CWR CONSERVATION STRATEGIES Nordic/ECPGR Joint

Workshop

19-22 September 2016, Vilnius, Lithuania

OBTAINING AND DIGITIZING GEOREFERENCED DATA

Necla TAŞ

Aegean Agriculture Research Research

Institute/TURKEY

Geo-referenced Data

Georeference = to translate a locality description into a mappable

representation of a feature

Geo-referenced Data

Geographical data, in addition to genetic data, to evaluate

diversity for a number of practical applications such as

o coordinating authenticity of accessions from collections

within the country of origin,

o identification of duplicates,

o planning explorations to find novel germplasm in the wild,

o identification of core or reference collections,

o determining potential sources of new alleles based on the

species’ original habitat

( Greene and Pederson,1996; Holbrook et al., 1993; Khoury et al., 2010; Ramı´rez-Villegas et al., 2010; Williams,2005).

DATA SOURCES

Well-established data

Portals

Genesys

EURISCO

Crop specific databases

GBIF

Collecting Missions

(Bioversity International)

o Herbaria,

o Gene bank databases

o Researchers archives

o National programs

o International agricultural

research centers

o Scientific literature

o Individual scientists

http://herbaryum.tagem.gov.tr/

http://bioversity.github.io/geosite/

Collecting Missions; Original passport

data of more than 220,000 samples

collected around the world during

Bioversity International supported

missions.

Geo-referenced about 150,000 samples

Species Occurrence Data

GBIF (Global Biodiversity Information Facility):

Free and Open Access to Biodiversity Data(www.gbif.org)

With more than 570 million records

GBIF is the biggest biodiversity

database on the Internet. Provide free

and open accsess taxon and accession

distribution, conservation and

environmental data

Data on Herbarium and National Collections Being

Digitized for Internet Access

Name Description Web Address

JSTOR Plant Science

images of specimens

from 155 institutions

http://plants.jstor.org

Databases on crop gene bank holdings

GENESYS

a global portal to

germplasm accession

holdings of plant

genetic resources for

food and agriculture

www.genesys-pgr.org

European Plant Genetic

Resources Search Catalogue

(EURISCO)

http://eurisco.ecpgr.org/nc/home_page.html

System-wide Information

Network for Genetic

Resources (SINGER)

www.ars-grin.gov/npgs/searchgrin.html

Castañeda Álvarez N. P., Vincent H. A., Kell S. P., Eastwood R. J. and Maxted N., 2011. Chapter 14: Ecogeographic surveys. Collecting Plant Genetic Diversity: Technical Guıdelines.

Data on Herbarium and National Collections Being

Digitized for Internet Access

Name Description Web Address

Wild plant species gene bank databases

ENSCONET http://enscobase.maich.gr

Botanic Garden Conservation

International (BGCI) database

www.bgci.org/plant_search.php

National programs

Russia AgroAtlas www.agroatlas.ru

Brazil CRIA www.cria.org.br

Japan NIAS www.gene.affrc.go.jp/databases_en.php

Mexico www.biodiversidad.gob.mx/genes/proyectoMaices.html

Other (Taxanomic groups, herbaria, etc.)

Harold and Adele Lieberman

Germplasm Bank (cereals)

www.tau.ac.il/lifesci/units/ICCI/genebank1.html

Manchester Museum http://emu.man.ac.uk/mmcustom/BotQuery.php

Millennium Seed Bank, Kew

www.kew.org/science-conservation/save-seed-

rosper/millennium-seed-bank/index.htm

Castañeda Álvarez N. P., Vincent H. A., Kell S. P., Eastwood R. J. and Maxted N., 2011. Chapter 14: Ecogeographic surveys. Collecting Plant Genetic Diversity: Technical Guıdelines.

Data on Herbarium and National Collections Being

Digitized for Internet Access

Name Description Web Address

Natural History Museum, UK

www.nhm.ac.uk/research-curation/collections/departmental-

collections/botany-collections/search/index.php

Royal Botanic Gardens Kew http://apps.kew.org/herbcat/navigator.do

Royal Botanical Garden of

Edinburgh

www.rbge.org.uk/databases

SolanaceaeSource www.nhm.ac.uk/research-

curation/research/projects/solanaceaesource

United States Virtual

Herbarium

http://usvirtualherbarium.org

Virtual Australian Herbarium

http://plantnet.rbgsyd.nsw.gov.au/HISCOM/Virtualherb/virtualh

erbarium .html#Virtual

Castañeda Álvarez N. P., Vincent H. A., Kell S. P., Eastwood R. J. and Maxted N., 2011. Chapter 14: Ecogeographic surveys. Collecting Plant Genetic Diversity: Technical Guıdelines.

There are different resources in order to georeference

collections. The basics, include: (Chapman and Wieczorek

2006).

A database and database software

Topographic maps (electronic, paper or both)

Access to a good gazetteer – (many are available free via the

internet, either for downloading, or via on-line searching)

Preferably internet access (as there are many resources on the

Internet that will help in georeferencing and locating places)

Suitable computer hardware

Geo-referenced Data

Conclusion

It is recommended that manual methods (which use book gazetteers

that list locations with latitude and longitude, and detailed maps) be

applied to small datasets (i.e., fewer than 100 records) because it is

very time consuming (Castañeda Álvarez et al., 2011).

Geo-referenced Data

Gazetteers

Acme Mapper: For looking for and locating addresses, place names, natural features and road names around the world.

http://www.geonames.org/

http://mapper.acme.com/

GeoNames: locating global postal

codes, largest cities, capitals, highest

mountains and other information for the

world.

http://dma.jrc.it/services/gazetteer/

FuzzyG: to find geographic features

even when you do not know their exact

names. Returns a list of similar names.

some form of gazetteer to establish the location more precisely

Conclusion

The larger datasets, reliable online services are

used.More-automated services are also available

through the internet (Castañeda Álvarez et al., 2011).

Geo-referenced Data

Google Geocoding API:provides geocoding (converting

addresses into geographic coordinates) and reverse geocoding

(converting geographic coordinates into a human-readable address)

of addresses

Georeferencing & GIS Tools

The GEOLocate project is an effort to develop software and services

for translating textual locality descriptions associated with biodiversity

collections data into geographic coordinates.

http://www.museum.tulane.edu/geolocate/web/WebGeoref.aspx https://developers.google.com/maps/documentation/geocoding/intro

Georeferencing & GIS Tools

DIVA-GIS: Free GIS Software,

especially good for ecological niche modeling or verification of georeferencing.

http://www.diva-gis.org/gdata

GEOQUAL: Assesses the quality of

the geo-referencing of the passport

data (collecting sites)

Google Maps

Google Earth

allows the user to retrieve information based on administrative and locality details.

provides information about the features that are present in the area (e.g., rivers,

populated areas, administrative divisions).

Georeferencing & GIS Tools

http://manisnet.org/gci2.html

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necla.tas@tarim.gov.tr http://arastirma.tarim.gov.tr/etae