nutrigenomics metadata 12_1_16_v4 (1)

Ben Busby, Ph.D.Genomics Outreach Coordinator

[email protected]

Recording Informative Metadata for Nutrigenomics!

Environmental Variation in the Rising Era of Individual Genome Sequence

Review of terminology and conceptsNext Generation Sequencing

Graphic Credit: Spencer Martin, UBC

Review of terminology and conceptsHow Genomes are Mapped and Assembled

© Martine Zilversmit 2013

http://1.usa.gov/1J1xmYs

NCBI NGS Online Workshop – Available on the NCBI YouTube Channel!

Review of terminology and conceptsHow Genomes are Mapped and Assembled

My View of Data Transfer Principles• Metadata Search

• Rapid NoSQL (for now)• Integration• Non-ambiguous identifiers

• Transferring Small amounts of Data• Data still gets transferred in the cloud• Underlying structure• Finding specific data from validated formats

• Democratization of Data• Rapid comparison by domain experts

• Reporting• Metrics to report data upload and [unique IP] download of datasets• Post-publication User Review

• The NCBI LinkOut Mechanism as a test suite

BioProject

BioSample

dbGaP

2007 2008 2009 2010 2011 2012 2013 2014 2015

14,20153,216

139,311

374,464

485,727

566,181

660,665

876,849

1,002,935

Subjects

Investigation of NGS:SRA BLAST!

Investigation of NGS:MagicBLAST!

Domain-specific SRA and BioSample Submission Templates

Domain-specific Bulk SRA and BioSample Submission

GenBank and RefSeq!

24

Submission to GenBank!

Superbankit!

Reporting

Food Borne Pathogens

Where to Get More Information!

The Future

The Future (in my opinion)

The Future (in my opinion)…

Is already here

Ontological Standardization

Integration into a Larger Data Discovery Framework

BD2K - bioCADDIE

Integration into a Larger Data Discovery Framework

Integration into a Larger Data Discovery FrameworkExample: GOLD (JGI)

E-Utilities (Eutils)

Video available at:http://www.ncbi.nlm.nih.gov/education/webinars/

42

E-Utilities (Eutils)

43

Introducing… Entrez DirectThe E-utilities on the UNIX

command line

esearch –db gene –query “foxp2[gene] AND human[orgn]” | \

elink –target protein –name gene_protein_refseq | \

efetch –format fasta

ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/

44

Moving from FTP-scraping cron jobs to on-demand APIs

45

Edirect Cookbook (DRAFT)

46

Generating apps that work with our APIs and Data Structures,

and Improve Metadata:

NCBI Hackathons!

2015-2016, 8 Hackathons

Many Functional Software Products 3 Days

An Educational Resource for RNAseq

Available to

anyone on AWS

Part of an Online Workshop

First 5 lectures

now available

on

HackathonsJanuary 2016 6 functional software products 3 days

Hackathons

In April, July, August and

October 2016

we built on

those projects .

Finding immunogenic peptides from single RNA-seq samples

DangerTrackDifficult to assess regions

Combined score is the average of SVs, mappability, GC..

NCBI region list

Encode blacklist

Get More Info!

On Twitter @NCBI@DCGenomics

In 2017 we will Build on Those Projects!

Biomedical Informatics Hackathon January 9th – 11th NIH Campus, Bethesda!

NCBI Genomics Hackathon March 20-22nd NIH Campus, Bethesda

nutrigenomics metadata 12_1_16_v4 (1)

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