1. EMODnet Biology Work Package 2
Mark Costello & Dan Lear

2. 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:
CITES
Habitats Directive
Birds Directive
OSPAR
IUCN

3. 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

4. 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

5. 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).

6. Task 2.2 Progress to date 6 pilot project (4 in progress)
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

7. Task 2.2 Progress to date Copenhagen Workshop on Traits (Aug 2013)
Produced a “wish list” for what a traits database should provide:
“Raw” data – not just coded/categorised data
Clear differentiation between ‘derived’ and/or ‘inferred’ traits and ‘measured’ traits
Redundancy and hierarchy
Clear definition of traits, traits categories and trait values, hence
An agreed vocabulary, hierarchy or ontology.
Genomic, molecular and/or physiological and ecotoxicology traits

8. 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

9. Potential for traits vocab to be hierarchical to increase
coverage and allow future refinement
Example traits hierarchy for reproduction from Reusser & Lee (2011) .

10. 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

11. 2.2 - Next 12 months
October Collation of existing glossaries and traits catalogues
Jan Produce a “flat” traits vocabulary for comment (with examples in a Semantic Media Wiki)
Feb Workshop in Paris (thanks to Ifremer) for discussion and development of vocab
Dec Further refinement and publication of vocab in standard format (SKOS/RDF) with initial trait values in WoRMS

12. Image courtesy of Science