Biodiversity Informatics

Sarah Faulwetter

Hellenic Centre for Marine Research

biodiversity informatics ≠ bioinformatics

organisms

genes

capture

storage

retrieval

analyses

deals with

individual organisms

species

populations

interactions between them

relationships between them

of data & information about

systematics

evolutionary biology

population biology

ecology

conservation biology

coming from disciplines such as

e x a m p l e s . . .

specimen / museum data

species occurrence data

taxonomic character data

taxonomy / classifications

quality control procedures

metadata standards

exchange protocols

data schemas and definitions

taxonomy / classifications

species occurrence data

species occurrence data

what occurs where?

why is it there?

why does it not occur in some other places?

has it been there before?

will it be there in the future?

are there other places it could occur?

taxonomy | classifications

finding

namingCafeteria roenbergensis

categorizing

describing

http://starcentral.mbl.edu/microscope/portal.php

n a m e s

scientific name:

Homo sapiens Linnaeus, 1758 genus name specific

epithetauthority year of

publication

names are labels for species

Aa paleacea

Limulus polyphemus

Kiwa hirsuta

Osedax frankpressiKingia australis

Pieris japponica

Pieris rapae

Trypanosoma brucei

Homo sapiens

names annotate data objects

names form the basis for an index

to search for and organize the totality of biological

content

Streptosyllis

names are inconsistent labels for species

p r o b l e m s

1one name has more than one meaning

Aotus trivirgatus

Aotus Illiger 1811

Aotus

Aotus Smith 1805

Aotus ericoides

.

2many names for the same organism

Koko

Горилла

Guerilla

Eastern Lowland Gorilla

Gorilla graueri

Gorilla berengei

Gorilla beringei Matschie

Gorilla beringei mikenensis

King kong

Gorilla gorilla

Virunga

Gorila

GorilleMountain gorilla

大猩猩

ゴリラ

THE ENCYCLOPEDIA OF LIFE

. . .

b u t w h a t a b o u t t h o s e

p r o b l e m s ?

t a x o n o m i c i n t e l l i g e n c e

disambiguation

& reconciliation

1one name has more than one meaning

disambiguation

= distinguish between different organisms with the same name

Aotus

monkey

primate

feet

eyes

vertebrate

plant

Fabaceae

leaves

flowers

Australia

2many names for the same organism

reconciliatio

n

= group names with the same meaning together

VERNACULAR NAMES    Gorilla English Mountain Gorilla English Eastern Gorilla English Eastern lowland gorilla English Gorille des plaines orientales French Grauer’s gorilla English Горилла Russian Gorila Spanish Bergsgorilla German Låglandsgorilla Swedish Bwindi Kinyarwanda Virunga Kinyarwanda 大猩猩 Chinese ゴリラ Japanese

OBJECTIVE SYNONYMS Gorilla beringei Gorilla beringei Matschie, 1902 Gorilla beringei mikenensis Lönnberg, 1917

MISSPELLINGS, SPELLING VARIATIONS,…Gorilla berengeiGorilla beringei Matschie, 1905Guerilla guerillaG. graueri MatschieG. graueri M. 1914

SUBJECTIVE SYNONYMS Gorilla graueri Matschie, 1914 Gorilla beringei graueri (Matschie, 1914) Gorilla gorilla

NameBank

over 10 million names

ClassificationBank

over 100 different classifications

b u t :

no classification has all names

many names are not placed yet into any classification

EOL needs

all names

to be able to index and show

all content

U N I O N

collect ALL names

use an existing classification

provide editing & annotation tools

insert all names

involve experts

indexing and navigational core of EoL

comprehensive – all names

taxonomically intelligent

access to multiple classifications

communal

always evolving, always current

names-based cyber-infrastructure

t h a n k y o u