tdwg at the university of tasmania
TRANSCRIPT
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Integrating Bio-Data
Lee BelbinManager, Infrastructure Project
TDWG (Biodiversity Information Standards)
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Who has heard of GBIF?
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GBIF
The Global Biodiversity Information Facility
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GBIF
International organisation established to share bio-data
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GBIF
Supported by ~42 countries (including Australia) and ~35
international organisations
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GBIF
The Australian hub is through ABRS (ABIF)
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Who has heard of TDWG?
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…that’s what I figured
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TDWG
Formerly: The Taxonomic Database Working Group
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…but more accurately referred to as
Biodiversity Information Standards
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Biodiversity Information Standards
International group responsible for standards and protocols for
sharing bio-data
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EOL?
Encyclopedia of Life
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ALA?
Atlas of Living Australia
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GBIF, EoL, ALA …
…are now or will be based on TDWG standards
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So what?
(…hence this talk…)
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Science is getting more collegiate
… a good thing.
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The Project
US$2 million over 2.5 years (Gordon & Betty Moore
Foundation)
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Aim
To improve the standards for sharing 'bio-data'
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Why?
The whole is (far) more than the sum of the parts…
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PeopleLee Belbin (Hobart: Manager), Roger Hyam (Edinburgh: Systems Architect), Ricardo Pereira (Brasilia: Software Engineer)Donald Hobern (Copenhagen: GBIF & now Manager of the ALA),Stan Blum (San Francisco, TDWG old timer!)
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Once … we had paper!
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and calculators!
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The attitude:
“It’s Mine!”
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Then..
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… but we are moving to
…far more open sharing and integration of data
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This will enable
…more effective environmental and species conservation / management
(among many other things)
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To do this, we need effective standards
…using ‘web 2.0’ technologies
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Video
‘The web is us’
http://www.youtube.com/watch?v=6gmP4nk0EOE
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Standards?
…Good ones are transparent to most who use them
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But for your education…I’ll give you a little insight … it will be
good for you.
Promise
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Standards to exchange bio-data have three components-
1. An ontology2. GUIDs
3. Transport protocols
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1. OntologyIs a data model that represents a formal set of concepts within a domain and the relationships
between those concepts
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Ontologies…are the basis of the Semantic Web where objects are given
meaning which computers and humans can understand
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Ontologies
…can be used by machines to reason about the objects
within that domain
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Resource Description Framework …
RDF is the language of the Semantic Web
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ALL data can be stored in the form of ‘RDF triples’ …
subject – predicate (verb) – objectWine – has vintage - 2005
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2. GUIDs
Globally Unique Identifiers
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GUIDs
Assigned by authorities to their (bio) objects
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GUIDs
…Remain attached to data objects(with attribution!)
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GUIDs
… When ‘clicked’ return ‘semantic’ metadata / data
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GUID of Choice …
Life Science Identifiers(LSIDs)
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Transport Protocols
…Map local data to global standards
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Transport Protocols
… Enable searching across geographically separated data repositories (based on different
systems)
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The transport protocol of choice …
TAPIRTDWG Access Protocol for
Information Retrieval
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Transport Protocol
Video
http://www.youtube.com/watch?v=x9404is3RJ8
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An Example
Antbase, Google, Genbank, PubMed ‘skimmed’ for RDF
and GUIDs using TAPIR
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… Emergent Properties…there are specimens that have been barcoded and which are labelled in GenBank as unidentified (i.e., names like "Melissotarsus sp. BLF m1"), but the same specimen has a proper name in AntWeb (e.g., casent0107665-d01 is Melissotarsus insularis).
We can then use this information to add value to GenBank. For example, a search of GenBank for sequences for Melissotarsus insularis find nothing, but it does have sequences for this taxon, albeit under the name "Melissotarsus sp. BLF m1".
Rod Page
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