Data Driven Innovation Interoperability Tech Track (#agridata) 18 - - PowerPoint PPT Presentation

Data Driven Innovation

Interoperability Tech Track (#agridata)

18 & 19 March 2015, Wageningen (@rfinkers)

Outline

§ Introduction “Interoperable Genetic Diversity” § Concept ”Bring Your Own Data” party § Aim BYOD Green Genetics? § Outcome BYOD Green Genetics § Hands on

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Climate change & Social disruption

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Photograph: ¡AFP/Getty ¡Images

http://www.theguardian.com/commentisfree/2015/mar/08/guardian-view-climate-change-social-disruption#img-1

Select a genetically diverse collection

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Legacy databases (e.g. Uniprot) Genome Sequence & Genome Annotation Genome Variation Data (re- sequencing collections) & SNP annotation Accession Passport Information Accession Phenotype Information

Web based aggregation of Information

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Interoperable Genetic Diversity

§ Genebanks should utilize genomics data

• But should not store them!

§ Genomics studies should make variant data available

• But need access to passport and

characterization & evaluation data.

§ Breeders needs tools to access diversity

Finkers, ¡van ¡Hintum et ¡al. ¡2014 ¡DOI: ¡10.1017/S1479262114000689

Genebank (s)

Genomics provider(s)

Intermezzo: Linked Open Data

Standardization makes the information interoperable

• Controlled vocabularies
• Machine readable
• Can all be queried by a single question vs. visiting

many websites

Interoperable Genetic Diversity (2)

§ Implications:

• Data can be stored at many different locations, but

can be found by computers

• Newly published information (in the correct format)

will be included automatically.

• Tools can be written to dedicated questions, such as

assessing allelic variation or utilize for collection management

Finkers, ¡van ¡Hintum et ¡al. ¡2014 ¡DOI: ¡10.1017/S1479262114000689

Genebank (s)

Genomics provider(s)

Interdisciplinary Approach Needed

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Genebanks Genomics provider(s)

Interdisciplinary Approach Needed

Need for Data Scientists & Domain Experts

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Genebanks Genomics provider(s)

Format: Bring your own Data Workshop

• 1. Users define the question(s)
• 2. Users and Linked data experts define concepts and
• ntologies
• 3. Experts help to create linked data and formulate

query

Bring Your Own Data Workshop

n More Info: http://www.dtls.nl/fair-data/byod/

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Data

• wners

Domain Experts Trainers Linked Data Experts

Example: Solanaceae Trait Ontology

BYOD in action

Select a genetically diverse collection

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Legacy databases (e.g. Uniprot) Genome Sequence & Genome Annotation Genome Variation Data (re- sequencing collections) & SNP annotation Accession Passport Information Accession Phenotype Information

Example Query

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PREFIX'rdf:'<http://www.w3.org/1999/02/22:rdf:syntax:ns#> PREFIX'rdfs:'<http://www.w3.org/2000/01/rdf:schema#> PREFIX'taxon:'<http://openlifedata.org/taxonomy_resource:> PREFIX'tdwg:'<http://rs.tdwg.org/dwc/terms/> SELECT'?acc ?label'(str(?lat)'as'?latitude)'(str(?long)'as' ?longitude) GRAPH'<http://cgngenis.wageningenur.nl>'{ ?acc taxon:species ?species'. ?species'rdfs:label ?label'. ?acc tdwg:decimalLatitude ?lat . ?acc tdwg:decimalLongitude ?long } }'order'by'?label

Outcome: Query Graph

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FAIRport* in VLPB?

*More on FAIRport in the presentation of Luiz Bonino, Thursday 10:30

Summary

§ Blueprint “Interoperable Genetic Diversity Shown” § BYOD resulted in interoperable data which could be

queried

• Request your own BYOD?

§ Public <-> Private integration possible

Select a genetically diverse collection

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Legacy databases (e.g. Uniprot) Genome Sequence & Genome Annotation Genome Variation Data (re- sequencing collections) & SNP annotation Accession Passport Information Accession Phenotype Information

Select a genetically diverse collection

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Legacy databases (e.g. Uniprot) Genome Sequence & Genome Annotation Genome Variation Data (re- sequencing collections) & SNP annotation Accession Passport Information Accession Phenotype Information

Working Prototype

§ screendump

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Questions?

Acknowledgements: BYOD team Theo van Hinthum & Frank Menting (CGN) Denis Guryunov & Martijn van Kaauwen (prototype)

• et. all.

HaploSmasher Hands On Session

§ HaploSmasher Prototype:

• genomic regions as input:

SL2.40ch03:10000..10200

• Solyc gene identifiers: Solyc10g085020
• Filter SNPs on impact type
• HIGH, MODERATE, LOW, MODIFIER

(SNPEff )

• No input validation yet
• Use correct notation, existing Solyc

gene ID’s

HaploSmasher

HaploSmasher

§ Query CGN FAIRdata graph

• Prototype is only generating links to CGN passport data now
• Graph data of three CGN accessions is available in our testset

HaploSmasher examples:

§ Haplotype Output

Example queries

§ http://www.plantbreeding.wur.nl/hs/ § Also, explore variation data & Linked resources

• http://www.tomatogenome.net

§ Examples:

• Beta-tubulin: Solyc10g085020
• HIGH & MODERATE vs. ALL effects
• Glutamate dehydrogenase Solyc05g052100
• Uridine kinase Solyc02g067880
• magnesium chelatase Solyc04g015750

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HaploSmasher examples:

§ Conserved housekeeping genes:

• Beta-tubulin Solyc10g085020 439 AA
• 1 SNP (HIGH & MODERATE effect) , two haplotypes

HaploSmasher examples:

• Beta-tubulin Solyc10g085020 439 AA
• 136 SNPs (all SNPEff impact types)
• Part of haplotype groups:

HaploSmasher examples:

• Glutamate dehydrogenase Solyc05g052100
• 13 SNPs (HIGH, MODERATE)

HaploSmasher examples:

• Uridine kinase Solyc02g067880
• 23 SNPs (HIGH, MODERATE)
• Example haplotype groups:

HaploSmasher examples:

• magnesium chelatase Solyc04g015750
• 21 SNPs (HIGH, MODERATE)
• Example haplotype groups: