A database on biological traits of polychaetes Sarah Faulwetter Hellenic Centre for Marine Research http://polytraits.lifewatchgreece.eu
Polytraits: A database on biological traits of marine polychaetes
May 15, 2015
Presentation of Polytraits at the EMODnet Traits Vocabulary workshop in Paris. The presentation gives a short overview of the polytraits database and discusses its problems.
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A database on biological traits of polychaetes
Sarah Faulwetter
Hellenic Centre for Marine Research
http://polytraits.lifewatchgreece.eu
background
● first started in-house in 2006
● aim: collecting traits to perform BTA
● initially: dataset with 102 polychaete species from Mediterranean lagoons
● manual text mining
● link to citation, original text snippet recorded
● data collection: purpose-driven, not systematic
http://polytraits.lifewatchgreece.eu
background
~ 1000 species-level taxa
950 literature sources
~ 20,000 records
current aim: data mobilisation
semantically described terms
background
background
~ 1000 species-level taxa
950 literature sources
~ 20,000 records
current aim: data mobilisation
semantically described terms
background
~ 1000 species-level taxa
950 literature sources
~ 20,000 records
current aim: data mobilisation
semantically described terms
trait selection
trait selection
mainly: BIOTIC, papers by Bremner et al., Annelid reproduction (Rouse & Pleijel)
Consultation of existing literature & databases
Creation of list of traits & modalities
Adaptation for polychaetes
Definitions & ontology mapping
All traits are categoricalEach trait has several modalitiesEach modality can be present or/and absent
Polychaete-specific traits, e.g. pharynx structure, epitoky, range of body sizes...
Clear definition of traits, mapped to existing ontology concepts where possible
trait selection
trait selection
47 traits, 252 modalities
ca. 5 traits “unsuitable”
adult traits reproductive traits larval traits
21 17 9
problems encountered
● Trait not applicable for polychaetes: “migration” there is no significant migration in polychaetes→
“Unsuitable” traits
problems encountered
● Trait “wrongly” defined e.g. “Sociability” should be either “solitary, gregarious...” or “commensal of ..., parasite of..., ….”
“Unsuitable” traits
● Trait not applicable for polychaetes: “migration” there is no significant migration in polychaetes→
problems encountered
Modalities too specialised
problems encountered
Modalities too specialised
problems encountered
Modalities too specialised
problems encountered
Modalities too specialised
needshierarchy
problems encountered
Traits with “endless” modalities
problems encountered
Traits with “endless” modalities
problems encountered
Traits with “endless” modalities
problems encountered
Overlap / Correlation of traits & modalities
problems encountered
Missing traits ( & modalities)
● Larval & adult dispersal potential
● Additional morphology traits, e.g. sensory organs
● Resistance to physical disturbance
● Environmental position (infauna, epifauna,...)
● Socio-economic traits
If I could do it again...
Wishlist
● Clearly define each trait and modality from the beginning, incl. examples
● Introduce hierarchy of traits
● Avoid conversion of numerical values into categories
● Weighting mechanism (e.g. “usually found on sand, rarely on mud”)
● Add flags for uncertainty
● Add geo-coding of origin of information (same species does different things in different areas)
● Introduce species interactions
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