amlc
TRANSCRIPT
Data dissemination tools for organism
attributes and new data records
EOL: data retrieval and use 101
Jen Hammock1, Katja Schulz1, Jorrit Poelen3
1- Smithsonian’s National Museum of Natural History
2- Global Biotic Interactions
preview TraitBank: organism attribute data
How can I get at it?
Example: tissue mineralization biogeography
Overview of available datasets
Ecological interactions data
Fresh Data- recent observations (sneak peek)
Global Access to Knowledge About Life on Earth
http://eol.org
Global Access to Knowledge About Life on Earthhttp://eol.org/data_search
Web service
http://www.eol.org/info/traitbank_api
eg: http://eol.org/api/traits/204729
Example: tissue mineralization
biogeography
www.iobis.org
Example: tissue mineralization
biogeography
Example: tissue mineralization
biogeography
• 70,106 hits out of 130,160 OBIS records
• 3659 out of 7943 taxa
Example: tissue mineralization
biogeography
Example: tissue mineralization
biogeographyAlso available: crystal structure, etc.
• Aragonite
• Calcite
• Apatite
• etc.
Example: tissue mineralization
biogeography
• Occurrence Data: OBIS (2015). Global biodiversity indices from the Ocean
Biogeographic Information System. Intergovernmental Oceanographic
Commission of UNESCO. Web. http://www.iobis.org (consulted on
2015/05/11)
• Mineralization types from 145 literature sources
• Trait Propagation from higher taxa according to WoRMS and AlgaeBase
Marine data summaryLarge datasets
Environmental data ranges- lat, long, depth, temperature, water chemistry (OBIS and World Ocean Atlas)
Geographic distribution keywords (marinespecies.org & marineregions.org)
Habitat keywords textmined from EOL articles
Ecological associations data (GloBI, aggregates from many sources, eg: GoMexSI)
Tissue mineralization
Other interesting datasets
Copepod life history and size
Phytoplankton cell mass, volume, shape
PolyTraits- polychaete life history, physical description
Mollusk shell dimensions
See all datasets
GloBI: Global Biotic
Interactions
Jorrit Poelen
http://www.globalbioticinteractions.org/browse/
http://www.globalbioticinteractions.org/browse/
http://www.globalbioticinteractions.org/browse/
Fresh Data
(Hammock, Poelen)
Robertson & Van Tassell D. & J., CC-BY-NC-SA
OBIS (2015). Global biodiversity indices from
the Ocean Biogeographic Information System.
Intergovernmental Oceanographic Commission
of UNESCO. Web. http://www.iobis.org
(consulted on 2015/05/18)
problem: so many places
records might appear
Citizen reporting platforms
NaturaLista/iNaturalist
iSpot
Reef Life Survey
Small, localized monitoring projects or research projects
Social media and random places on the internet??!!!??
Museums and other natural history collections
Government agency surveys
Fresh Data- a community search index
Query the index for occurrence data (powered by GBIF +…)
Available to anyone
Geographical selection
Taxonomic filter
Save query
Initially only available to registered curators
Provide a sentence or two describing your interest in the data
Set email notification preferences (daily/weekly/etc.)
Anonymous or contactable?
Receive notifications when fresh data appears
Data providers will be notified that their data was sent to
someone
Engaging the public in scientific
research
What we know from recent studies of citizen science:
Data fit for use? This is a reasonable expectation, though it will not necessarily take less effort to train and manage volunteers as it would take to gather the data yourself.
Added benefit: inspired scientific literacy. *Not* necessarily taught by the citizen science project. Participants are motivated to go out and acquire more information.
Danielsen, F., P.M. Jensen, N.D. Burgess, R. Altamirano, P.A. Alviola, H. Andrianandrasana, J.S. Brashares, A.C. Burton, et al. 2014. A Multi-Country Assessment of Tropical Resource Monitoring by Local Communities. BioScience, 64:236-251. [pdf]
Fortson, Lucy, Karen Masters, Robert Nichol, E. M. Edmondson, C. Lintott, J. Raddick, and J. Wallin. "Galaxy Zoo." Advances in machine learning and data mining for astronomy (2012): 213-236.
also…. ask Jen!
Thanks
This work was supported by:
The Smithsonian’s National Museum of Natural History
The Sloan Foundation
David M. Rubenstein
Jen: [email protected]