New trend of Biodiversity Informatics based on Global Biodiversity
Information Facility (GBIF) and Barcode of Life (BoL)
Yasumasa Shigemoto1) , Yoshikazu Kuwana2), Hideaki Sugawara3)
1Fujitsu Limited, 2Tokai Software, 3National Institute of Genetics◆ Summary of GBIF

Contact us: hsugawar@genes.nig.ac.jp◆ Examples of specimen or observation data

 In 2011, GBIF will provide 1 billion data of specimen exsitu or observation on 1.8 million species.
 GBIF is managed by the GBIF member countries.
 Biodiversity data is open to the public by organizations inthe GBIF member countries or NGOs.
 Statistics as of Dec. 2009
Data provider such as university
or museum

303 organizations/ 39 countries

Biodiversity information such asspecimen or observation

190 million

 Ranking of data contribution by countries
No.

Country

Number ofprovider

1
2
3
45United States
SwedenGreat Britain
FranceGermany

Number of biodiversity
data
89
69 millions
123 millions
1017 millions
1510 millions
19
6.9 millions

…

…

…

…

17

Japan

4

1.6 millions

…

…

…

…

◆ Roles of National Institute of Genetics (NIG)
 NIG collects domestic specimen/observation data andregister to international GBIF database.
From 20 domestic organizations such as Tokyo university,
national science of museum, Hyogo museum and so on.
510 thousands of specimen/observation data such as
mouse, insect, plant and Lact bacillus are registered to
GBIF from NIG.
 Promote the activity of biodiversity informatics in Japan.
Annual symposium
GBIF Japan Portal site

Acceptance of GBIF data Scientific name:
Mus musculus Linnaeus, 1758
 Taxonomic information:
Kingdom: Animalia, Phylum: Chordata, …
 Common name in each country
House Mouse (English)
Souris Commune (French) Year, month and day on which the specimen was collected.
 Location of specimen collected or observation such as
latitude, longitude, country, state and county.
 Display of distribution of specimen or observation
Please refer to the under left distribution chart of Barn
Swallow observation.
 Images of specimen or observation data

◆ Procedure of data registration to GBIF
1. To map your specimen/observation data to Darwin Core
which is the GBIF data standard.
Examples of 48 Darwin Core items（Most parameters are optional.) Catalogue number (e.g. C1-119467)
 Code of provider’s organization such as university ormuseum (e.g. HYO in the case of Hyogo Museum) Record type (e.g. observation/specimen/livingorganism/germplasm/seed) Scientific name and taxonomy (e.g. Kingdom, Phylum,Class, Order, Family, Genus, Species)
2. To send the GBIF Japan node the data in an Excel or atab delimited file which conform with Darwin Core.
3. The GBIF Japan node checks the file as follows.
 Whether the required items are filled in.
 Whether values are valid. For example, latitude andlongitude should be numeric.
 Whether catalog number is unique within the data set.
4. To send the GBIF Japan node your overview of
specimen/observation such as abstract, keywords and nameof administrator.
5. The GBIF Japan node registers and configures the data to
NIG server by using DiGIR provider software, then contact
GBIF headquarter by NIG.
Data provider 303
organization

Users

GBIF search box(Japanese common
name is acceptable.)

GBIF headquarter(Denmark)
retrieval

Dataexchange

Global index

http://gbif.ddbj.nig.ac.jp/◆GBIF search by Japanese common name Translation from scientific name to Japanese common nameis done by a dictionary developed by Database Center forLife Science.
 GBIF headquarter does not accept Japanese common name.
 GBIF Japan Portal site translate from Japanese name toscientific name and search specimen/observation data.
Example of searching by Japanese “TUBAME (Barn Swallow)”◆Species Identifying System by Barcode
 Barcode of Life project is building a database of partial
DNA sequences of Cytochrome Oxidae Subunit 1 (COXI) as
barcodes for the identification of animal species.
 When two high school girls of New York collected fishes in
the restaurant and analyzed them by fish BoL database ina university, it turned out that 14 fishes of 56 were
“Imitation” and it was reported by New York Times etc.
 Species Identifying System by using BoL data and 16S
rRNA for bacteria is open to the public by GBIF Japan
portal site.
Phylogenetic tree ofSpecies Identifying System
identifying species

Distribution chart of TUBAMEGBIF Japan portal site is supported by National BioResource Project (NBRP））.