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About Kotka

Kotka is a collection management system for Finnish natural history collections and botanical gardens. Kotka has been developed in-house in the Finnish Museum of Natural History Luomus since 2011 and the development continues as part of the services provided by the Finnish Biodiversity information Facility FinBIF. Developing and maintaining Kotka is part of Luomus' national responsibilities and thus Finnish natural history museums & collections can use Kotka free of charge.


It aims to:

  • Make collection work more efficient and streamlined
  • Make collections and specimen data more accessible, and therefore increase their scientific and other use
  • Increase the quality of collections and specimen data

Kotka includes browser-based tools to:

  • Enter, edit and view data about
    • collections - metadata about biological collections
    • specimens - diverse data about museum specimens
    • datasets - used to tag and group specimens for different purposes
    • samples/preparations - data about DNA and tissue samples and vertebrate preparations
    • living collection accessions and events -  botanical gardens
    • organizations - contact details for transaction management
    • transactions - loans, donations and exchanges of museum specimens
    • ABS - tools to manage compliance with the Nagoya Protocol and other Access and Benefit sharing regulations
  • Import specimen data from Excel
  • Validate data
  • Search specimens, create statistics and reports
  • Search samples and garden branches
  • Export data to Excel
  • Print & design different kind of labels: LabelDesigner
  • Help with loan management
  • Share data to FinBIF's data warehouse

Principles

  • Kotka stores primary data. The data recorded into Kotka is not updated anywhere else
  • All users of Kotka see all the data, but can edit only their own department's data
  • All data recorded to Kotka is stored permanently. Old versions of data can therefore be reverted to
  • The data structure of Kotka is flexible and stresses rapid development and usefulness in different kind of situations
    • The format is loosely based on ABCD standard, but uses many proprietary fields. Mapping the fields to Darwin Core is relatively simple
    • Format is extended as needed. Only few fields are mandatory
    • Format is hierarchical, allowing multiple organisms, identifications, samples and type specimen information per one specimen (for example, a herbarium sheet with multiple plants, each with multiple identifications)
    • Most data is denormalized (for example, any kind of species name or collector name can be used)
    • Allows recording both specimens and observations
  • Taxonomy management, user authentication and some validation services are outsourced to other FinBIF's services
  • According to FinBIF's data policy, the data recorded to Kotka are available as open data, with few exceptions (e.g. sensitive species)
  • All data identified by HTTP URI's (see examples below)
  • Accessible to all Finnish natural history museums

Development principles

  • Development using agile methods. New features are published when needed
  • Test-driven development and continuous integration to staging server (kotkatest.luomus.fi)
  • Modern browser based user interface (kotka.luomus.fi)
  • Flexible non-relational database with mostly denormalized data
  • Data querying, sharing, publishing through search server (Elastic) containing secondary copy of the data in a format optimized for querying
  • Utilization of pre-existing tools; FinBIF's information systems, ontologies, Excel tools, open source front- & back-end libraries etc.
  • Simplicity and flexibility
  • Code published as open source with MIT license at https://bitbucket.org/luomus/kotka/src/master/

Technology

  • Backend with PHP and Zend Framework
  • Frontend with Bootstrap, jQuery and multiple other open source libraries
  • Primary data currently (12/2015) in an ontology database based on Oracle relational database. Migration to more efficient Oracle JSON document database is being planned.
  • Search functionality based on ElasticSearch
  • Data published through FinBIF's data warehouse (Vertica)
  • Code on Bitbucket: https://bitbucket.org/luomus/kotka
  • Based mostly on RESTful API's

Examples of data

Users

Kotka is being used at the following Finnish institutions (09/2020):

  • Finnish Museum of Natural History Luomus, University of Helsinki
  • Zoological and Botanical Museum, University of Oulu
  • Zoological and Botanical Museum, University of Turku
  • Kuopio Natural History Museum
  • Natural History Section, Jyväskylä University Museum, University of Jyväskylä
  • Kieppi, Kokkola Museum of Natural History 
  • Natural Science Collections, Ostrobothnia museum
  • Regional Museum of Lapland
  • Satakunta Museum, City of Pori
  • Forssa Museum of Natural History
  • HAMBI culture collections, University of Helsinki
  • Tampere Natural History Museum

Manual

Contact

Kotka is being built at Finnish Museum of Natural History Luomus

Product Owner: Anniina Kuusijärvi, lead developer Ville-Matti Riihikoski
kotka(ät)luomus.fi

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