EMODnet Biology Work Package 2
Mark Costello & Dan Lear
[email protected]
[email protected]
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Task 2.1 Deliverables
D2.1 List of species tagged with role and importance within MSFD
reporting and the linked descriptor for inclusion in ERMS/WoRMS
(M6).
D2.2.EU-wide assessment of those species and communities
identified by national MSFD leads as required for MSFD monitoring
and reporting (M18).
Pan-European Species directories Infrastructure (PESI) has already
tagged entries in WoRMS with:
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CITES
•
Habitats Directive
•
Birds Directive
•
OSPAR
•
IUCN
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Descriptor 1: Biological diversity
Descriptor 2: Non-indigenous species
Descriptor 3: Population of commercial fish / shell fish
Descriptor 4: Elements of marine food webs
Descriptor 6: Sea floor integrity
OSPAR well advanced in indicator development (ICG-COBAM).
The stage of indicator development not clear for the other
Regional Sea Commissions.
Some indicators relate to habitats/communities/beds/reefs –
where possible these will be tagged against species as “candidate
indicators”
Deliverables depend on the agreement and publication of
indicators for all RSC’s – phased approach to the list
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
2.1 - Next 12 months
Post-doc at MBA will
• Review, asses and update existing lists for EU and Int Legislation and
Conventions to include species included in HELCOM, Barcelona & Bucharest
Conventions
•
Liaise with Regional Sea and national MSFD leads for indicators
• Carry out initial assessment of indicator status and timeline for delivery
• Populate matrix linking Species -> MSFD Region -> Indicator -> Descriptor
• Publish tagged species list for inclusion in WoRMS
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Task 2.2 Deliverables
D2.3: Organization of a data attributes workshop to discuss a
standardized vocabulary and prioritize the biological attribute and
trait information, in collaboration with WoRMS taxonomic editors
(M6).
D2.4: Publication of proposed standardized species attributes
vocabulary (M24).
D2.5: Selected European marine species tagged with relevant
species attributes information and available through WoRMS and on
the EMODnet biological portal (M36).
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Task 2.2 Progress to date
6 pilot project (4 in progress)
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•
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Planktonic Copepods
Planktonic Taxa
Benthic Taxa
Sea & Coastal Birds
Macro-algae (starts Oct 2013)
Invasive species (Completed)
Common terms compared
Already highlighting issues of confused or conflicting terminology
and the need for a vocabulary
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Task 2.2 Progress to date
Copenhagen Workshop on Traits (Aug 2013)
Produced a “wish list” for what a traits database should provide:
1. “Raw” data – not just coded/categorised data
2. Clear differentiation between ‘derived’ and/or ‘inferred’ traits
and ‘measured’ traits
3. Redundancy and hierarchy
4. Clear definition of traits, traits categories and trait values, hence
5. An agreed vocabulary, hierarchy or ontology.
6. Genomic, molecular and/or physiological and ecotoxicology traits
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Task 2.2 Discussions
Standards for traits are being development
GBIF are developing Plinian Core (extension of Darwin Core)
TDWG also have a group working on traits
Need to agree an interoperable publication method
Semantic Media Wiki allows comment/discussion on
definitions and export to RDF or SKOS
BODC Vocab Server – integration with SeaDataNet
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Potential for traits
vocab to be
hierarchical to increase
coverage and allow
future refinement
Example traits
hierarchy for
reproduction from
Reusser & Lee (2011) .
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Task 2.2 Discussions
Traits “coding” – the aggregation of traits to a single value (eg Depth
Range)
Traits should be stored as multiple values per trait per species to
facilitate different coding requirements and allow intra-species
analysis
Plus each value should be referenced
Has implications for storage and display in WoRMS
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
2.2 - Next 12 months
October 2013 - Collation of existing glossaries and traits catalogues
Jan 2014 - Produce a “flat” traits vocabulary for comment (with
examples in a Semantic Media Wiki)
Feb 2014 - Workshop in Paris (thanks to Ifremer) for discussion and
development of vocab
Dec 2014 - Further refinement and publication of vocab in standard
format (SKOS/RDF) with initial trait values in WoRMS
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013
Image courtesy of Science
EMODnet Biology Kick-off Meeting – VLIZ, Oostende 11-12 September 2013