Presentation of the Global Biodiversity Information Facility (GBIF) knowledge organization system (KOS) work program for the National Center for Biomedical Ontology (NCBO) Web seminar series in October 2012. Available at http://www.bioontology.org/GBIF-vocabulary-management-for-biodiversity-informatics

1. NCBO Webinar series
Knowledge Organization System (KOS) for
biodiversity information resources
- GBIF KOS work program
Dag Endresen
Knowledge Systems Engineer, Node manager for GBIF Norway
Natural History Museum, University of Oslo
Éamonn Ó Tuama
Senior Programme Officer, Inventory, Discovery, Access (IDA)
Global Biodiversity Information Facility (GBIF)
17 October 2012

2. GBIF enables free and open access to biodiversity
data online.
We’re an international government-initiated and
funded initiative focused on making biodiversity data
available to all and anyone, for scientific research,
conservation and sustainable development.
Status data portal
October 2012
Presented
by Éamonn

3. The OECD origin…
OECD Global Science Forum recommendation (1999):
“Establish and support a distributed system of interlinked
and interoperable modules (databases, software and
networking tools, search engines, analytical algorithms,
etc.) that together will form a Global Biodiversity
Information Facility (GBIF)”
“This facility will enable users to navigate
and put to use vast quantities of
biodiversity information, thereby:
 advancing scientific research…
 serving the economic…
 providing a basis from which our
knowledge of the natural world
Presented
can grow rapidly…” by Éamonn

4. 1. Information infrastructure – an
Internet-based index of a globally
distributed network of
interoperable databases that
contain primary biodiversity data.
1. Community-developed tools,
standards and protocols – the
tools data providers need to format
and share their data.
1. Capacity-building and training –
and access to a global expert
community.
Presented
by Éamonn

5. http://data.gbif.org/
Presented
by Éamonn

6. Web services (REST)
Advanced search for occurrence records
• Scientific names and classification
• http://data.gbif.org/ws/rest/taxon
• Species occurrence data
• http://data.gbif.org/ws/rest/occurrence
• Species occurrence data aggregated, 1 degree cell
• http://data.gbif.org/ws/rest/density
• Metadata on data providers
• http://data.gbif.org/ws/rest/provider
• Metadata on datasets
• http://data.gbif.org/ws/rest/resource
• Metadata on data networks
• http://data.gbif.org/ws/rest/network
Presented
Open and free use of data! by Éamonn

7. Slide developed by Donald Hobern
GBIF’s unique role
• Registry of biodiversity data resources
• Tools and support for biodiversity data publication
• Network development at national, regional and
global levels
• Global virtual natural history collection
• Cross-domain linkage between data from
collections, ecology and genomics
• Access to biodiversity data for GIS analysis and
environmental monitoring
– Aggregated presence data Presented
by Éamonn
– Site-based survey data (samples, presence/absence)

8. Unifying species data
Ecological
Genomics
Monitoring
Darwin Core
Integrated access for
records of the
occurrence of any
species:
• What?
• When? Collections
• Where?
• What evidence?
• Data owner?
• Link to full record
Presence only
Slide developed by Donald Hobern

9. Darwin Core – a glossary of terms
Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, De Giovanni R, Robertson T, and Vieglais D (2012)
Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7(1): e29715.
doi:10.1371/journal.pone.0029715

10. TDWG
Ontology
The TDWG
Ontology was
developed and
maintained
between 2007
and 2009.
http://rs.tdwg.org/ontology

11. GBIF KOS
task group
report
http://links.gbif.org/gbif_kos_whitepaper_v1.pdf
Presented
by Éamonn
11

12. GBIF KOS work program, 2011 and 2012
Description of work:
• “a flexible, user-friendly ontology management
environment, enabling users to create, define, extent
and share their own terms and concepts where
needed, providing options for discussions and
annotation, while supporting re-use of terms from
standardized ontologies wherever possible”.
• Extent the functionalities of existing vocabulary services (like
GBIF).
• Collaborative community interface for users and user-
networks, bottom-up, user-friendly and non-technical.
• Flexibility for biologists to express their knowledge regardless
of whether the terminology has been standardized yet or not.
12

13. Data standards
Important principle: Re-use of terms from
standardized terminologies wherever possible.
13 The cartoon is from XKCD: http://xkcd.com/927/ CC-BY-NC

14. Term versus Concept
“The SKOS (simple knowledge organization system) format is designed to present
KOS data in a format that is suitable for machine inferencing and particularly for
use in the Semantic Web (….) concepts – units of thought – and distinguishes
these from the terms that are used to label these concepts.
Will, L. (2012). The ISO 25964 Data Model for the Structure of an Information Retrieval Thesaurus. Bulletin of the
American Society for Information Science and Technology 38(4): 48-51.
Dextre Clarke, S.G. and L. Zeng (2012). From ISO 2788 to ISO 25964: the evolution of thesaurus Standards towards
Interoperability and data modeling. ISQ Information Standards Quarterly 24(1): 20-26.
14

15. Why use a flat vocabulary ?
• Maximize the reuse of terms, focus on the definition
and labels for basic terms.
• Low threshold for non-technical biologists and
biodiversity domain experts to access terms and
contribute (compared to richer ontologies).
• Preferred technology: RDF (resource description
framework) and SKOS (simple knowledge organization
system).
• Construction and maintenance of OWL ontologies are
demanding in respect to expertise, effort and costs.
• Maintaining SKOS vocabularies are less demanding.
• RDF resources are designed to be easily extended.
• Ontologies (OWL) can be based on (extend) terms
declared by a RDF/SKOS vocabulary.
• SKOS became a W3C recommendation in 2009.
15

16. Why use OWL (web ontology language) ?
• OWL DL supports machine reasoning through machine
accessible formal semantics.
• OWL provides by default an URI as identifier for classes,
properties, relations and instances.
• E.g. OBO target practical solutions in the biomedical /
biology domain, while OWL is more generic and provide
cross-domain interoperability.
• OWL 1.0 became a W3C recommendation in 2004,
• OWL 2.0 in 2009.
• http://www.w3.org/2007/OWL/
• Recommendation:
• REUSE terms declared by concept vocabularies…
• Start with SKOS - then explore OWL…
16

17. Governance structure (TDWG VoMaG)
http://community.gbif.org/pg/groups/21382/
17

18. http://kos.gbif.org
18

19. Vocabulary management (work-flow)
1. Mint and maintain concepts and terms, in domain-
Wiki expert working groups.
Vocabulary 2. Release final version as a Concept Vocabulary.
3. REUSE terms from published concept
Management vocabularies and ontologies when designing new
1 DwC-A controlled term and value vocabularies. 4
4. Publish at the GBIF Resources Repository.
5. Browse at the GBIF Resources Browser. Resources
Repository
2
ISOcat Concept
Vocabulary Vocabulary GBIF 5
Management (rdf, skos) Resources
1 Browser
proposed
template
processor
DwC-A
controlled GBIF Vocabularies
Excel, text, etc… vocabularies
Evaluation of 3 as a collaborative
Template for management tool for
collaborative
Vocabularies 1 management tools Darwin Core Archive
http://kos.gbif.org/ controlled term and value
GBIF Vocabularies
vocabularies.
19

20. GBIF Vocabulary Server (Drupal)
Wiki
Vocabulary
Management
Concept
Vocabulary Resources
ISOcat
Vocabulary (rdf, skos) Repository
Management
MS Excel
Template for
Vocabularies GBIF IPT
Evaluation of various tools for DwC-A term
collaborative management of and value
concept vocabularies. vocabularies
GBIF Vocabularies GBIF Vocabularies
as a collaborative
management tool for Darwin Core Archive
controlled terms and value
Darwin Core Archive vocabularies
controlled terms and The GBIF
Vocabulary
controlled value Server is based
vocabularies. on Drupal 6 /
Scratchpads v1
20

21. Semantic wiki forum for terms
Wiki
Vocabulary
Management
Concept
ISOcat
Vocabulary Resources
Vocabulary
(rdf, skos)
Management
Repository
MS Excel
Template for
Vocabularies GBIF IPT
Evaluation of various tools for
collaborative management of DwC-A
concept vocabularies. term and value
vocabularies
?
Wiki forum for terms as an open
community platform for description
Wiki Forum and maintenance of existing
terms.
for Terms
Replacement tool also for the
GBIF Vocabulary Server?
21

22. GBIF Term browser
Wiki
Vocabulary
Management
Concept
Concept vocabularies
ISOcat
Vocabulary Resources stored/deposited at
Vocabulary
(rdf, skos) http://rs.gbif.org/terms/
Management
Repository
MS Excel
Template for
Vocabularies
Evaluation of various tools for
collaborative management of
concept vocabularies.
The GBIF Term Browser allows a
user to browse for terms defined in
widely used concept vocabularies
such as Darwin Core, Dublin Core,
FOAF, etc., including where
available, translations.
http://kos.gbif.org/termbrowser/
22

23. Biodiversity ontology management
REUSE terms from
Concept concept vocabularies
Vocabulary Ontologies
(rdf, skos) (rdf, owl)
Evaluation of Evaluation of
tools for the biodiversity
development ontology
of biodiversity repository
ontologies. solutions.
1 Wiki tool 2 Resources
(incl. ontology Repository
development?) (incl. ontologies?)
23

24. BioPortal ontology repository
Proposal: establish a biodiversity “slice” at the NCBO BioPortal.
• Loading biodiversity ontologies into the NCBO BioPortal promotes
mapping (and reuse of terms) between bio-medical and biodiversity
ontologies.
• An instance of the BioPortal software for biodiversity requires long-term
obligations to host and maintain the resource – does e.g. GBIF have the
resources to offer to host a BioPortal instance?
http://bioportal.bioontology.org/projects/168
24

25. GBIF KOS resources
Concept vocabularies (skos:conceptSchema, RDF)
• Darwin Core, Darwin Core “extensions”, NCD, GNA,
Audubon Core (and other concept vocabularies).
as a basis and foundation for
Software application schema (XML, XML schema)
• Darwin Core Archive (DwC-A) controlled terminology
and controlled value vocabularies.
• Resources such as the DwC-A controlled term and
value vocabularies REUSE terms (by URI) from a
concept vocabulary.
25

26. Biodiversity KOS (based on Darwin Core)
Darwin Core (DwC) provides a flat list of concepts and terms,
expressed using RDF.
 DwC “extensions” (vocabularies for the declaration of
complementary and additional concepts).
 Reuse concepts from other vocabularies whenever possible.
Darwin Core Archive (DwC-A) has a star schema model.
• DwC-A core(s), extensions and controlled value vocabularies
• declared as XML lists of terms.
• DwC-A resources should always REUSE terms from Darwin Core
and other concept vocabularies.
• New DwC-A core types (data types), eg. sample? Formalize
class entities (ontology). [Current types: Taxon &
Occurrence]
 Formalize a governance structure for maintaining KOS resources based on the
principles established for Darwin Core (towards TDWG VoMaG).
26

27. Darwin Core Archive (DwC-A)
 DwC-A publish DwC records including terms
from DwC-A extensions.
 Simple text based format.
 Zipped single file archive.
Germplasm.txt
27

28. Darwin Core Archive extension (XML term list)
28 http://rs.gbif.org/sandbox/extension/audubon.xml

29. GBIF Vocabulary Server
The GBIF Vocabulary
Server can assist a
user to create and
manage DwC-A
extensions or
controlled value
vocabularies.
However, it is not
designed to create
RDF/SKOS concept
vocabulary resources
with reusable
concepts.
edit interface It can export XML, but
not RDF.
It is based on
XML export Scratchpads (v1), aka.
Drupal v 6.
29

30. Concept vocabulary (RDF/SKOS)
In progress:
XSLT -> HTML for
human readable
version.
30 http://rs.gbif.org/terms/geotime/geotimeConcept.rdf

31. Global Names Architecture (GNA)
Many of the GNA term URI identifiers does
not resolve (404 not found).
The rowType identifiers simply resolve to
the software application schema (to the
DwC-A extension).
We propose to formalize the GNA concept
declarations using RDF/SKOS for
improved re-usability of the GNA terms
and concepts.
31

32. Global Names Architecture (GNA)
RDF/SKOS
XML
The Global Names Architecture (GNA) terms were originally simply declared
by the DwC-A extension. We propose to formalize the GNA concept
32 declarations using RDF/SKOS for improved re-usability of the GNA terms.

33. Global Names Architecture (GNA)
RDF/SKOS
We propose to formalize the GNA concept declarations using
RDF/SKOS for improved re-usability of the GNA terms.
33

34. Darwin Core Archive extensions
• Global Names Architecture (GNA)
• Audubon Core (multimedia)
• Invasive species (GISIN)
• Genetic Resources (Germplasm)
• EOL species profile
• Taxonomic Concept Schema (TCS)
• Genomics Standards Consortium (GSC)
• Meta-genomics (?)
• ABCD (?)
• …
34

35. Controlled value vocabularies
• Country codes
• Language
• Basis of record
• Taxonomic rank
• Nomenclatural status
• Life form
• Life stage
• Geological time periods
• chronostratigraphy
• magnetostratigraphy
• Species interactions
• saproxylic interactions
• pollinators
• …
35

36. Example: master SKOS/RDF resource
en [
es
[
zh [
ja [
Presented
by Éamonn
36 http://rs.gbif.org/terms/dwc/dwc_translations.rdf

37. Semantic
MediaWiki
single
term
view
Presented
by Éamonn

38. Recommendations for the GBIF KOS work programme
• GBIF Resources Repository (http://rs.gbif.org/)
• Further development of new DwC-A extensions and controlled value vocabularies.
• Workflow for the translation of term descriptions.
• Versioning of terms/vocabularies.
• Continue the evaluation of collaborative tools for management of flat
vocabularies of terms (RDF/SKOS).
• Semantic MediaWiki, ISOcat, Protégé (web-protégé), …
• New semantic Wiki for the description of terms / glossary of terms /
community-driven discussion forum (with JKI, Gregor Hagedorn).
• Discussion, discovery and REUSE of existing terms.
• NCBO BioPortal as a repository for biodiversity ontologies.
• Explore BFO based OWL version of Darwin Core…?
• KOS governance structure developed and formalized by the (TDWG)
Vocabulary Management Task Group (VoMaG).
• Roadmap for KOS into the GBIF infrastructure, portal, tools…!
38

39. Furthermore, I
think that we
need persistent
identifiers!
Cato the Elder ended all his speeches in
the senate of Rome with: "Ceterum
autem censeo Carthaginem esse
delendam" (English: "Furthermore, I
think Carthage must be destroyed").
39 Available at http://www.bioontology.org/GBIF-vocabulary-management-for-biodiversity-informatics