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Using Wikibase �as a Platform to Develop a �Semantic Biodiversity Standard

David Fichtmueller�Botanic Garden and Botanical Museum Berlin

NFDI Wikibase Workshop, 23 February 2021

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The ABCD Standard

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The ABCD Standard

  • Access to Biological Collection Data

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The ABCD Standard

  • Access to Biological Collection Data
  • XML Schema�

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The ABCD Standard

  • Access to Biological Collection Data
  • XML Schema
  • >1800 Concepts (XPaths)�

NFDI Wikibase Workshop, 23 February 2021

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The Challenge

  • Convert it to a semantic standard (OWL Ontology) with the same expressiveness

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The Challenge

  • Convert it to a semantic standard (OWL Ontology) with the same expressiveness
  • Keep existing documentation, restrictions, connections

NFDI Wikibase Workshop, 23 February 2021

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The Challenge

  • Convert it to a semantic standard (OWL Ontology) with the same expressiveness
  • Keep existing documentation, restrictions, connections
  • Collaborative Platform for many users

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The Solution

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The Solution

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The Properties

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The Properties

  • 25 Wikibase Properties to describe the Items

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The Properties

  • 25 Wikibase Properties to describe the Items

Label Description Aliases

is part of

in Vocabulary

Usage Notes

subclass of

is coupled with

Concept Name

additional Description

Created

subproperty of

excludes usage of

has range

in Concept Group

Modified

has Meta Property

is mandatory

has datatype

Example

associated Property

is Meta Property of

Functional Property

allowed value

Example (localized)

associated Concept

is inverse of

has domain

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The Workflow

  • Import:

Schema Parser OpenRefine QuickStatements

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The Workflow

  • Import:

Schema Parser OpenRefine QuickStatements

                • Editing:

Manually reduced concepts: 1800+ ~550

Automated Edits: Query Service + QuickStatements

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The Workflow

    • Validation:

Maintenance Queries

Manual Review

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The Workflow

    • Validation:

Maintenance Queries

Manual Review

    • Export:

Python Script using the Query Service to fill � OWL Templates

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The Result

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The Result

  • Success!

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The Result

  • Success!
  • Similar approach for the Modelling Framework in the DiSSCo Project (Distributed System of Scientific Collections)

NFDI Wikibase Workshop, 23 February 2021

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The Advise

  • Only install Wikibase using the Docker image

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The Advise

  • Only install Wikibase using the Docker image
  • Be aware: Many Wikidata tools require adjustments to properly work with other Wikibase instances (e.g. QuickStatements)

NFDI Wikibase Workshop, 23 February 2021

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The Advise

  • Only install Wikibase using the Docker image
  • Be aware: Many Wikidata tools require adjustments to properly work with other Wikibase instances (e.g. QuickStatements)
  • It is easy to automate steps, use it as much as possible.

NFDI Wikibase Workshop, 23 February 2021

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The Last Slide

https://wiki.bgbm.org/bdidata/index.php/BDI_Data:Main_Page

Thank you for your attention!

Questions?

Feel free to contact me: d.fichtmueller@bgbm.org

�Source of background image: https://www.youtube.com/watch?v=x3Cvn1vNQ98 created by M-Create for DFG (License CC-BY)

NFDI Wikibase Workshop, 23 February 2021