Collecting and sharing framework ofmarine biodiversity data in the NorthWestern Pacific region

Takashi Hosono
Global Oceanographic Data Center (GODAC),Japan Agency for Marine-Earth Science and Technology (JAMSTEC)

Self introduction
1998-2005: Population dynamics of epifaunal caprellids in algal bed
2006-2010: Ecology of by-catch species in longline fisheries
2010-2014: Detecting suitable habitat for foraminiferal species incoral reef
2014: Data manager of OBIS Japan

https://obis.org/contact/Today's outline- Global activities on integrating biodiversity information (GBIF &OBIS)- Key factors in OBIS framework: data format and database forscientific name
- OBIS node activities in Japan- Data use-caseToday's outline- Global activities on integrating biodiversity information (GBIF &OBIS)
Biodiversity information are composed from biological occurrence
data
https://obis.org/products/maps/202002/species_
pacific_5.png

Observations=Biological occurrence records

Points of the records

Species distribution/
Community structure

Past (XXXX-2000)
Textual information in scientific papers (paper media) → limited data source

Heptner, M. V. 1963. Reproductive biology and life cycle of Caprella septentrionalis Kroyer (Amphipoda,Caprellidae) in the White Sea (In Russian with English summary). Zoologicheskii Zhurnal 42:1619-1630.

Arimoto, I. 1976. Taxonomic studies of caprellids (Crustacea,Amphipoda, Caprellidae) found in the Japanese and adjacentwaters. Special Publications from the Seto Marine BiologicalLaboratory Ser. III:1-229.

Present (2000-2020)
・Many global-scale database such as GBIF or OBIS etc. have been lunched.

http://beta.iobis.org/

http://www.gbif.org/

Currently, we can easily accessmany distribution data on target
species through global scaledatabases

OBIS and GBIF

http://beta.iobis.org/Target
Records
Data format
Data platform
Data sharing

Marine only
63,695,682
DarwinCore
IPT
Shared with GBIF<<<==

http://www.gbif.org/

Land and Marine
1,634,289,915
DarwinCore
IPT
Shared with OBIS

Data flow in OBIS

cited from OBIS node training materials

OBIS nodes in Asia-Pacific region
Total 8 nodes
OBIS China
OBIS JapanIndOBISSEA OBISOBIS Malaysia
OBIS Indonesia

SWP OBISOBIS Australia

https://obis.org/contact/Today's outline- Global activities on integrating biodiversity information (GBIF &OBIS)- Key factors in OBIS framework: data format and database forscientific name
- OBIS node activities in Japan- Data use-caseSummary of OBIS data
presence records: 63,695,682
Datasets: 3,689
Accepted species: 146,970
https://mapper.obis.org/

To integrate large datasetsmoothly,
OBIS use-data standard: Darwin Core
-common scientific name DB: WoRMS
cited from OBIS node training materials

Darwin Core (by TDWG)

Darwin Core is a body of standards for biodiversity informatics.
It provides stable terms and vocabularies for sharing biodiversity data.
OBIS Node data manager always check data from data providers andmodify the data to correct DwC format (Taxon; Location; Date, etc.).

https://dwc.tdwg.org/terms/#location

44 terms related to location information
https://obis.org/manual/darwincore/WoRMS for scientific nameSome species have many synonymized name.
WoRMS provides- correct spelling- validity of the names- scientific name ID as URN style- web service to check scientific namehttp://www.marinespecies.org/aphia.php?p=taxdetails&id=165853

Example of DwC data
8 required terms in OBIS framework:・scientificName・scientificNameID・occurrenceID・eventDate
・decimalLatitude
・decimalLongitude
・occurrenceStatus・basisOfRecord
scientificName

scientificNameID

occurrenceID

eventDate decimalLatitude decimalLongitude occurrenceStatusbasisOfRecord

Arca zebra

urn:lsid:marinespecies.org:taxname:420713 MCNUSB_001

1999-01-01-10.7413-63.8791 Present

PreservedSpecimen

Perna viridis

urn:lsid:marinespecies.org:taxname:367822 MCNUSB_002

1999-01-01

10.7413-63.8791 Present

PreservedSpecimen

Phyllonotus pomum urn:lsid:marinespecies.org:taxname:419944 MCNUSB_003

1999-01-01

10.7413-63.8791 Present

PreservedSpecimen

Strombus pugilis

urn:lsid:marinespecies.org:taxname:419695 MCNUSB_047

1999-01-01

10.8737-63.8805 Present

PreservedSpecimen

Trachycardium

urn:lsid:marinespecies.org:taxname:203976 MCNUSB_075

1999-01-01

10.8477-68.2424 Present

PreservedSpecimen

Chione cancellata

urn:lsid:marinespecies.org:taxname:397040 MCNUSB_006

1999-01-01

10.6886-63.8514 Present

PreservedSpecimen

Atrina seminuda

urn:lsid:marinespecies.org:taxname:420740 MCNUSB_007

1999-01-01

10.6886-63.8514 Present

PreservedSpecimen

Lyropecten

urn:lsid:marinespecies.org:taxname:203879 MCNUSB_004

1999-01-01

10.7413-63.8791 Present

PreservedSpecimen

iOBIS (2017) “Slides on OBIS data formats File” at OBIS Nodes Training Course (2017) accessthrough https://classroom.oceanteacher.org/mod/resource/view.php?id=7459

Today's outline- Global activities on integrating biodiversity information (GBIF &OBIS)- Key factors in OBIS framework: data format and database forscientific name
- OBIS node activities in Japan- Data use-caseOBIS Japan has developed original DB: BISMaL

A database specific to the region-Local language UI for local dataproviders-Taxonomic information around
Japan (39,445 taxa)

Marine biodiversity data around Japan

2,300,399 records (present/absent)
14,144 species
form various type of data providers (Scientists/ NPO/NGO/ Government)
Coastal monitoring/ Vessel investigation/ Literature-based data/ etc.

In BISMaL, data providers can-use DwC check tools-have their own dataset page

QC tool for data providers

Dataset page

BISMaL can estimates past environments forrecords by referring ocean reanalysis dataset

Hosono et al. (2020) WCMB_2020

Today's outline- Global activities on integrating biodiversity information (GBIF &OBIS)- Key factors in OBIS framework: data format and database forscientific name
- OBIS node activities in Japan- Data use-caseCollecting and sharing data enable us to-calculate biological index-analyze data gap-provide useful information for policy maker&-perform data driven science in global scale
Scientific Papers using OBIS data in 2020

Simple usage of occurrence data withestimated environmental data
Two common arrow worms with no environmental information
Krohnitta pacifica
K. subtilis

Extract old observation (in 1982-1992) from BISMaL
K. pacifica 904
K. subtilis
1136
Estimate temperature for these records using BISMaL function

Simple usage of occurrence data withestimated environmental data

Hosono et al. (2020) WCMB_2020

Estimated thermal habitats for two Krohnitta species.
The thermal habitats of two species are mostly overlapped, but Kernel density
plots detect habitat differences at lower temperature zone.

Today‘s outline- Global activities on integrating biodiversity information (GBIF & OBIS)- Key factors in OBIS framework: data format and database for scientific name
- OBIS node activities in Japan- Data use-case

In addition to the node activities,
we made educational materials for kids.

Produced by Naoto Higa (JAMSTEC, GODAC)

http://www.godac.jamstec.go.jp/j-obis/e/img/jobis_video_en.mp4