Metadata analysis of germplasm collections

The case of agINFRA

Dr. Vassilis ProtonotariosAgricultural Biotechnologist, PhDAgro-Know Technologies, Greece

e-Conference on Germplasm Data InteroperabilitySession 2: “Status of data and metadata for germplasm”

Structure of the presentation

1. The agINFRA germplasm data sources– Chinese Crop Germplasm Information System– Italian National Germplasm Database

2. Current status– Mappings– Linked Data approach

3. Conclusions

The agINFRA germplasm data sources

agINFRA germplasm data sources

• Italian Germplasm Database (CRA)– Data available through EURISCO -> GENESYS– Uses EURISCO set of descriptors– Data also available through GBIF

• Chinese Crop Germplasm Information System (CGRIS/CAAS)– Data unavailable through aggregators– Own schema used for description of germplasm

accessions– Metadata exposure in CSV

agINFRA germplasm data analysis

1. Analysis of agINFRA germplasm data sources2. Analysis of metadata schemas used3. Identification of external schemas– Review of existing work

4. Definition of a base schema (descriptors)5. Mappings of various schemas to the base one6. Development of a linked data approach for

linking germplasm data sources

1. Chinese Crop Germplasm Information System (CGRIS / CAASD)

Chinese Crop Germplasm Information System (CGRIS)

• Provided by: Chinese Academy of Agricultural Sciences• A central repository for all type of plant genetic resources

information. It consists of six subsystems: 1. The management system of the National Crop Gene Bank (NCGB), 2. The management system of the long-term storage in Qinghai, 3. The management system of National germplasm Resources Nursery, 4. The crop characterization and evaluation database system,5. The database system for germplasm exchange at home and abroad

and 6. The management system of the medium-term storage in Beijing.

URL: http://icgr.caas.net.cn/cgrisintroduction.html

CGRIS: Data

At present, CGRIS owns• > 2000 MB data on 180 kinds of crops– including food crops, fibre plants, oil crops,

vegetable, fruit tree, tea, mulberry, tobacco, sugar, green manure crops, tropical crops etc.),

• 390,000 accessions of germplasm

CGRIS: Accessions (indicative list)

http://icgr.caas.net.cn/cgrisintroduction.html

Crop Germplasm Classification

Info on wheat varieties

Info on wheat varieties

CGRIS: Germplasm Data Query

CGRIS: Germplasm Data Query

CGRIS Metadata

• CGRIS germplasm descriptors based on own schema – can be seen as the de facto standard for

germplasm accession information in China. – Based on metadata scheme standards such as

developed by IPGRI (Bioversity) and GRIN

CGRIS: Basic Descriptors

CGRIS: Wheat descriptors

CGRIS Metadata: Next steps

• A mapping to the Multi-crop Passport Descriptors (MCPD) standard is intended– According to CAAS subject experts such a mapping

should be rather easy to produce.

CGRIS: Exposing data

• Data stored in relational DBs • Hosted in an SQL server• Exposure of data as CSV files (partially in

Chinese)

CGRIS: IPR information

• The CGRIS website is public and accessible for everybody. The information is provided free of charge but based on copyright.

• With regards to data exchange there is no explicit policy to follow.

• CGRIS does not have an Open Access mandate and the members of the CGRIS network apply their own institution policy.

2. Italian Germplasm Database (CRA)

Italian Germplasm Database

• Provided by: Italian Council for Research and Experimentation in Agriculture

• Developed in the context of the “Plant Genetic Resources/FAO” project in 2004 – Research Centres and Units of the CRA – The Institute of Plant Genetics of the CNR in Bari, – NGO “Rete Semi Rurali”– University collections (Perugia, Potenza etc.)

URL: http://fru.entecra.it

CRA Germplasm: Data

Current status of germplasm data (CRA)• 20,954 records from Italy are included in

EURISCO of which 17,212 from CRA • 28,509 records for 275 plant species in the

National Inventory (in general)– does not allow for identifying the number of CRA

germplasm records

CRA: Accessions (indicative list)

URL: http://fru.entecra.it/accessioni.php

Info on specific species

EURISCO descriptors

CRA Metadata

• Most CRA institutional databases use the MCPD– however, in the records provided to the National

Inventory several fields are often not filled. • Some CRA collections also use descriptors

defined by – the Union for the Protection of New Varieties of

Plants (UPOV) and – the National Register of New Varieties.

• Ensure mapping to the Multi-crop Passport Descriptors (MCPD)/EURISCO

CRA: IPR information

• The CRA website is public and accessible for everybody. The information is provided free of charge but based on copyright

• The Multilateral System (MLS) of the Treaty demands free availability of the information on the PGRFA that are under the management and control of the Contracting Parties and in the public domain (Treaty, Art. 11.2).

• This excludes – germplasm accessions that are subject to IPR and – other legally binding protection which restricts the Contracting

Party’s control over the material. – Accessions that are not covered by IPR include old and

autochthonous varieties, crop wild relatives and other material found in in-situ conditions, new cultivars not protected by IPR and cultivars whose IPR have expired.

Conclusions

Current status

• First version of mappings is available• EURISCO descriptors used as base schema– MCPD– Darwin Core for Genebanks– ABCD– CGRIS– CRA

Mapping table

Mapping table

Development of decision trees

Development of decision trees

Linked Data

• A linked data approach will be used by agINFRA for linking germplasm data sources

• OpenAGRIS already aggregates germplasm data using AGROVOC

Conclusions

• Both schemas / sets of descriptors can be mapped to the EURISCO ones

• Linked Data approach will facilitate linking of germplasm data from CRA/CGRIS

• EURISCO descriptors to be published as linked data– To be used as the base of passport data

• Linking to other germplasm standards– e.g. Darwin Core for Genebanks*

*https://code.google.com/p/darwincore-germplasm/wiki/DarwinCoreGermplasmMapping

Take home message

• The identification of common properties between different metadata schemas will facilitate the linked data framework

(Indicative) List of References

• agINFRA Deliverable D2.3 “Review of Content Requirements”

• agINFRA Deliverable D5.3 “Conceptual specification of linked agricultural data framework”

• agINFRA Germplasm Working Group Wiki http://wiki.aginfra.eu/index.php/Germplasm_Working_Group

• EURISCO passport descriptors http://www.ecpgr.cgiar.org/germplasm_databases.html

• Draft Mapping of EURISCO Descriptors to ABCD 2.06 http://www.bgbm.org/TDWG/CODATA/Schema/Mappings/EURISCO-2-ABCD.pdf

Source: http://verastic.com/social/why-do-people-not-say-thank-you.html

Contact me: vprot@agroknow.gr