User:Adojaan/PlutoF

PlutoF is a web-based workbench, developed by scientists of the University of Tartu for managing, storing, analysing and publishing biodiversity data during its whole life cycle.

Registred users can manage various data from single observations to DNA-based molecular data, including collections, specimens, samples, sequences, projects, publications and more - everything in an integrated way.

Being universal by nature, PlutoF enables to manage data of different taxonomic groups - fungi, plants, animals, birds, insects, thus contributing to collaboration of researches from various fields.

PlutoF workbench is built using Ember.js and Django REST frameworks and PostgreSQL+PostGIS database. Workbench is developed by the workgroup of biodiversity informatics and digital archives of Natural History Museum, University of Tartu (Estonia).

Structure
PlutoF workbench consists following modules: projects, collections, monitoring and conservation, taxonomy, ecology.

Projects
Modul of Projects is meant for organizing research data. Project can be related to different data - observations, specimens, samples, sampling areas, etc. There is a flexible rights management functionality enabling to fine-tune access and usage of the data.

Besides research data PlutoF can also be used for citizen science projects. Data gathered during various citizen science projects is published in Estonian eBiodiversity portal (eElurikkus) and via Global Biodiversity Information Facility (GBIF).

Collections
It is possible to create digital archives representing objects in natural history collections, either large museum collections or small private ones. Functionality of the module includes printing labels, managing loans, creating reports and publishing data in GBIF or elsewhere. Collection data can be about pinned insects, herbarium specimens, living cultures of microorganisms and environmental samples.

Monitoring and conservation
Conservation and monitoring projects can link different types of taxon occurrences, based on observations, samples, DNA, specimens, references, etc. It is also possible to manage assessments of endangered species based on IUCN categories.

Taxonomy
It is possible to manage classifications, either to use global ones (for example from GBIF taxonomical backbone) or own classifications shared within a workgroup or published via API. Taxon occurrences may be linked simultaneously to different classifications.

Ecology
Managing datasets about soil, water, air, tissue and other samples related to DNA sequences obtained with Sanger of High Throughput Sequencing methods. Datasets can be used along with linked observation or experiment data.

Workbench
PlutoF workbench is divided in two main parts: Taxon Occurrences and Laboratories; additionally there are several elements supporting data management (Projects, Persons, Organizations etc).

Taxon Occurrences
The module of Taxon Occurrences enables to enter various data, related to particular taxon.


 * Observations are used in monitoring, citizen sciene and other projects where taxa can be identified visually, via sound or by specific devices.
 * Specimens, including living organisms stored in natural history collections, biobanks or monitored in nature
 * References. Taxon occurrences can be traced and databased from the published literature.
 * DNA sequences of speciments and eDNA are important in taxon identification analyses and DNA-based monitoring.

All the different data can be supplied with the data of involved persons, location, time, date, environment, substrate, interactions with other taxa etc.

Laboratories
File repository

It is possible to add various files to taxon occurrence records - photos, audio files, video recordings, documents. File usage rights can be specified using CC licences.

Collections

Management of natural history collections and related workflow, including transactions, loans, deposits, assessments, etc.

Publishing

There are several ways to publish data managed in PlutoF. It is possible to request Digital Object Identifier (DOI) for the dataset or publish the data in global portal GBIF. It is also possible to manage references, keywords and publications.

Taxonomy

The Taxonomy module is meant for creating and managing taxonomic lists, taxon descriptions and names. Species hypotheses from UNITE database can also be viewed there.

Analyses

PlutoF features an analysis module by providing analytical services for molecular sequence identification and species discovery from eDNA samples. For example, software like ITSx (http://microbiology.se/software/itsx/), ATOSH ja massBLASTer can be used.

Experiments

This module enables to manage data of laboratory experiments such as DNA extraction, PCR, DNA sequencing.

GIS

GIS is an essential part of the workbench enabling to manage sampling areas.

Story of the name
Kessy Abarenkov who created PlutoF workbench as a part of her doctoral thesis has described it as follws:

"Choosing the name of the workbench coincided with the time when Pluto had just been kicked out of the list of planets and the topic was actively covered by the press. I kind of felt sorry for the former planet and decided to name the desktop after it. F was the first letter in the alphabet to match Pluto without infringing Disney's copyright"

Data volume
The data of PlutoF database is physically stored on EOSC infrastructure.


 * need data!!

Users
Users of PlutoF workbench are


 * museums and institutions from all over the World using it for managing natural history collections (see Natarc.ut.ee);
 * researchers (taxonomists, ecologists), communities and organizations (UNITE database, ToxGen, Marine Biodiversity Observation Network);
 * citizen scientists, their organizations and data portals (nt BirdLife Estonia, eElurikkus, Estonian Naturalists' Society);

PlutoF workbench has more than 3000 registred users from different countries. Besides domestic users most active are researches from USA, Great Britain and Sweden.