1 of 24

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

2 of 24

The ABCD Standard

�

NFDI Wikibase Workshop, 23 February 2021

3 of 24

The ABCD Standard

�

  • Access to Biological Collection Data

NFDI Wikibase Workshop, 23 February 2021

4 of 24

The ABCD Standard

�

  • Access to Biological Collection Data
  • XML Schema�

NFDI Wikibase Workshop, 23 February 2021

5 of 24

The ABCD Standard

�

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

NFDI Wikibase Workshop, 23 February 2021

6 of 24

The Challenge

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

NFDI Wikibase Workshop, 23 February 2021

7 of 24

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

8 of 24

The Challenge

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

NFDI Wikibase Workshop, 23 February 2021

9 of 24

The Solution

NFDI Wikibase Workshop, 23 February 2021

10 of 24

The Solution

NFDI Wikibase Workshop, 23 February 2021

11 of 24

The Properties

NFDI Wikibase Workshop, 23 February 2021

12 of 24

The Properties

  • 25 Wikibase Properties to describe the Items

NFDI Wikibase Workshop, 23 February 2021

13 of 24

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

NFDI Wikibase Workshop, 23 February 2021

14 of 24

The Workflow

  • Import:

Schema Parser → OpenRefine → QuickStatements

NFDI Wikibase Workshop, 23 February 2021

15 of 24

The Workflow

  • Import:

Schema Parser → OpenRefine → QuickStatements

                • Editing:

Manually reduced concepts: 1800+ → ~550

Automated Edits: Query Service + QuickStatements

NFDI Wikibase Workshop, 23 February 2021

16 of 24

The Workflow

    • Validation:

Maintenance Queries

Manual Review

NFDI Wikibase Workshop, 23 February 2021

17 of 24

The Workflow

    • Validation:

Maintenance Queries

Manual Review

    • Export:

Python Script using the Query Service to fill � OWL Templates

NFDI Wikibase Workshop, 23 February 2021

18 of 24

The Result

NFDI Wikibase Workshop, 23 February 2021

19 of 24

The Result

  • Success!

NFDI Wikibase Workshop, 23 February 2021

20 of 24

The Result

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

NFDI Wikibase Workshop, 23 February 2021

21 of 24

The Advise

  • Only install Wikibase using the Docker image

NFDI Wikibase Workshop, 23 February 2021

22 of 24

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

23 of 24

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

24 of 24

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