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Community Standards and Tools for Biodiversity Science
NIEHS Workshop for the Development of a Framework for Environmental Health Science Language
September 15, 2014Ramona Walls
iPlant [email protected]
The biodiversity standards landscape
ECOLOGY
field surveysobservationsenvironments
MUSEUM COLLECTIONS
specimenschecklists
GENOMICS
moleculesspecimens
The biodiversity standards landscape
ECOLOGY
ISO/OGCO&M
OBO-E
MUSEUM COLLECTIONS
DwC/TDWGGBIF
GENOMICS
GSCINSDC
Changing landscape
ECOLOGY
GENOMICS
MUSEUM COLLECTIONS
Overview of existing standards
• Darwin Core (DwC)
• Minimum Information for any (x) Sequence (MIxS)
• Extensible Observation Ontology (OBO-E) and the Observation and Measurements (O&M)standard
Darwin Core
• Positives:
– widely used
– comprehensive
– available as RDF
• Negatives:
– ambiguous definitions
– no logical structures
Minimum Information for any (x) Sequence (MIxS)
MIxS
• Positives:
– easy to use
• truly minimal
• spreadsheet is familiar
– available as RDF
• Negatives:
– no logical structures
– minimum not always sufficient for re-use
Extensible Ontology for Observations (OBO-E) is an ontology that is consistent with the Observation
and Measurement (O&M) schema
Madin et al. 2007 Ecol. Informatics doi: 10.1016/j.ecoinf.2007.05.004
OBO-E:
O&M:
OBO-E with extensions for modeling data on crabs that live on corals measured along a transect
Madin et al. 2007 Ecol. Informatics doi: 10.1016/j.ecoinf.2007.05.004
OBO-E
• Positives:
– consistent with widely used standard (O&M)
– logical structure
– extensible to many kinds of observations
• Negatives:
– not easily accessible to many scientists
– not yet widely used or tested
– not yet aligned with other biological ontologies
Understanding GxPxE requires us to work at the intersection of disciplines
ECOLOGY
GENOMICS
MUSEUM COLLECTIONS
The Biological Collections Ontology (BCO) aims to integrate biodiversity data across
sources and sub-disciplines
Moorea Biocode
bioinventory event
Museum
specimens
Tissue sample at
Smithsonian Institution
Gut sample Metagenomic sequences
at CAMERA portal
Genbank
sequence
Digital image stored
on Morphbank
identification
John DeckJohn WieczoreckRobert Guralnick+ many more!
Challenge: getting existing datasets into a form where we can query them the way we want
NEON soil sample data mapped to BCO
Scaling up: bringing the metagenomicdata into the iPlant Data Commons
Bonnie HurwitzKen Youens-ClarkiPlant staff
Scaling up: bringing the metagenomicdata into the iPlant Data Commons
Bonnie HurwitzKen Youens-ClarkiPlant staff
Step 1: validate workflow with existing data
Step 2: production workflow with “traditional” technology
alternative: leverage iRODS technology
iPlant Data Commons: workflows for the entire data lifecycle
project creation
iPlant Data Commons: workflows for the entire data lifecycle
specimencollection
project creation
iPlant Data Commons: workflows for the entire data lifecycle
specimencollection
analysis
project creation
iPlant Data Commons: workflows for the entire data lifecycle
specimencollection
analysis
project creation publication
Acknowledgements
