What can Bioinformaticians learn from YouTube?

Data

New project. New schema.

EMBL: 20 different data formats

“A biologist would rather share their toothbrush than their (gene) names”

Mike Ashburner

YouTube loves to share

100 million views per day

114 apps

<rdf:RDF xmlns="http://www.affymetrix.com/community/publications/affymetrix/tmsplice#"

<Gene rdf:about="#1110002A21Rik"> <chr>chr1</chr> <hasVariant rdf:parseType="Resource"> <representedBy rdf:resource="#gi13385627"/> </hasVariant> <hasVariant rdf:parseType="Resource"> <representedBy rdf:resource="#gi18043402"/> </hasVariant> <strand>+</strand> </Gene>

RDF, OWL, SPARQL, GRDDL, WTF?

The semantic web, not The Semantic Web

Lower case ‘s’, lower case ‘w’

<tr><th class="two-column">Gene</th><td class="two-column"><table width="100%" cellpadding="4"><tr><td><strong><a href="http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?hgnc_id=1101">BRCA2</a></div></strong> (HGNC Symbol)</td><td><span class="small"> To view all Ensembl genes linked to the name <a href="/Homo_sapiens/featureview?type=Gene;id=BRCA2">click here</a>.</span></td></tr></table><p>This gene is a member of the Human CCDS set: <a href="http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&amp;DATA=CCDS9344">CCDS9344</a> </p></td></tr>

<tr class="hgene"><th class="two-column">Gene</th><td class="two-column"><table width="100%" cellpadding="4"><tr><td><strong><a href="http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?hgnc_id=1101" rel="hgnc_name">BRCA2</a></div></strong> (HGNC Symbol)</td><td><span class="small"> To view all Ensembl genes linked to the name <a href="/Homo_sapiens/featureview?type=Gene;id=BRCA2" rel="gene_list" >click here</a>.</span></td></tr></table><p>This gene is a member of the Human CCDS set: <a href="http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&amp;DATA=CCDS9344" rel="ccds">CCDS9344</a> </p></td></tr>

Can our web site be our API?

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618

my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );

my $gene = fetch_by_gene_stable_id( 'ENSG00000139618' );

More data on our sites than through the API

(we’re not the only ones)

RSS

iCal

XML

RESTful service

Representational state

transfer

psd-production/projects

psd-production/projects

GET

RETRIEVE

<projects>

<project> <id type="integer">8</id> <created-at type="datetime">2007-10-22T09:43:30+01:00</created-at> <family-id type="integer">3</family-id> <name>Test BAC</name> <updated-at type="datetime">2007-10-22T09:43:30+01:00</updated-at> <user-id type="integer">1</user-id> <workspace-id type="integer"/> </project>

</projects>

psd-production/projects

POST

CREATE

http://psd-production/projects/67

http://psd-production/projects/67

POST

UPDATE

http://psd-production/projects/67

DELETE

DESTROY

http://psd-production/projects/67

No installationNo setup

No fancy protocols

All you need is curl

Perl API

Ruby API

Tools

ToolsWorkflows

It’s all about the workflow

Trace archive vs SSAHA

Workflows are memes

Users add value

YouTube knows memes

Not invented here!

Reproducibility

Go with the flow

Quickly define workflows

Quickly reuse services

Data

Explore

Service Service

Data

Reuse workflows

YouTube for workflows+

Yahoo! Pipes for biological data

=Never having to write another BLAST parser

Design

Stop hacking

Program to interfaces

“The interface is a contract between data provider and

data consumer” Lincoln Stein

Design for reuse

Code for maintenance

Foster “accidental development”

114 YouTube apps

However...

Designing for reuse is hard

With great power comesgreat responsibility

With great power comesgreat responsibility

Available

Accessible

Reliable

Discoverable:where is your web site?

Design is for humans

YouTube is ‘only’ an online video site

A good UI outweighs smart features

“Monolithic solutions always fail”

Graham Cameron

Loose coupling rules

Don’t reinvent Eclipse

Thank you

GREENISGOOD.CO.UK