2014.04.01 shorthouse redm400

Biodiversity Informatics

David P. Shorthouse, Université de Montréal

© Mr.checker (CC-SA 3.0 Unported)

What is biodiversity informatics?How are biodiversity data used?How are biodiversity data made available?What are the key challenges?What are its organizations?Where can I go for more?

Bioinformaticsfocused on the *omics

Biodiversity Informaticsinteroperability of scientific names,

classifications

History of “Biodiversity Informatics”

John S. Whiting

Canadian BiodiversityInformatics Consortium (1993)

Johnson Norm F. 2007. Biodiversity informatics. Annu Rev Entomol. 52:421-38.

DOI 10.1146/annurev.ento.52.110405.091259

Who, What,Where, When?

How are biodiversity data used?

Chapman, A. D. 2005. Uses of Primary Species-Occurrence Data, version 1.0. Report for the Global Biodiversity Information Facility, Copenhagen.

http://www.gbif.org/resources/2834

1 Taxonomy: research, indices, floras/faunas, field guides, phylogenies

2 Biogeography: distributional atlases, species distribution modeling, species decline

3 Life Histories and Phenologies4 Endangered, Migratory, and Invasive Species5 Impact of Climate Change6 Ecology, Evolution and Genetics: habitat loss,

ecosystem function7 Environmental Planning: impact assessments

Uses of Primary Occurrence Data

Uses of Primary Occurrence Data8 Conservation Planning: rapid biodiversity assessments,

identifying priority areas, reserve selection, sustainable use

9 Health and Public Safety: disease and disease vectors, bioterrorism, biosafety, parasitology

10 Bioprospecting11 Border Control and Wildlife Trade12 Education and Public Outreach13 Ecotourism14 Society and Politics: data repatriation15 Recreational activities

DOI 10.7717/peerj.11

DOI 10.1038/nature12872

How are biodiversity data made available?

The Process

CollectPrepareDigitizeStandardizePublish

Collect

© Ainsley Seago

PrepareCreating a long-term voucher

for scientific research

Specimen labelPrimary biodiversity data

What, when, where & who

DigitizeRecording specimen information

in a digital format

StandardizeDifferent database systems

Different formatsDifferent languages

Darwin CoreA common biodiversityinformation language

bit.ly/DarwinCore

175 terms

Darwin Core ArchiveA common biodiversity

information format

PublishMake available online

GBIF Integrated Publishing Toolkit (IPT)

What Other Kinds of Data?

ImagesObservationsPhylogenetic TreesGraphsUnstructured textsTaxonomic lists

What are the key challenges?

Scientific Names

DOI 10.1007/11530084_8

Homonymssame name for many taxa

Synonymsdifferent names for same taxa

Variant representationsorthography, spelling,differences in authority

DOI 10.1016/j.tree.2010.09.004

Globally Unique Identifiers

Data Quality and Fitness-for-Use

Giving Credit for Participation & Metrics of Success

What are (a few of) the Biodiversity Informatics organizations?

*.globalnames.org

Edit

http://gnite.org

Index

http://gni.*

Atomize…{genus: { epitheton: "Pardosa" },species: { basionymAuthorTeam: { year: "1892”, authorTeam: "Banks", author: ["Banks”] }, epitheton: "moesta", authorship: "Banks, 1892" }}…

Resolve

http://resolver.*

Find

http://gnrd.*

Global Names

What about Canadian Organizations?

Federal Biodiversity Information PartnershipCanadian Biodiversity Information FacilityOBIS Canada

canadensys.net

Academic11 universities, 5 botanical

gardens & 2 museums35+ researchers

30 collectionsPlants, insects and fungi

Canadensys HeadquartersUniversité de MontréalBiodiversity Centre

13 mil. specimens2 out of 3 are insects

GoalMobilize 3 million specimen

records (20%)

DownloadPer dataset

Not very flexible

ChecklistsData about taxa (vs specimens)

also supported byDwC-A, GBIF & IPT

VASCANDatabase of Vascular Plants of Canada

data.canadensys.net/vascan

Biological Survey of CanadaThe Biota of Canada

http://www.biologicalsurvey.ca

Data licenseAllow data to be used

bit.ly/cc0-for-data

Where can I go for more?

Social Venues

TAXACOMTDWGCanadensys Google GroupiDigBioECN-LGitHubTwitter

What Skills/Technologies Might I Need?

Web programming: HTML5, cssRelational databases: PostgreSQL/PostGIS, MySQLNoSQL data stores: Neo4j, CouchDBProgramming languages: R, Python, ruby, Java, JavaScriptCreativity with data: dynamic visualizations

Biodiversity Informatics Commercialization

iekho.comBranché

What is biodiversity informatics?How are biodiversity data used?How are biodiversity data made available?What are the key challenges?What are its organizations?Where can I go for more?

www.canadensys.net@canadensys@dpsSpiders

david.shorthouse@umontreal.ca

David P. Shorthouse