Difference between revisions of "DWB training environment"

From Diversity Workbench
Jump to: navigation, search
 
(13 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
[[Image: DWB components.png|450px|right|DWB components © SNSB IT Center'']]
 
[[Image: DWB components.png|450px|right|DWB components © SNSB IT Center'']]
  
−
The DWB training environment at the [http://www.snsb.info SNSB IT Center] is complemeenting the [[Training materials]]. It includes the following 15 databases with examplary data from real life biodiversity and geodiversity projects as well as with a number of terminologies, gazetteers and taxonomies which are useful as structural templates for creating new ontologies. The data is for training purposes only; the content from real life projects is mostly outdated. Other pieces of content are created for the DWB training in particular and are very patchy.
+
The DWB training environment at the [http://www.snsb.info SNSB IT Center] complements the [[Training materials|DWB training materials]]. It offers access to the 15 pre-configured databases listed below with exemplary data from real life biodiversity and geodiversity projects as well as with exemplary data from a number of terminologies, gazetteers and taxonomies which are useful as structural templates for creating new ontologies. The data is for training purposes only. The content from real life projects is mostly outdated. Other pieces of content are created for the DWB training in particular and are very patchy.
  
 
The bio- and geodiversity data and the nature science ontologies might be modified/ changed/ re-organised/ enriched/ deleted by users who have a common log-in. The content of the databases is set back to the initial state every half year or on request. The DWB training environment is available for your personal training purposes and is used to train the participants in the [http://www.snsb.info/Workshops.html regular DWB workshops].
 
The bio- and geodiversity data and the nature science ontologies might be modified/ changed/ re-organised/ enriched/ deleted by users who have a common log-in. The content of the databases is set back to the initial state every half year or on request. The DWB training environment is available for your personal training purposes and is used to train the participants in the [http://www.snsb.info/Workshops.html regular DWB workshops].
  
−
In near future, this [[DWB training environment]] will be "mirrored" to a GFBio server environment at the [https://www.gwdg.de/de GWDG] in Göttingen. New configurations and scripts will facilitate the direct SSO access via the [https://www.gfbio.org/ GFBio portal].
+
The databases of the [[DWB training environment]] are regularly "mirrored" to a GFBio/ NFDI4Biodiversity server environment at the [https://www.gwdg.de/de GWDG] in Göttingen. New configurations and scripts will facilitate the direct SSO access via the [https://www.gfbio.org/ GFBio portal].
  
 
----
 
----
Line 18: Line 18:
 
*''Password: available on request''
 
*''Password: available on request''
  
−
Please contact [http://www.snsb.info/staff_weibulat.html Tanja Weibulat] as reference person for DWB user within the [https://www.gfbio.org/ GFBio] initiative.
+
Please contact [http://www.snsb.info/staff_weibulat.html Tanja Weibulat] as contact person for DWB users.
  
  
Line 37: Line 37:
  
 
==DiversityDescriptions_Workshop==
 
==DiversityDescriptions_Workshop==
−
*DWB project "Tutorial" for the following local example projects:
+
*projects:
 +
**"MyDatadesc" is an empty project for starting with own data.
 
**"An Interactive Key to Species of Erythroneura" (© 2003-2006 D. Dmitriev & C. Dietrich) The SDD version is released under the Creative Commons non-commercial, by attribution, share-alike license in version 2.5. Imported from SDD file published at http://wiki.tdwg.org/twiki/bin/view/SDD/RealWorldExamples_SDD1dot1
 
**"An Interactive Key to Species of Erythroneura" (© 2003-2006 D. Dmitriev & C. Dietrich) The SDD version is released under the Creative Commons non-commercial, by attribution, share-alike license in version 2.5. Imported from SDD file published at http://wiki.tdwg.org/twiki/bin/view/SDD/RealWorldExamples_SDD1dot1
 
**"SDD of ETI reptiles and amphibians" (© 2008 ETI) The SDD version is released under the Creative Commons non-commercial, by attribution, share-alike license (Creative Commons 3.0 NC-BY-SA unported). Imported from SDD file published at http://wiki.tdwg.org/twiki/bin/view/SDD/RealWorldExamples_SDD1dot1
 
**"SDD of ETI reptiles and amphibians" (© 2008 ETI) The SDD version is released under the Creative Commons non-commercial, by attribution, share-alike license (Creative Commons 3.0 NC-BY-SA unported). Imported from SDD file published at http://wiki.tdwg.org/twiki/bin/view/SDD/RealWorldExamples_SDD1dot1
−
**"BactDescDSMZ" (© Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures) 5 descriptions of bacterial strains from DSMZ
+
**"DSMZbacdivedesc" (© Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures) 5 descriptions of bacterial strains from DSMZ
 
**"BFLheilpflanzendesc" (© 2016 Staatliche Naturwissenschaftliche Sammlungen Bayerns) Medical plants of Bavaria
 
**"BFLheilpflanzendesc" (© 2016 Staatliche Naturwissenschaftliche Sammlungen Bayerns) Medical plants of Bavaria
−
*Project "LIASlight" (© BSM, München, Germany)) excerpt of 421 items from LIAS light - A Database for Rapid Identification of Lichens Imprint: http://liaslight.lias.net/About/Impressum.html  
+
**"LIASlight" (© BSM, München, Germany)) excerpt of 421 items from LIAS light - A Database for Rapid Identification of Lichens Imprint: http://liaslight.lias.net/About/Impressum.html  
−
*Project "DEEMY" (© 2004–2015 by Reinhard Agerer, Ludwig-Maximilians-Universität München) excerpt of 76 items from DEEMY - An Information System for Characterization and Determination of Ectomycorrhizae. www.deemy.de
+
**"DEEMY" (© 2004–2015 by Reinhard Agerer, Ludwig-Maximilians-Universität München) excerpt of 76 items from DEEMY - An Information System for Characterization and Determination of Ectomycorrhizae. www.deemy.de
−
* Project "MOD-CO" (CC BY-SA 4.0) Schema v. 1.0: Towards an integrative and comprehensive standard for meta-omics data of collection objects. https://www.mod-co.net
+
**"MODCOschema1dot0desc" (CC BY-SA 4.0) Schema v. 1.0: Towards an integrative and comprehensive standard for meta-omics data of collection objects. https://www.mod-co.net
  
 
Files for import:
 
Files for import:
 +
*Starting with client version 4.5.0 the demo files for import can be copied to the local resrources directory with menu item "''Administration''" - "''Tutorial files ...''". In subdirectory "Import\Tutorial" the file "ReadMe.txt" gives an overview of the provided files. 
 +
 +
Alternatively the files are available online:
 
* SDD structured dataset of trait data of Ulmus for import: https://github.com/SNSB/DWB-Contrib/tree/master/DiversityDescriptions/Import/Schemas/Tutorial-SDD   
 
* SDD structured dataset of trait data of Ulmus for import: https://github.com/SNSB/DWB-Contrib/tree/master/DiversityDescriptions/Import/Schemas/Tutorial-SDD   
 
* CSV/ TXT structured dataset of biomass (BEF China) with DD import schema as description: https://github.com/SNSB/DWB-Contrib/tree/master/DiversityDescriptions/Import/Schemas/BEFCHINAhlpbiomass/Biomass-as-description
 
* CSV/ TXT structured dataset of biomass (BEF China) with DD import schema as description: https://github.com/SNSB/DWB-Contrib/tree/master/DiversityDescriptions/Import/Schemas/BEFCHINAhlpbiomass/Biomass-as-description

Latest revision as of 16:16, 3 July 2023

DWB components © SNSB IT Center

The DWB training environment at the SNSB IT Center complements the DWB training materials. It offers access to the 15 pre-configured databases listed below with exemplary data from real life biodiversity and geodiversity projects as well as with exemplary data from a number of terminologies, gazetteers and taxonomies which are useful as structural templates for creating new ontologies. The data is for training purposes only. The content from real life projects is mostly outdated. Other pieces of content are created for the DWB training in particular and are very patchy.

The bio- and geodiversity data and the nature science ontologies might be modified/ changed/ re-organised/ enriched/ deleted by users who have a common log-in. The content of the databases is set back to the initial state every half year or on request. The DWB training environment is available for your personal training purposes and is used to train the participants in the regular DWB workshops.

The databases of the DWB training environment are regularly "mirrored" to a GFBio/ NFDI4Biodiversity server environment at the GWDG in Göttingen. New configurations and scripts will facilitate the direct SSO access via the GFBio portal.


Access data to the DWB training environment

  • IP-Adresse: training.diversityworkbench.de
  • Port: 5432
  • SQL-Server authentification
  • User: WORKSHOP
  • Password: available on request

Please contact Tanja Weibulat as contact person for DWB users.


DiversityAgents_Workshops

  • project: Copy of BSMcollectors (version for training purposes only; content outdated or very patchy)

DiversityCollection_Workshop

  • projects:
    • Copy of BSMwohlfcoll (water colours; version for training purposes only; content outdated or very patchy)
    • DWBbarcodingcoll: Single examplary units (= records, = “datasets sensu DC“) from GBOL and ZSM barcoding projects
    • DWBmonitoringcoll: 18 examplary units (observation records) from monitoring projects
    • DWBsamplescoll: 46 examplary units (specimen or sample records)

DiversityCollectionCache_Workshop

DiversityDescriptions_Workshop

  • projects:
    • "MyDatadesc" is an empty project for starting with own data.
    • "An Interactive Key to Species of Erythroneura" (© 2003-2006 D. Dmitriev & C. Dietrich) The SDD version is released under the Creative Commons non-commercial, by attribution, share-alike license in version 2.5. Imported from SDD file published at http://wiki.tdwg.org/twiki/bin/view/SDD/RealWorldExamples_SDD1dot1
    • "SDD of ETI reptiles and amphibians" (© 2008 ETI) The SDD version is released under the Creative Commons non-commercial, by attribution, share-alike license (Creative Commons 3.0 NC-BY-SA unported). Imported from SDD file published at http://wiki.tdwg.org/twiki/bin/view/SDD/RealWorldExamples_SDD1dot1
    • "DSMZbacdivedesc" (© Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures) 5 descriptions of bacterial strains from DSMZ
    • "BFLheilpflanzendesc" (© 2016 Staatliche Naturwissenschaftliche Sammlungen Bayerns) Medical plants of Bavaria
    • "LIASlight" (© BSM, München, Germany)) excerpt of 421 items from LIAS light - A Database for Rapid Identification of Lichens Imprint: http://liaslight.lias.net/About/Impressum.html
    • "DEEMY" (© 2004–2015 by Reinhard Agerer, Ludwig-Maximilians-Universität München) excerpt of 76 items from DEEMY - An Information System for Characterization and Determination of Ectomycorrhizae. www.deemy.de
    • "MODCOschema1dot0desc" (CC BY-SA 4.0) Schema v. 1.0: Towards an integrative and comprehensive standard for meta-omics data of collection objects. https://www.mod-co.net

Files for import:

  • Starting with client version 4.5.0 the demo files for import can be copied to the local resrources directory with menu item "Administration" - "Tutorial files ...". In subdirectory "Import\Tutorial" the file "ReadMe.txt" gives an overview of the provided files.

Alternatively the files are available online:

DiversityExsiccatae_Workshop

(not part of the regular training schedule!)

  • no projects: copy from the productive database (version for training purposes only; content outdated or very patchy)

DiversityGazetteers_Workshop

  • projects:
    • LfUnaturraumBYhegaz (Landesamt für Umweltschutz, Naturräume Bayern, Haupteinheiten)
    • LfUnaturraumBYeigaz (Landesamt für Umweltschutz, Naturräume Bayern, Einheiten)
    • LfUnaturraumBYuegaz (Landesamt für Umweltschutz, Naturräume Bayern, Untereinheiten)
    • DTK25BYgaz (Digitale Topographische Karte Bayern, 1:25.000)
    • BKG2001GN250gaz (geographische Namen 250.000er Karte, Bundesamt für Kartographie und Geodäsie)
    • DTK25DEgaz (Digitale Topographische Karte Deutschland, 1:25.000)

DiversityProjects_Workshop

  • 113 projects, including a lot of TaxRef lists

DiversityReferences_Workshop

  • project:
    • GBIFmyxlit: copy from the productive database (version for training purposes only; content outdated or very patchy)

DiversitySamplingPlots_Workshop

  • projects:
    • IBFmergplots: 9 vector shapes with metadata of excursion areas of O. Mergenthaler
    • SMNKspiderplots: 579 vector shapes with hierarchically structured metadata and additional information (Exposition, Höhe, etc.) from SMNK

DiversityScientificTerms_Workshop

  • terminologies (versions for training purposes only; content outdated or very patchy)
    • Terminologica Anatomica (TA) - excerptum (few entries for bones of the hand)
    • Chronostratigraphy
    • European Nature Information System (EUNIS)
    • Geographic regions
    • Gesteine (few entries for rocks; following an internal terminology)
    • Lebensraumtypen
    • Lithostratigraphy
    • Mineralien (few entries for minerals; roughly following the terminology of https://www.mindat.org/)
    • Pflanzengesellschaften

DiversityTaxonNames_Fungi_Workshop

  • project:
    • DGfMnames (version for training purposes only; content outdated or very patchy)
  • list:
    • TaxRef_DGfM_Fungi_DE

DiversityTaxonNames_Insecta_Workshop

  • project:
    • GBOLnames (version for training purposes only; content outdated or very patchy)
  • list
    • TaxRef_GBOL_Auchenorrhyncha_DE

DiversityTaxonNames_Myxomycetes_Workshop

(not part of the regular training schedule!)

  • projects
    • GBIFnomenmyx (version for training purposes only; content outdated or very patchy)
  • no lists

DiversityTaxonNames_Plants_Workshop

  • projects:
    • BFLnames (version for training purposes only; content outdated or very patchy)
    • GBOLnames (version for training purposes only; content outdated or very patchy)
  • lists:
    • TaxRef_BFL_VPlants
    • TaxRef_GBOL_Mosses_DE

DiversityTaxonNames_Vertebrata_Workshop

  • project:
    • GBOLnames (version for training purposes only; content outdated or very patchy)
  • lists:
    • TaxRef_GBOL_Pisces_DE


Back to: Training materials

Retrieved from "https://diversityworkbench.net/w/index.php?title=DWB_training_environment&oldid=22759"