,  3) Create/Import Specimens, 4) Search/Manage/Share/Publish,  5) Collection Transactions (loans, borrows, assessments, treatments)

Citizen Science Projects: 1) Create and Configure Project (Areas, Input Forms, Taxon Restrictions, Public Page),  2) Gather Taxon Occurrence Data (ODK Collect, mobile applications, web workbench),  3) Moderate/Search/Manage/Publish

Barcoding Projects: 1) Create Project, 2) Create Sampling Areas,  3) Create/Import Specimens and Sequences,  4) Search/Manage/Share/Publish

Interactions: 1) Create Project, 2) Create Sampling Areas,  3) Create/Import Specimens,  4) Create Interactions Between Taxon Occurrences

Metabarcoding Projects: 1) Create Project,  2) Create Sampling Areas,  3) Create/Import Material Samples,  4) Upload HTS Representatives,  5) Search/Manage/Share/Publish

For further help:

  • Read the PlutoF manuals available in English and Estonian
  • Watch video tutorials which will guide you through the different functionalities of the tool


Standards used

Darwin Core (DwC), Ecological metadata language (EML), Genomic Standards Consortium (GSC): MIMARKS, MIxS, MCL


Pros and Cons of the tool

The advantage of  PlutoF  is  that  all  data  are  automatically  linked  and  therefore  can  be  searched, analysed and  published  as  a  unified  dataset. All  data  from  other  public  or  shared  projects  are  also available in the same way. Sharing data with selected users is just few mouse clicks away. Datasets are easily published through GBIF or Pensoft journals, while Digital Object Identifiers (DOIs) may be obtained through the system. Users can also create a variety of reports and checklists.

Additional resources: