NGSonto and TypOn

João André CarriçoICBO 2015 Genomics Workshop

jcarrico@fm.ul.ptTwitter: @jacarrico

Disclaimers

• Work in Progress (kind of stalled to be honest)

• I’m not an ontology expert…

Motivation

• High Throughput Sequencing changed the Molecular Epidemiology field

• Raw sequencing data deposits:- Sequence Read Archive- European Nucleotide Archive- DNA Data Bank Japan

MotivationVery hard to traceback the processes performed on a sequencing study

sample → ????????? → reads →???? → contigs (draft genome) / SNPs

DRY LABWET LAB

NGSonto

• www.phyloviz.net/NGSonto• Split in 3 modules:

• NGS process pipeline• Protocols workflow• Study structure

NGS processes pipeline

Protocols Workflow

Study structure

Reused concepts

Reused termsFOAF agent

OBI plan specification,data itemprotocolsoftwaresoftware methodsoftware scriptstudy designDNA sequencerDNA extractDNA sequence datamaterial sampleDNA extractionDNA sequencinglibrary preparationinvestigation

SO contigread

Biosamples Sample

TypOn Isolate

EDAM parametersequence cuttingsequence

assemblysequence

assembly (de-novo), sequence assembly (mapping)

NGSonto termsdata processing protocolfiltering protocolsequence cutting protocolDNA extraction protocollibrary preparation protocolde-novo assembly protocolmapping assembly protocolsequencing protocolmessagelibrary,processed readsraw readsNext Generation Sequencing processdata processingfilteringstepExecution stepNGS workflow step

TypOn: the microbial typing ontology

http://bioportal.bioontology.org/ontologies/TYPON

http://code.phyloviz.net/typon

http://purl.phyloviz.net/ontology/typon

http://purl.phyloviz.net/ontology/20140910/typon ->Versioning

TypOn: the microbial typing ontology

Acknowledgments

• Mickael Silva IMM,FM,UL

• Francisco Couto FCUL• Alexandre Francisco INESC-ID, IST,UL • Cátia Vaz ISEL• Mário Ramirez IMM,FM,UL

Acknowledgments

PATHO Ngen Trace – Next Generation Genome Based High Resolution Tracing of Pathogens http://patho-ngen-trace.eu/

IRIDA – Integrated Rapid Infectious Disease Analysis http://www.irida.ca/