Last modified by Mikko Heikkinen on 2024/04/18 10:01
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1 == About Kotka ==
2
3 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>>url:https://laji.fi/en||shape="rect"]]. Developing and maintaining Kotka is part of Luomus' national responsibilities and thus Finnish natural history museums & collections can use Kotka free of charge.
4
5 === Aims ===
6
7 Kotka **aims** to:
8
9 * Make collection work more efficient and streamlined
10 * Make collections and specimen data more accessible, and therefore increase their scientific and other use
11 * Increase the quality of collections and specimen data
12
13 === Tools ===
14
15 Kotka includes browser-based **tools** to:
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17 * Enter, edit and view data about
18 ** collections - metadata about biological collections
19 ** specimens - diverse data about museum specimens
20 ** datasets - used to tag and group specimens for different purposes
21 ** samples/preparations - data about DNA and tissue samples and vertebrate preparations
22 ** living collection accessions and events -  botanical gardens
23 ** organizations - contact details for transaction management
24 ** transactions - loans, donations and exchanges of museum specimens
25 ** ABS - tools to manage compliance with the Nagoya Protocol and other Access and Benefit sharing regulations
26 * Import specimen data from Excel
27 * Validate data
28 * Search specimens, create statistics and reports
29 * Search samples and garden branches
30 * Export data to Excel
31 * Print & design different kind of labels: LabelDesigner
32 * Help with loan management
33 * Share data to [[FinBIF>>url:http://laji.fi/en||shape="rect"]]'s data warehouse
34
35 === Principles ===
36
37 * Kotka stores primary data. The data recorded into Kotka is not updated anywhere else
38 * All users of Kotka see all the data, but can edit only their own department's data
39 * All data recorded to Kotka is stored permanently. Old versions of data can therefore be reverted to
40 * The data structure of Kotka is flexible and stresses rapid development and usefulness in different kind of situations
41 ** The format is loosely based on ABCD standard, but uses many proprietary fields. Mapping the fields to Darwin Core is relatively simple
42 ** Format is extended as needed. Only few fields are mandatory
43 ** 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)
44 ** Most data is denormalized (for example, any kind of species name or collector name can be used)
45 ** Allows recording both specimens and observations
46 * Taxonomy management, user authentication and some validation services are outsourced to other FinBIF's services
47 * According to FinBIF's data policy, the data recorded to Kotka are available as open data, with few exceptions (e.g. sensitive species)
48 * All data identified by HTTP URI's (see examples below)
49 * Accessible to all Finnish natural history museums
50
51 ==== Development principles ====
52
53 * Development using agile methods. New features are published when needed
54 * Test-driven development and continuous integration to staging server ([[kotkatest.luomus.fi>>url:http://kotkatest.luomus.fi/||shape="rect"]])
55 * Modern browser based user interface ([[kotka.luomus.fi>>url:https://kotka.luomus.fi/||shape="rect"]])
56 * Flexible non-relational database with mostly denormalized data
57 * Data querying, sharing, publishing through search server (Elastic) containing secondary copy of the data in a format optimized for querying
58 * Utilization of pre-existing tools; FinBIF's information systems, ontologies, Excel tools, open source front- & back-end libraries etc.
59 * Simplicity and flexibility
60 * Code published as open source with MIT license at [[https:~~/~~/bitbucket.org/luomus/kotka/src/master/>>url:https://bitbucket.org/luomus/kotka/src/master/||shape="rect"]]
61
62 === Technology ===
63
64 * Backend with PHP and Zend Framework
65 * Frontend with Bootstrap, jQuery and multiple other open source libraries
66 * (% style="color:#ff0000" %)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.
67 * Search functionality based on ElasticSearch
68 * Data published through FinBIF's data warehouse (Vertica)
69 * Code on Bitbucket: [[https:~~/~~/bitbucket.org/luomus/kotka>>url:https://bitbucket.org/luomus/kotka||shape="rect"]]
70 * Based mostly on RESTful API's
71
72 === Examples of data ===
73
74 * Collections of Luomus: [[http:~~/~~/tun.fi/HR.128>>url:http://tun.fi/HR.128||shape="rect"]]
75 * Insect specimen: [[http:~~/~~/id.luomus.fi/GL.3951>>url:http://id.luomus.fi/GL.3951||shape="rect"]]
76 * Lichen specimen: [[http:~~/~~/id.luomus.fi/HA.H9506963>>url:http://id.luomus.fi/HA.H9506963||shape="rect"]]
77 * Type specimens at Luomus: [[https:~~/~~/kotka.luomus.fi/types/by-collection?uri=http:~~/~~/tun.fi/HR.128>>url:https://kotka.luomus.fi/types/by-collection?uri=http://tun.fi/HR.128||shape="rect"]]
78
79 == Users ==
80
81 Kotka is being used at the following Finnish institutions (09/2021):
82
83 * Finnish Museum of Natural History Luomus, University of Helsinki
84 * Zoological and Botanical Museum, University of Oulu
85 * Zoological and Botanical Museum and Botanic garden, University of Turku
86 * Kuopio Natural History Museum
87 * Natural History Section, Jyväskylä University Museum, University of Jyväskylä (+ Botanic garden)
88 * Kieppi, Kokkola Museum of Natural History
89 * Natural Science Collections, (% style="color:#515151" %)Ostrobothnia museum
90 * Regional Museum of Lapland
91 * Satakunta Museum, City of Pori
92 * Forssa Museum of Natural History
93 * HAMBI culture collections, University of Helsinki
94 * Tampere Natural History Museum
95 * Porvoo museum, natural history collections
96 * Iisalmi Natural history museum
97
98 == Manual ==
99
100 * **[[Manual of Kotka>>doc:digit.Kotka Collection Management System.Manual for Kotka.WebHome]]**
101
102 == Contacts and communication ==
103
104 Kotka is being built at Finnish Museum of Natural History [[Luomus>>url:http://www.luomus.fi/en||shape="rect"]]
105
106 Product Owner: Anniina Kuusijärvi, kotka(at)luomus.fi
107
108 Kotka has a **Yammer group and also a mailing list**, where you can join to get the latest information about Kotka developments and maintenance breaks etc. Contact kotka(at)luomus.fi to request to join the mailing list or the Yammer group.
109
110 == Addresses ==
111
112 * **Kotka: [[https:~~/~~/kotka.luomus.fi>>url:https://kotka.luomus.fi/||shape="rect"]]**
113 * **Kotkan testing version: [[https:~~/~~/kotkatest.luomus.fi>>url:https://kotkatest.luomus.fi/||shape="rect"]]** - This can be used to practise using Kotka and imaginary data can be added there. Ask for the user name and password to access the testing site from the admins.
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