Introduction to Biodiversity Informatics

Biodiversity Informatics

David P. Shorthouse, Université de Montréal

Trochosa ruricola (De Geer, 1778)Trochosa terricola Thorell, 1856

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?

http://www.simplemappr.net

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.

Uses of Primary Occurrence Data

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 assessments8 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

Uses of Primary Occurrence Data

DOI 10.7717/peerj.11

Dr. Jeremy Kerr, University of Ottawa

How are biodiversity data made available?

The Process

CollectPrepareDigitizeStandardizePublish

CollectWhy do we collect specimens?

PrepareCreating a long-term voucher

for scientific research

Specimen labelPrimary biodiversity data

What, when, where & who

What?Scientific name & classification

• Anemone narcissiflora• Anemone parviflora• Anemone richardsonii• Arabis lyrata• Caltha leptosepala• Campanula lasiocarpa• Cardamine umbellata• Carex aquatilis• Carex capillaris• Carex enanderi• Carex gynocrates• Carex podocarpa• Carex vaginata• Claytonia sarmentosa• Corydalis pauciflora• Dodecatheon frigidum• Draba crassifolia• Dryas integrifolia• Epilobium anagallidifolium• Epilobium latifolium• Equisetum variegatum• Eriophorum angustifolium• Eriophorum brachyantherum• Eriophorum scheuchzeri• Festuca altaica• Huperzia haleakalae

When?Date -> trends

Where?Locality, elevation & habitat

GeoreferencingLocality description -> Coordinates

Who?Collector -> history

Locked in paper formatNot easily accessible

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

Database

DarwinCoreArchive

Tapir protocol

Standardize & publish

GBIF’scentral index

Harvest

User

Simplify

PublishMake available online

GBIF Integrated Publishing Toolkit (IPT)

What are the key challenges?

DOI 10.1016/j.tree.2010.09.004

DOI 10.1007/11530084_8

Homonymssame name for many taxa

Synonymsdifferent names for same taxa

Variant representationsorthography, spelling,differences in authority

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

Applying Global Names Tools

# N

ames

foun

d

Data Packages Published PDF0

10

20

30

40

50

60

70

t220 =, 3.68 p = 0.0003

Coming Soon

What about Canadian Organizations?

Federal Biodiversity Information PartnershipCanadian Biodiversity Information FacilityOBIS Canada

canadensys.net

A networkOf people and collections

Academic11 universities, 5 botanical

gardens & 2 museums

Canadensys HeadquartersUniversité de MontréalBiodiversity Centre

35+ researchersMainly systematists

30 collectionsPlants, insects and fungi

13 mil. specimens2 out of 3 are insects

GoalMobilize 3 million specimen

records (20%) by 2013

Carole SinouData Publication Support Professional

DownloadPer dataset

Not very flexible

ChecklistsData about taxa (vs specimens)

Now also supported byDwC-A, GBIF & IPT

VASCANDatabase of Vascular Plants of Canada

data.canadensys.net/vascan

Data licenseAllow data to be used

bit.ly/cc0-for-data

Where can I go for more?

Biodiversity Informatics Commercialization

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?

Thanks!www.canadensys.net

@canadensys@dpsSpiders

david.shorthouse@umontreal.ca

David P. Shorthouse