The document discusses knowledge management of experimental data through the ISA ecosystem. It describes the ISA-tab format and software suite that allows annotation and curation of experimental metadata. As a use case, it analyzes a dataset on metabolite profiling from a study of fatty acid amide hydrolase knockout mice. The ISA tools can represent investigations and assays, convert data to standardized formats, and facilitate sharing and analysis of experimental data.

1. The
open
source
ISA
soOware
suite
and
its
internaQonal
user
community:
Knowledge
management
of
experimental
data
Alejandra
González-­‐Beltrán
Senior Software Engineer, ISATeam
Oxford
e-­‐Research
Centre,
University
of
Oxford
Oxford,
UK
NETTAB
2012
–
Integrated
Bio-­‐Search,
Como,
Italy,
November
14-­‐16

2. Outline
• Knowledge
management
of
experimental
data
– SeSng
the
scene
– The
ecosystem:
ISA-­‐tab,
tools,
community
– Use
case
• Latest
addiQons
• Related
projects
&
main
points

3. SeSng
the
scene
health
agro
env
tox/pharma
Source
of
the
figure:
EBI
website
Bioscience
is
mulQ-­‐domain…

4. SeSng
the
scene
health
agro
env
tox/pharma
Source
of
the
figure:
EBI
website
Bioscience
is
mulQ-­‐domain…
Petabytes
of
data

5. SeSng
the
scene
health
agro
env
tox/pharma
Source
of
the
figure:
EBI
website
Bioscience
is
mulQ-­‐domain…
Petabytes
of
data
Experimental
metadata
in
Lab
books

6. inves&ga&on
study
assay
• Assist
in
the
annotaQon
and
management
of
experimental
data
at
source
• Deal
with
data
from
high-­‐throughput
studies
using
one
or
a
combinaQon
of
omics
and
other
technologies
• Empower
users
to
uptake
community-­‐defined
checklists
and
ontologies
• Facilitate
data
sharing,
reuse,
comparison
and
reproducibility
of
experiments,
submission
to
internaQonal
public
repositories

7. The
ecosystem

8. The
ecosystem
ISA software suite: supporting standards-compliant Towards interoperable bioscience data
experimental annotation and enabling curation at the Sansone et al, 2012
community level
Nature Genetics
Rocca-Serra et al, 2010
Bioinformatics

9. General
purpose
&
flexible
format
Domain
agnosQc
Captures
metadata
in
omics
experiments
and
tradiQonal
experiments
(e.g.
clinical
chemistry
and
histology)

10. faahKO
dataset
• Available
in
BioConductor
• Subset
of
the
original
data
on
global
metabolite
profiling
Saghatlian
et
al.
Biochemstry.
2004
• LC/MS
peaks
from
the
spinal
cords
of
6
wild-­‐type
and
6
FAAH
(facy
acid
amyde
hydrolase)
knockout
mice

11. -­‐
Define
key
enQQes
(e.g.
factors,
protocols,
parameters)
-­‐
Grouping
of
studies
-­‐
Relate
studies
and
assays
faahKO
invesQgaQon

12. -­‐ Subjects
studied:
source(s),
sampling
methodology,
characterisQcs
faahKO
study
-­‐ treatments/manipulaQons
performed
to
prepare
the
specimens
NEWT
UniProt
Taxonomy
Database
Mouse
Genome
InformaQcs

13. -­‐ Subjects
studied:
source(s),
sampling
methodology,
characterisQcs
faahKO
study
-­‐ treatments/manipulaQons
performed
to
prepare
the
specimens
Mouse
Adult
Gross
Anatomy

14. -­‐ measurement
type,
e.g.
metabolite
profiling
-­‐ technology,
e.g.
mass
spectrometry
faahKO
assay

18. Report
and
edit
the
descripQon
of
the
invesQgaQon
using
Google
Spreadsheets.
Use
Google
Spreadsheets
in
combinaQon
with
ISA-­‐
Tab
templates
(created
through
imporQng
the
Excel
file
from
the
ISAconfigurator)
and
OntoMaton
(for
ontology
search
and
tagging
support)
to
report
an
invesQgaQon.

19. -­‐ collaboraQve
annotaQon
-­‐ distributed
groups
of
users
-­‐ version
control
&
history
Ontology
Search
and
Tagging
in
Google
Spreadsheets

20. Create
templates
detailing
the
steps
to
be
reported
for
different
invesQgaQons,
complying
to
community
standards
(listed
at
),
e.g.
configuring
fields
to
be
(i)
ontology
terms,
(ii)
text
(with/without
regular
expression
tesQng),
(iii)
numbers
etc.

21. From
the
ISA-­‐Tab
we
can
perform
analysis,
convert
to
RDF/OWL
and
other
formats
for
submission/
sharing
to
local/remote
repositories,

22. From
the
ISA-­‐Tab
we
can
perform
analysis,
convert
to
RDF/OWL
and
other
formats
for
submission/
sharing
to
local/remote
repositories,
+
VisualisaQon
Methods

23. faahKO
Groups
faahKO
Workflow
Maguire
E,
Rocca-­‐Serra
P,
Sansone
SA,
Davies
J
and
Chen
M.
Taxonomy-­‐based
Glyph
Design
-­‐-­‐
with
a
Case
Study
on
Visualizing
Workflows
of
Biological
Experiments,
IEEE
Transac9ons
on
Visualiza9on
and
Computer
Graphics,
volume
18,
2012
(in
press)

24. • R
package
available
in
BioConductor
2.11
hcp://bioconductor.org/packages/release/bioc/html/Risa.html
• ISAtab
class
• Read
ISAtab
files
into
ISAtab
objects
and
save
ISAtab
files
• Build
xcmsSet
(xcms
package)
objects
from
mass
spectrometry
assays
• Augment
the
ISAtab
dataset
aOer
analysis
•
source
&
issues
tracking
hcps://github.com/ISA-­‐tools/Risa

25. • faahKO
package
v.
2.12
contains
ISAtab
files
describing
the
experiment
faahkoISA
=
readISAta(find.package("faahKO"))
assay.filename
<-­‐
faahkoISA["assay.filenames"][[1]]
xset
=
processAssayXcmsSet(faahkoISA,
assay.filename)
…
updateAssayMetadata(faahkoISA,
assay.filename,"Derived
Spectral
Data
File","faahkoDSDF.txt"
)
• MTBLS2
processing
and
analysis
using
Risa,
xcms
and
CAMERA
BioConductor
packages
Metabolights – an open access general-purpose repository for
metabolomics studies and associated meta-data
Haug et al, 2012
Nucleic Acids Research

26. ISA
syntax
&
Underlying
Material/Data
workflows
Input
Material
or
Output
Material
or
Data
Node
Data
Node
Characteris9cs[…]
Factor
Value[…]
Characteris9cs[…]
Factor
Value[…]
Protocol
REF
Parameter
Value
[…]
26

27. • Make
the
semanQcs
of
ISAtab
explicit,
including
materials
&
data
enQQes
&
processes
• Exploit
the
semanQc
annotaQons
available
in
ISAtab
datasets
• Augment
ISA
syntax
with
new
elements
(e.g.
groups),
facilitaQng
the
understanding
&
querying
of
experimental
design
• Facilitate
data
integraQon
&
knowledge
discovery/reasoning

28. ISAtab
datasets
as
linked
data
• Connect
to
the
growing
Linked
Data
universe
RDF
=
Resource
DescripQon
Framework,
OWL
=
Web
Ontology
Language
• CollaboraQons
with
Toxbank
(
)
&
W3C
Health
Care
&
Life
Sciences
Interest
Group
(HCLSIG)
<subject,
predicate,
object>
<lipoprotein>
<parQcipates_in>
<inflammatory
response>
<PRO:212342352>
<BFO_0000056>
<GO:0006954>

29. ISAtab
dataset
ISAtab
Graph
Parser
Analysis
ISA
Mapping
Parser

30. ISA-­‐OBO-­‐mapping

31. has
specified
input
type
material
enQty
Saghantelian_1
sample
collecQon
derives
from
has
specified
output
type
type
KO1
has
specified
input
processed
material
derives
from
extracQon
material
processing
type
has
specified
output
KO1_extract
has
specified
input
type
InformaQon
derives
from
mass
content
enQty
spectrometry
has
specified
output
type
./cdf/KO/ko15.CDF

32. Increasing
level
of
structure…
…different
target
audiences
Notes
in
Lab
books
Spreadsheets
&
Tables
Facts
as
RDF
statements
(informaQon
for
humans)
(ISAtab
metadata)
(informaQon
for
machines)

33. core
organizaQon
in
the
UK
Node

34. Implementation at Harvard
ISA
hcp://discovery.hsci.harvard.edu/

35. Implementation at the EBI
hcp://www.ebi.ac.uk/metabolights
Metabolights – an open access general-purpose repository for
metabolomics studies and associated meta-data
Haug et al, 2012
Nucleic Acids Research
35

36. The
ecosystem

37. @isatools
@biosharing
Isa-­‐tools.org
isacommons.org
biosharing.org