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Difference between revisions of "DiversityNaviKey"

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The software application DiversityNaviKey (DNK) is intended to identify organisms or other items (digital objects) as well as item groups which are part of or related to biodiversity or geodiversity research, by means of a set of pre-defined characteristics. It allows for interactive and sophisticated search on highly structured datasets with descriptive data (trait data with descriptors and states/values) to identify items and item groups according to (modified) states/values and other criteria, consecutively selected during the identification process.  
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{| border="0" align="right" style="border-collapse:collapse; background-color:transparent;" cellpadding="50"
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|[[File:DNK-Bildkomposition-scaled.jpg|right|500px|DiversityNaviKey © SNSB IT Center'']]
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DiversityNaviKey is the reimplementation of the multi-lingual java applet/application [http://navikey.net NaviKey] which is also an integrated part of the [http://www.diversitynavigator.net/ DiversityNavigator] database client.
 
  
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The new application will be implemented as a „Progressive Web Application (PWA)“. Thus it is platform independent and will run on every common browser (Firefox, Chrome, Edge, Safari). The pages are responsive and adjusted to the user device (desktop, tablet, smartphone). By using caching mechanism of modern browsers, like ServiceWorker and IndexedDB, the main tasks of the application will also be available in offline mode.  
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The software application DiversityNaviKey (DNK) is a generic tool primarily designed for any kind of diagnosis and interactive identification of organisms or other items as well as item groups which are part of or related to biodiversity, geodiversity or environmental research, by means of a set of pre-defined characteristics. It allows for sophisticated selection based on highly structured data sources (datasets) with descriptive data (trait data with descriptors, descriptor categorical states, descriptor values). The browser-based tool is optimized to build and run determination keys based on the consecutive selection of descriptors, descriptor states and values during the identification process. Selection criteria might be predefined by individual user or changed during the identification process.
  
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DiversityNaviKey will use SDD structured data sources and PostgreSQL cache database mechanisms as established for [[DiversityDescriptions]].  
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The new application is realised as a „Progressive Web Application (PWA)“. Thus, it is platform independent and is running on every common browser (Firefox, Chrome, Edge, Safari). The pages are responsive and adjusted to the user device (desktop, tablet, smartphone). On smartphones it looks like a native app. By using caching mechanism of modern browsers, like ServiceWorker and IndexedDB, the main tasks of the application will also be available in offline mode. The access to the tool might be organised as part of existing web portals and information systems.
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DiversityNaviKey is using SDD structured data sources offered via PostgreSQL cache database mechanisms and REST web services as established for [[DiversityDescriptions]]. It is the reimplementation of the well-known multi-lingual java applet/application [http://navikey.net NaviKey] which is also an integrated part of the [http://www.diversitynavigator.net/ DiversityNavigator] database client.
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For current software releases see '''https://divnavikey.snsb.info'''.
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Code Repository: https://github.com/SNSB/DiversityNaviKey
  
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Future extension to cover [https://diversityworkbench.net/Portal/DiversityMobile DiversityMobile] functions is envisaged.
 
  
 
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DiversityNaviKey will be presented at the [https://informatik2021.gi.de/informatik2021 INFORMATIK 21 Konferenz Berlin & online], Workshop [https://www.nfdi4biodiversity.org/cs4biodiversity/ Computer Science for Biodiversity].
 
  
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DiversityNaviKey was presented 2021
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*at the [https://informatik2021.gi.de/informatik2021 INFORMATIK 21 Konferenz Berlin & online], Workshop [https://www.nfdi4biodiversity.org/cs4biodiversity/ Computer Science for Biodiversity] with DNK presentation [https://www.nfdi4biodiversity.org/documents/5/CS4BioDiversity_Talk_DiversityNaviKey_ArianeGrunz.pdf here] and abstracts [https://informatik2021.gi.de/informatik2021/workshops/cs4biodiversity here].
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*at the [https://www.snsb.info/SNSBInfoOpenWiki/Wiki.jsp?page=DivWorkbenchWorkshop_42 42. Diversity Workbench Workshop].
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See also paper:
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*Triebel, D., Grunz, A., Seifert, S., Link, A. & Rambold, G., (2021). DiversityNaviKey, a Progressive Web Application for interactive diagnosis and identification. In: , . (Hrsg.), INFORMATIK 2021. Gesellschaft für Informatik, Bonn. (S. 517-538). [https://dl.gi.de/handle/20.500.12116/37705 DOI: 10.18420/informatik2021-040]
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SNSB Press release 2022: [https://snsb.de/diversitynavikey/ SNSB entwickelt neue Diagnose-App für Forschung und Sammlungen] with English version [https://snsb.de/diversitynavikey/?lang=en SNSB develops new diagnostic app for natural science objects]
 
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==Six exemplary data sources which will be available for diagnosis and identification via DiversityNaviKey starting with October 2021==
 
  
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The numbers of items, descriptors, values are those in the productive DiversityDescriptions databases (SNSB installations) which might be larger than the numbers available for DNK access.
 
  
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{|border=1 cellpadding="5" style="margin:1em 1em 1em 0; background:#FFFFFF;border:1px #AAA solid; border-collapse:collapse; empty-cells:show;"
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==Data sources ==  
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|-style="text-align:left; background:#D3D3D3;"
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! DiversityNaviKey code
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! Title of the data source (dataset)
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! Description of the data source
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! Number of items, number of item values
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! Number of descriptors, number of categorical descriptor states
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! Number of linked images and documents hosted by SNSB
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! Linked internet resources
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! Access point with citation (e.g. re3data, DOI)
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! Responsible/ author(s)
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! Creative Common Licenses (textual data and hosted images)
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! References and notes
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|BELMONTsurveydesc (1)||Belmont Forum Open Data Survey 2014||Belmont Forum Open Data Survey, September until November 2014, by the Open Data working group of the E-Infrastructure and Data Management Collaborative Research Action (https://www.belmontforum.org/). Survey design worked out by the Open Data working group of the E-Infrastructure and Data Management Collaborative Research Action. The data are stored in DiversityDescriptions since 2015.  ||1,328 items with 63,123 categorical state values and 1,490 text values  ||80 descriptors with 69 categorical descriptors (238 categorical states), 11 free text descriptors ||-||-||Raw data as csv-files under https://zenodo.org/record/16384# ||Schmidt, Birgit; Gemeinholzer, Birgit; Treloar, Andrew; Hodge, Jonathan; Santanchè, André; Oakley, Kim||CC BY || Schmidt, B., Gemeinholzer, B., Treloar, A (2016): Open Data in Global Environmental Research: The Belmont Forum's Open Data Survey. PLOS One, DOI: 10.1371/journal.pone.0146695; https://data.snsb.info/dataset/gfbio/projects_gfbio/968
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|- style="background:#F5F5F5;"
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|BFLheilpflanzendesc (2)|| Artenquiz zum Thema Heilpflanzen in Bayern||Das Wissen über die rund 300 in Bayern vorkommenden Heilpflanzen und vor allem die Fähigkeit sie in der Natur zu erkennen geht immer mehr verloren. Dabei finden sich in vielen Pflanzenarten wertvolle medizinische Wirkstoffe. Auch sind sie gar nicht so selten zu finden. Im Artenquiz "Heilpflanzen in Bayern" unter http://artenquiz.bayernflora.de/ können Sie sich zum einen selbst testen und sehen wie gut Sie die verschiedenen Heilpflanzen bereits erkennen, zum anderen können Sie sich durch genaues Betrachten der Bilder und Auswählen der richtigen Merkmale neues Wissen aneignen. Der Datenbestand wird in DiversityDescriptions gemanagt. ||-||- ||xxx images of items, xxx images of descriptors, xxx images of categorical states||+||-||Hagedorn, Gregor; Plank, Andreas; Leininger, Iris; Link, Anton||CC BY ... CC BY SA|| see also under [https://diversityworkbench.net/Portal/DiversityDescriptions_Implementations DiversityDescriptions_Quiz] and [http://biowikifarm.net/meta/Artenquiz_documentation Artenquiz Documentation]
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|DEEMY|| An Information System for Characterization and DEtermination of EctoMYcorrhizae ||DEEMY is collecting descriptive data on ectomycorrhizae. The data are stored in DiversityDescriptions. The online output of the database offers definitions of the descriptors (characters) of ectomycorrhizae used, morphological descriptions of the ectomycorrhizae, original hand drawings and photographs. Currently, DEEMY is comprising more than 500 types of ectomycorrhizae characterized by 498 often multi-state descriptors (characters). It includes more than 850 drawings of characters and 177 images of ectomycorrhizae (http://www.deemy.de/).||554 items with 63,806 categorical state values, 38,270 quantitative values, 928 text values ||498 descriptors with 341 categorical descriptors (1,336 categorical states), 154 quantitative, 3 free text descriptors||177 images of items, 59 images of descriptors, 596 images of categorical states, accessed via URIs from SNSB image webserver ||- ||re3data.org: DEEMY; editing status 2019-01-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZF5V last accessed: 2021-08-04||Agerer, Reinhard; Rambold, Gerhard||CC BY-NC-ND||
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|DSMZbacdivedesc (1)||Mobilisation of data for GFBio services - Bacterial Descriptions Use Case ||The description of five comprehensively annotated bacterial strains have been imported into the DiversityDescriptions in the course of the project GFBio (www.gfbio.org). The purpose of this mobilization is the availability of taxon-related descriptive information for the GFBio data portal following various standard schemas, e.g. SDD, for the test and development of data pipelines and work flows. The data has been manually annotated out of species descriptions derived by results of recently completed and ongoing projects carried out and published by researchers at the DSMZ. The ecological and environmental relevance of these strains is given by their participation in nitrogen and carbon cycles (significant exoenzyme activity) within their particular habitat. The detailed documented metabolic and physiologic profile of each strain indicates their significant adaptation to the soils of different climates. Hence, these strains are important biotic components of their environment.||5 items with 589 categorical state values, 158 quantitative values, 208 text values, 4 molecular sequence values  ||310 descriptors with  200 categorical descriptors (680 categorical states), 56 quantitative, 54 free text descriptors, 1 sequence descriptor ||-||?||Access points in [http://bacdive.dsmz.de BacDive - The Bacterial Diversity Metadatabase] under [http://bacdive.dsmz.de/index.php?site=search&rd=23454 Blastocatella fastidiosa Foesel et al. 2013  A2_16], [http://bacdive.dsmz.de/index.php?search=24777 Aridibacter kavangonensis Huber et al. 2014 Ac_23_E3], [http://bacdive.dsmz.de/index.php?site=search&rd=24776 Aridibacter famidurans Huber et al. 2014 A22_HD_4H], [http://bacdive.dsmz.de/index.php?site=search&rd=133 Edaphobacter aggregans Koch et al. 2008 emend. Dedysh et al. 2012 Wbg-1], [http://bacdive.dsmz.de/index.php?site=search&rd=132 Edaphobacter modestus Koch et al. 2008 Jbg-1]
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|| Söhngen, Carola; Bunk, Boyke; Podstawka, Adam; Gleim, Dorothea; Overmann, Jörg||CC BY ||https://data.snsb.info/dataset/gfbio/projects_gfbio/967
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|LIASlight||LIAS light – A Database for Rapid Identification of Lichens ||The lichen trait database LIAS light (http://liaslight.lias.net/) is a component of the LIAS information system. It is a considerable pool of descriptive data based on 71 different qualitative, quantitative, and text characters, for more than 10,000 lichen taxa, being phylogenetically classified according to the current  outline for fungi (Wijayawardene et al. 2020). It includes information on morphological, ecological and chemical traits. The descriptor and descriptor state backbone is translated in more than 20 languages. LIAS light data are accessible in DELTA format to be used locally. For utilisation with the browser-based Java applet NaviKey see http://liaslight.lias.net/Identification/Navikey/World/en_GB/index.html.||more than 10,000 items with xxx categorical state values, xxx quantitative values, xxx text values ||71 descriptors with 58 categorical descriptors (2,961 categorical states), 6 quantitative, 7 free text descriptors||-||+||re3data.org: LIAS; editing status 2019-02-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3134N last accessed: 2021-08-04 ||Rambold, Gerhard; Davydov, Evgeny; Elix, John A.; Nash III, Tom H.; Scheidegger, Christoph; Zedda, Luciana||CC BY-NC-ND||lichen names managed in [http://liasnames.lias.net/ LIAS names], lichen vocabulary managed in [https://glossary.lias.net/wiki/ LIAS glossary]
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|LIASmetabolites||  LIAS metabolites – A Database for the Rapid Identification of Secondary Metabolites of Lichens||http://liaslight.lias.net/Identification/Navikey/Metabolites/index.html||-||-||-||+||-||Elix, John A.; Kalb Klaus; Rupprecht Johanna; Schobert, Rainer; Rambold, Gerhard  ||CC BY-NC-ND|| see also http://www.anbg.gov.au/abrs/lichenlist/Chem%20Cat%203.pdf
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(1) data curation, enrichment and data publication done as part of the the DFG-funded project [https://www.gfbio.org/ GFBio]
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Currently six data sources are open and freely available for diagnosis and identification purposes with use of DiversityNaviKey and data access via the [https://www.snsb.info SNSB IT Center]. They are from different scientific fields (botany, mycology, lichenology, bacteriology, chemistry, sociology). The by far largest dataset is that on lichen trait data provided by the long-term information system [http://www.lias.net/ LIAS].
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The table under [[DWB DiversityNaviKey data sources]] describes the single datasets.
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Future extension to cover [https://diversityworkbench.net/Portal/DiversityMobile DiversityMobile] functions is envisaged. DiversityNaviKey might also become part of the wider [https://www.nfdi4biodiversity.org/ NFDI4Biodiversity] RDC cloud tool network.
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(2) data curation, enrichment and data publication done as part of the project [https://wiki.bayernflora.de/web/Hauptseite Flora von Bayern]
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Back to [[DWB DiversityNaviKey data sources]]

Latest revision as of 08:40, 7 September 2023

DiversityNaviKey © SNSB IT Center


The software application DiversityNaviKey (DNK) is a generic tool primarily designed for any kind of diagnosis and interactive identification of organisms or other items as well as item groups which are part of or related to biodiversity, geodiversity or environmental research, by means of a set of pre-defined characteristics. It allows for sophisticated selection based on highly structured data sources (datasets) with descriptive data (trait data with descriptors, descriptor categorical states, descriptor values). The browser-based tool is optimized to build and run determination keys based on the consecutive selection of descriptors, descriptor states and values during the identification process. Selection criteria might be predefined by individual user or changed during the identification process.

The new application is realised as a „Progressive Web Application (PWA)“. Thus, it is platform independent and is running on every common browser (Firefox, Chrome, Edge, Safari). The pages are responsive and adjusted to the user device (desktop, tablet, smartphone). On smartphones it looks like a native app. By using caching mechanism of modern browsers, like ServiceWorker and IndexedDB, the main tasks of the application will also be available in offline mode. The access to the tool might be organised as part of existing web portals and information systems.

DiversityNaviKey is using SDD structured data sources offered via PostgreSQL cache database mechanisms and REST web services as established for DiversityDescriptions. It is the reimplementation of the well-known multi-lingual java applet/application NaviKey which is also an integrated part of the DiversityNavigator database client.


For current software releases see https://divnavikey.snsb.info.

Code Repository: https://github.com/SNSB/DiversityNaviKey



DiversityNaviKey was presented 2021

See also paper:

  • Triebel, D., Grunz, A., Seifert, S., Link, A. & Rambold, G., (2021). DiversityNaviKey, a Progressive Web Application for interactive diagnosis and identification. In: , . (Hrsg.), INFORMATIK 2021. Gesellschaft für Informatik, Bonn. (S. 517-538). DOI: 10.18420/informatik2021-040

SNSB Press release 2022: SNSB entwickelt neue Diagnose-App für Forschung und Sammlungen with English version SNSB develops new diagnostic app for natural science objects


Data sources

Currently six data sources are open and freely available for diagnosis and identification purposes with use of DiversityNaviKey and data access via the SNSB IT Center. They are from different scientific fields (botany, mycology, lichenology, bacteriology, chemistry, sociology). The by far largest dataset is that on lichen trait data provided by the long-term information system LIAS.

The table under DWB DiversityNaviKey data sources describes the single datasets.


Future extension to cover DiversityMobile functions is envisaged. DiversityNaviKey might also become part of the wider NFDI4Biodiversity RDC cloud tool network.

Back to DWB DiversityNaviKey data sources

Retrieved from "https://diversityworkbench.net/w/index.php?title=DiversityNaviKey&oldid=23126"