Hagedorn 2013: Beyond Darwin Core - Stable Identifiers and then quickly beyond towards linked open...
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Transcript of Hagedorn 2013: Beyond Darwin Core - Stable Identifiers and then quickly beyond towards linked open...
Stable Identifiers
and thenQuickly Beyond
(towards Linked Open Data)
Gregor Hagedorn
© U.Kils, CC BY-SA 3.0; from Wikimedia Commons
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All slides published under Creative Commons BY-SA 3.0 (unless marked otherwise)
Identifiers
SpecimenCollection
SpecimenCollection
BotanicalNomenclatural
Classical Identifiers
SpecimenCollection
Taxon = Abies alba Mill.
SpecimenCollection
Taxon = Abies alba Mill.
BotanicalNomenclatural
Literatur
Taxon = Abies alba Mill.
Classical Identifiers
SpecimenCollectionDatabase
Taxon = 6e8bc430-9c3a-
11d9-9669-0800200c9a66
SpecimenCollectionDatabase
Taxon = 6e8bc430-9c3a-
11d9-9669-0800200c9a66
BotanicalNomenclatural
Database
Taxon = 6e8bc430-9c3a-
11d9-9669-0800200c9a66
Newer Identifiers
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
BotanicalNomenclatural
Database
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
Newer Identifiers
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
BotanicalNomenclatural
Database
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
Not actionable ___________If this
found:
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
BotanicalNomenclatural
Database
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
Not actionable ___________If this
found:
And this
found:
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
SpecimenCollectionDatabase
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
BotanicalNomenclatural
Database
Taxon = urn:uuid:6e8bc430-9c3a-
11d9-9669-0800200c9a66
Not actionable ___________If this
found:
And this
found:
Then relation
detected:
This is already useful!
But „linking“(dereferencing)would also be
useful
Solution 1: LSIDs
= building a proprietary Biodiversity-derefencing
service
Solution 2: Semantic Web /
Linked Open Data
SpecimenCollectionDatabase
Taxon = http://id.pesi.org/tax/6
e8bc430-9c3a-11d9-9669-
0800200c9a66
SpecimenCollectionDatabase
Taxon = http://id.pesi.org/tax/6
e8bc430-9c3a-11d9-9669-
0800200c9a66
BotanicalNomenclatural
Database
@ http://id.pesi.org/tax/6
e8bc430-9c3a-11d9-9669-
0800200c9a66
Semantic WebIf this
found: Then relation
derefenced
SpecimenCollectionDatabase
Taxon = http://id.pesi.org/tax/6
e8bc430-9c3a-11d9-9669-
0800200c9a66
SpecimenCollectionDatabase
Taxon = http://id.pesi.org/tax/6
e8bc430-9c3a-11d9-9669-
0800200c9a66
BotanicalNomenclatural
Database
@ http://id.pesi.org/tax/6
e8bc430-9c3a-11d9-9669-
0800200c9a66
Semantic Web
Micro-citation of data!
Semantic Webuses
http URIs
The Simple Rules1. Use URIs as names for things2. Use HTTP URIs so that people can look
up those names.3. When someone looks up a URI,
provide useful information, using the standards (RDF*, SPARQL)
4. Include links to other URIs. so that they can discover more things.(Tim Berners-Lee , 2006, http://www.w3.org/DesignIssues/LinkedData.html)
Stable URI Identifier Patterns?1. Anything goes!!!2. It is just more or less difficult to keep stable3. Google for: “Best practices for stable URIs”
(pro-iBiosphere paper)
– http://objects. myorg.edu/id/1C4EDC178AD79DD7F1A5AB856E8C5BCA
– http://concepts.myorg.edu/id/123– http://id.plazi.org/specimen/123
Respect your resources.
Be selective.
Stability is a management
decision!
Beyond: Linked Open Data
Linked Open Data Cloud (LOD 2011)
Linked Open Data Cloud (LOD 2011)
Why Linked Open Data?– Distributed Web Model
• using w3c standards (xml, rdf, owl) • Machine usable data (automatic analysis & reasoning)• Physical object, RDF, HTML linked (content negotiation)
Why Linked Open Data?– Distributed Web Model
• using w3c standards (xml, rdf, owl) • Machine usable data (automatic analysis & reasoning)• Physical object, RDF, HTML linked (content negotiation)
– Anyone can say anything about anything, anywhere• Usages that the data providers never anticipated• Third parties connect concepts between data sets• Particular needs contribute to global achievement
Why Linked Open Data?– Distributed Web Model
• using w3c standards (xml, rdf, owl) • Machine usable data (automatic analysis & reasoning)• Physical object, RDF, HTML linked (content negotiation)
– Anyone can say anything about anything, anywhere• Usages that the data providers never anticipated• Third parties connect concepts between data sets• Particular needs contribute to global achievement
– Flexible to adapt to almost any form of data– Information managed at source plus annotated globally
Why Linked Open Data?– Distributed Web Model
• using w3c standards (xml, rdf, owl) • Machine usable data (automatic analysis & reasoning)• Physical object, RDF, HTML linked (content negotiation)
– Anyone can say anything about anything, anywhere• Usages that the data providers never anticipated• Third parties connect concepts between data sets• Particular needs contribute to global achievement
– Flexible to adapt to almost any form of data– Information managed at source plus annotated globally– Queries and other analysis can combine arbitrary sets of
data, anywhere and owned by anyone– Common and diverse vocabularies can be used together
and related to each other (creativity, science!)
Strategy:1. Stable Identifiers Now (Semantic Web compatible, http-dereferenceable)2. Semantic Web Later ...
LSID, ARK, DOI, etc.?
DOI as anexample
DOIResolver
Human use Machine use
RDF (Meta)data
Content Data
Legend:
DOI Resolution Provider
Content Provider
ssssssssssssssssssssssssssssssssssssssssssssssssss
ssssssssssssssssssssssssssssssssssssssssssssssssss
Global Stability Mapping
Web serverredirection
DOIResolver
Human use Machine use
RDF (Meta)data
Content Data
RDF Data
ContentData/Html
Legend:
DOI Resolution Provider
Content Provider
HTTP Content Provider
ssssssssssssssssssssssssssssssssssssssssssssssssss
ssssssssssssssssssssssssssssssssssssssssssssssssss
ssssssssssssssssssssssssssssssssssssssssssssssssss
ssssssssssssssssssssssssssssssssssssssssssssssssss
Global Stability Mapping
Web-server-based content negotiation (MIME-type request based)
Local Stability Mapping
© G. Hagedorn, CC BY 3.0ff
DOIResolver
Infrastructure
3. Human resources required to manage the huge global list of redirection rules
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
Community-owned DOI infrastructure:1. Loads on central redirect (handling all global
taxon-related knowledge discovery!)2. GBIF-DOI is single point of failure when
used for Semantic Web (where doi-resolver must be included)
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
RDF (Meta)data
Content Data
Content Provider
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ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss ssssssssss
© G. Hagedorn, CC BY 3.0ff
Web serverredirection RDF
Data
ContentData/Html
DOI Provider Content Provider
DOIResolver
ssssssssssssssssssssssssssssssssssssssssssssssssss
ssssssssssssssssssssssssssssssssssssssssssssssssss
ssssssssssssssssssssssssssssssssssssssssssssssssss
ssssssssssssssssssssssssssssssssssssssssssssssssss
© G. Hagedorn, CC BY 3.0ff
Take home message:
Implementing stable SemWeb/LOD-compliant URI identifiers NOW is not a waste of resources should we all decide to do DOIs!