Informatics for the International Mouse Phenotyping Consortium

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22 Οκτ 2013 (πριν από 3 χρόνια και 7 μήνες)

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Users

can

now

register

interest

in

genes



Will

receive

updates

on

knockout

strain

production

mousephenotype.org

The IMPC home page that provides access to IMPC online resources

THE IMPC WEB PORTAL

IMPReSS
-

Standardized protocols


The

web

portal

for

standardized

phenotyping

protocols


Protocols

based

on

conferences,

calls,

and

an

online

forum


IMPReSS

will

provide

mappings

between

measurements

and

phenotypes


The

International

Mouse

Phenotyping

Consortium

(IMPC)

is
:


Generating

a

knockout

mouse

strain

for

almost

every

protein
-
coding

gene

in

the

next

decade


Characterizing

each

strain

using

a

standardized,

broad
-
based

phenotyping

pipeline
.


Supported

by

the

MPI
2

consortium

consisting

of

experts

from

EMBL
-
EBI,

MRC

Harwell,

and

the

Wellcome

Trust

Sanger

Institute


The

MPI
2

consortium

is
:



Centralizing,

analyzing,

and

integrating

all

phenotype

data

generated

by

IMPC

partners


Standardizing

phenotype

protocols

to

allow

comparison

of

data

across

centers


Using

dedicated

‘data

wranglers’

to

work

with

IMPC

partners

to

ensure

proper

transfer

and

quality

control

of

data

occurs
.



Developing

a

statistical

analysis

pipeline

that

will

automate

genotype
-
to
-
phenotype

associations
.


Annotating

all

data

with

biomedical

ontologies

to

enhance

data

integration
.




The

community

is

invited

to

sign

up

to

receive

strain

production

updates

and

to

evaluate

the

presentation

of

data

as

we

develop

the

IMPC

web

portal
:


www
.
mousephenotype
.
org

Overview


The

MPI
2

consortium

is

involved

in

all

aspects

of

the

IMPC

pipeline

from

tracking

mouse

production

to

data

integration

and

dissemination

efforts



Genotype
-
to
-
phenotype

associations

will

be

made

by

an

automated

statistical

pipeline



The

IMPC

web

portal

is

under

a

rapid

development

cycle

with

features

being

added

after

user

testing
.

For

the

latest

see
:


beta.mousephenotype.org




Data

from

the

first

knockout

mouse

lines

phenotyped

as

part

of

the

IMPC

project

will

be

available

for

analysis

soon

Conclusion

Funding

1
)

Mallon

AM,

et

al

Accessing

data

from

the

International

Mouse

Phenotyping

Consortium
:

state

of

the

art

and

future

plans
.

Mamm

Genome
.

2012

Oct
;
23
(
9
-
10
)
:
641
-
.

PMID
:

22991088
.


2
)

Brown

SD,

Moore

MW
.

The

International

Mouse

Phenotyping

Consortium
:

past

and

future

perspectives

on

mouse

phenotyping
.

Mamm

Genome
.

2012

Oct
;
23
(
9
-
10
)
:
632
-
40
..

PubMed

PMID
:

22940749
.


User

driven

design
-

We

test

all

of

our

online

components

with

biomedical

researchers

to

improve

the

utilit

and

ease

of

use

of

the

IMPC

web

portal
.

References


This

resource

is

developed

and

maintained

by

the

MPI
2

consortium


Funding

supported

by

the

NIH

Common

Fund

Mechanism
:

U
54

HG
006370


Mouse

Phenotyping

Informatics

Infrastructure



MPI
2


The

imits

resource

was

initially

developed

developed

by

the

I
-
DCC,

supported

by

the

European

Union

(Project

number
:

223592
)


Mouse
production

centers

LIMS

IMPC

databases

Disseminate

IMPC

Pipeline


Export


Analysis

Standardizing

Procedures

& Tracking

Troubleshooting

&

Quality

Control

Statistical

Pipeline

&

Data
Integration













iMitS

Andrew Blake (1), Terrence Meehan (2) , Steve Brown (1), Paul
Flicek

(2), Ann
-
Marie Mallon (1), Helen Parkinson (2), William
Skarnes

(3
) and members of the IMPC consortium

(1) MRC Harwell, Harwell, UK, (2) EMBL
-
EBI,
Hinxton
, UK, (3)
Wellcome

Trust Sanger Institute,
Hinxton
, UK

Informatics for the International Mouse
Phenotyping

Consortium


The

MPI
2

consortium

coordinates

production

of

mice,

harmonize

protocols

and

data

export

across

centers
,

associate

genes

to

phenotypes

using

an

automated

statistical

pipeline,

and

performs

data

integration

to

gain

new

insights

into

human

disease
.


The Many Roles of the IMPC Informatics Team

Key IMPC Resources

Data

Wranglers
-

Dedicated

personnel

that

work

with

mouse

centers

to

ensure

data

is

uploaded

correctly

and

of

high

quality
.

Online

forum
-


A

forum

focused

on

production

and

phenotyping

protocols

for

the

IMPC

community

with

over

a

hundred

users
.

Ontology

Use
-

Data

is

annotated

to

widely

used

ontologies

including

the

MP,

MA,

EMAPA

to

aid

in

data

integration

efforts
.

Automated

Statistical

Analysis
-

A

statistical

package

in

the

widely

used

R

environment

is

being

developed

to

automate

genotype
-
to
-
phenotype

associations
.

QC Tools

Comprehensive Search Features

Acknowledgements


We

would

like

to

acknowledge

members

of

the

MPI
2

consortium

including
:

Julian

Atienza
-
Herrero
1
,

Chao
-
Kung

Chen
2
,

Armida

Di

Fenza
1
,

Richard

Easty
3
,

Simon

Greenaway
1
,

Alan

Horne
3
,

Vivek

Iyer
3
,

Natasha

Karp
3
,

Gautier

Koscielny
2
,

Jeremy

C
.

Mason
2
,

David

Melvin
3
,

Hugh

Morgan
1
,

Asfand

Qazi
3
,

Mathew

Redden
1
,

Ahmad

Retha
1
,

Luis

Santos
1
,

Duncan

Sneddon
1
,

Jonathan

W
.
G
.

Warren
2
,

Henrik

Westerberg
1
,

Robert

Wilson
3
,

Gagarine

Yaikhom
1

Contact us

www.mousephenotype.org
/contact
-
us


The

tracking

interface

used

by

IMPC

partners


Production

centers

register

intent

to

create

a

knockout

strain


Metrics

available

to

centers

and

funding

agencies


QC

tools

are

available

to

data

providers


Unusual

data

patterns

are

highlighted

as

part

of

quality

control


Data

wranglers

will

sign

off

on

data

after

passing

QC

Registration of Interest


Data

is

indexed

using

ontologies



Allow

users

to

drill

down

to

the

data

they

want

Beta Site


New

features

are

tested

on

a

beta

site


Includes


gene

page


phenotype

page


Data

visuallization