Virtual BiodiversityViBRANT

WP4 Standards meeting:setting the agenda

Vince SmithNatural History Museum, London

vince@vsmith.info

ViBRANTVirtual Biodiversity

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Virtual BiodiversityViBRANT

Background to WP4Overarching objectives & vision

1. Facilitate integration and harmonisation of distributed data-sets

2. Provide management and dissemination facilities for the necessary ontologies

3. Provide biologists with the necessary flexibility to express their knowledge regardless of whether the terminology has been standardized yet or not. API service

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Our job is to clarify what this means…

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Virtual BiodiversityViBRANT

Background to WP4Overarching objectives & vision

1. Facilitate integration and harmonisation of distributed data-sets

2. Provide management and dissemination facilities for the necessary ontologies

3. Provide biologists with the necessary flexibility to express their knowledge regardless of whether the terminology has been standardized yet or not. API service

Our job is to clarify what this means…

15

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Virtual BiodiversityViBRANT

1. Untangling WP4 objectivesFacilitate integration and harmonisation of distributed data-sets

i.e. linking up the Scratchpad archipelago

How do we do this?

Sites: 200+

Users: 2340+

Pages: 205k

Circa 2 new sites/wk.

Since Mar. ‘07

10% access per mnth

40% accessed per mnth

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Options for linking up the Scratchpads

• Search

Planned via Apache Lucene in WP2 (issues for distributed servers)

• A registry listing all the Scratchpads

Planned in WP2 (several options for doing this)

• Integrating data

Planned in WP4 via the CDM

A key objective of this meeting is to detail options for the registry & the CDM

1. Untangling WP4 objectivesFacilitate integration and harmonisation of distributed data-sets

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Associated deliverables:

D4.1) Scratchpad common access point: Develop an initial set of API services to link the Scratchpad communities to the resources of the CDM, to facilitate data exchange. [month 12] - NB Too early

D4.3) Ongoing services enhancements:Develop robust services, based on usage statistics and user feedback, that enhance the prototype tools delivered under D4.1 & D4.2 [month 36]

1. Untangling WP4 objectivesFacilitate integration and harmonisation of distributed data-sets

15

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Virtual BiodiversityViBRANT

Background to WP4Overarching objectives & vision

1. Facilitate integration and harmonisation of distributed data-sets

2. Provide management and dissemination facilities for the necessary ontologies

3. Provide biologists with the necessary flexibility to express their knowledge regardless of whether the terminology has been standardized yet or not. API service

Our job is to clarify what this means…

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Virtual BiodiversityViBRANT

2. Untangling WP4 objectivesProvide mang. & dissemination facilities for the necessary ontologies

i.e. providing a more standardised approach to vocabularies

Controlledvocabulariesin a Scratchpad

How do we get people to share these lists?

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Initial approach to sharing vocabularies in WP4

• Explore needs

Ongoing via GBIF

• Develop prototypes

Being planned by GBIF (DR) now

• Embed vocabularies into Scratchpads

Need to work out the details

2. Untangling WP4 objectivesProvide mang. & dissemination facilities for the necessary ontologies

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Virtual BiodiversityViBRANT

Associated deliverables:

D4.2) Ontology tools:Develop the GBIF ontology tool and produce an equivalent tool based on a semantic wiki. Deliver a single user interface for ontology creation and editing based on user-acceptance of the alternative technologies. [month 24]

D4.3) Ongoing services enhancements:Develop robust services, based on usage statistics and user feedback, that enhance the prototype tools delivered under D4.1 & D4.2 [month 36]

2. Untangling WP4 objectivesProvide mang. & dissemination facilities for the necessary ontologies

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Virtual BiodiversityViBRANT

Background to WP4Overarching objectives & vision

1. Facilitate integration and harmonisation of distributed data-sets

2. Provide management and dissemination facilities for the necessary ontologies

3. Provide biologists with the necessary flexibility to express their knowledge regardless of whether the terminology has been standardized yet or not. API service

Our job is to clarify what this means…

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Virtual BiodiversityViBRANT

3. Untangling WP4 objectivesFlexible service to express knowledge regardless of whether terminology has been standardized

i.e. wiki-based system for managing ontologies

Need to clarify?

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Controlled anatomical vocabularies

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Demonstrate and deploy the advantages of Semantic Mediawiki as a base layer for vocabulary management

Controlled per site Controlled across sitesDemonstrators via

1. Wiki, 2. Semantic wikii

Now ViBRANT Post ViBRANT

3. Untangling WP4 objectivesFlexible service to express knowledge regardless of whether terminology has been standardized

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Associated deliverables:

D4.2) Ontology tools:Develop the GBIF ontology tool and produce an equivalent tool based on a semantic wiki. Deliver a single user interface for ontology creation and editing based on user-acceptance of the alternative technologies. [month 24]

D4.3) Ongoing services enhancements:Develop robust services, based on usage statistics and user feedback, that enhance the prototype tools delivered under D4.1 & D4.2 [month 36]

3. Untangling WP4 objectivesFlexible service to express knowledge regardless of whether terminology has been standardized

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