1. Bespoke
data
integra/on
using
open
source
&
seman/c
technologies
Nadia
Anwar,
Mar/jn
van
Iersel

2. What
do
we
do?
Direct
support
of
scien.sts
in
research
Data
Acquisi.on,
Management
and
Stewardship
Data
Integra.on
Answering
specific
and
complex
Bioinforma.cs
ques.ons
Tool
kit
deployment
and
maintenance
for
use
in-­‐house

3. Goals
 Integrate
data
- Typically,
using
linked
data
 Answer
biological
ques/ons
- Through
useful
visualisa/ons
 Reproducible
- Everything
is
scripted,
version
controlled
and
tracked
 Flexible
- Using
Mul/ple
Specialized
Tools
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

4. You
have
data,
I
have
data...now
what?
* Adapted from http://xkcd.com/208/ (CC-BY-NC)
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

5. hVp://fly.cloud.generalbioinforma/cs.com
FlyAtlas FlyCyc 1) Transform
into
triples
 Fly
Expression
Data
 Fly
Pathway
Data
2)
Infer
some
more
triples
3)
Visualize
triples

Pathways

Networks
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

6. 1st
you
need
some
triples
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

7. Then,
you
need
some
magic
 Transi/ve
Proper/es
 flyatlas:ProbeData
- A-­‐B-­‐C
→
A-­‐C
subclass
BP:DNAregion
 Class
Subsump/on
- FlyAtlas
to
BioPAX
 flyatlas:1234_at
is
a
flyatlas:ProbeData,
 Node
Integra/on
- iden/fiers.org
URI's
 flatlas:1234_at
is
a
BP:DNARegion
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

8. Next,
the
preVy
bit:
Visualisa/on
 PathVisio
 Cytoscape
 And
other
views
….
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

9. Finally...
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

10. <Posi/on
about:Flexiblilty/>
 Flexible
data
integra/on
- Use
Linked
Data
- Use
Iden/fiers.org
- Don’t
be
afraid
to
extend
Ontologies,
that’s
the
point
- Be
reasonable
with
what
you
integrate,
you
can
always
add
more
later...
 Use
tools
that
best
answers
the
biological
ques/ons
 Script
everything,
you
will
probably
have
to
redo
it!
 It
needs
to
be
flexible,
this
is
research
and
is
not
about
building
the
best
Enterprise
like
“one
fits
all”
solu/on.
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts

11. We
are
hiring!
www.generalbioinforma/cs.com
Nadia
Anwar,
Mar/jn
van
Iersel
Expert
Bioinforma/cs
from
Bioinforma/cs
Experts