mged-toxico — MIAME for Toxicogenomics experiments

[Mged-toxico] suggestion for a checklist for exchange of data with a toxicogenomics study / microarray data

[Fostel, J. \(NIH/NIEHS\) [C] <fo...@ni...>]

we have been working on a checklist of what is "almost" minimal
information for exchange with toxicogenomics data, to support
interpreting the data in context of the study.
we have a draft paper and two example data files, and are opening it up
to comment via the MGED toxicogenomcis WG.list.
you can request a copy since these are too big to attach.  please reply
for a copy
we hope to invite journal editors and database repositories to endorse
this, and will deposit in the MICheck MIBBI site collecting other
minimal information checklists.

we look forward to your comments.
thanks for your attention!

regards,

...jennifer

Jennifer Fostel, Ph.D.
CEBS Scientific Administrator
NIEHS ITSS contractor

National Center for Toxicogenomics
PO Box 12233 Mail Drop F1-05
111 Alexander Drive
Research Triangle Park NC 27709-2233

phone 919 541 5055
fax 919 541 1460

[Mged-toxico] Virtual Conference: Live video streaming Onto and Toxicogenomics Track

[<wil...@or...>]

As part of the Virtual Conference on Genomics and Bioinformatics we will
be broadcasting live the session on Genomics of Cancer and
Bioinformatics for Toxicogenomics. You can submit your questions
directly please use
http://www.virtualgenomics.org/vcgb/program_2005.htm and click on submit
your question.

Please download or use WINDOW MEDIA PLAYER or
THEN go to FILE
THEN OPEN URL and then TYPE IN THE ADDRESS:

http://141.142.204.218:8080

Genomics of Cancer and Bioinformatics for Toxicogenomics
Discussion Leader: Maricel Kann, National Institutes of Health

The goals of the toxicogenomics track is to feature researchers trying
to elucidate molecular mechanisms of involved in studying: a) cellular
responses to environmental stresses, b) how responses to environmental
stressors extrapolate from one species to another; c) identify
toxicant-specific and adverse effects-specific patterns of gene
expression; d) develop gene expression-based biomarkers to particular
toxic components; e) develop a bioinformatic tools to integrate genomic
data dealing with the effects of toxicological compounds.

Susanna-Assunta Sansone. The European Bioinformatics Institute. UK
ToxicogenOMICS Omics standards, resources and data at EBI

Daniel Rubin, Stanford University. USA
Moving Beyond Ontology Libraries: Integrating and Accessing Biomedical
Ontologies to Annotate Experimental Data

Vladimir A. Kuznetsov., Genome Institute of Singapore. Singapore
A Scale-Dependent Statistic of Expressed Genes in MicroArray
Transcriptome Reveals Breast Cancer Phenotypes

Dennis Quan. IBM T. J. Watson Research Center. USA
How the Semantic Web Will Revolutionize Informatics Data Integration

Keith Dunker University of Indiana. USA
Intrinsic disorder in Cell-Signaling and Cancer-associated Proteins

Susan Wilson. Australian National University. Australia
Some Fundamental Considerations in Interpretation of Gene-expression
Profile Data with Applications to Cancer Research

[Mged-toxico] Toxicogenomics Track: Virtual Conference

[<ann...@vi...>]

 Fifth Virtual Conference on Genomics and Bioinformatics
October 25-28, 2005
Sharing Knowledge with the World

The Virtual Conference central broadcasting location is The Alliance
Center for Collaboration, Education, Science and Software (ACCESS).
From this location several speakers will be presenting their research...
This site will host a maximum of 150 researchers and students.

No registration fees

http://www.virtualgenomics.org/vcgb/conference_2005.htm

The virtual conference on genomics and bioinformatics (V-VCGB) is an
advanced collaborative environment featuring top researchers involved
in the fields of Computational Biology, Structural Genomics,
Toxicogenomics and Cancer Research, Databases, Infectious Diseases,
Ethics and Education and Nanobiotechnology. The main objectives of the
Virtual Conference are:

* Transcend geographical and economical barriers for the exchange of
ideas that facilitates the interaction and collaboration among
scientists and educators around the world.
* Address the benefits and limitations of the newest developments in
post-genomic technologies.
* Explore the social and ethical implications of genomic and
bioinformatic research.
* Establish new ways to introduce the high school community to today's
multidisciplinary science.

In order to accomplish our objectives, the Virtual Conference on
Genomics and Bioinformatics is completed without registration fees. The
conference is broadcast around the world using Access Grid and real-time
video streaming technologies. In addition to the real-time virtual
conference, presentations (visual and audio) are available on the web
for delayed streaming. Threaded discussion sessions with the invited
speakers and additional peer-reviewed paper sessions follow the
conference.

Who Should Attend?

Students, Bioinformatics' project leaders, Statisticians, Artificial and
Synthetic Life, Computational Biologists, Computational Chemists, IT
leaders and Genomic database administrators, Biotechnology business
analysts and anyone involved in the analysis of the genomic structure
and dynamics of living systems

To register to one of the Virtual Sites around the world:
http://www.virtualgenomics.org/vcgb/registration.php

To check the program:
http://www.virtualgenomics.org/vcgb/program_2005.htm

[Mged-toxico] CEBS update

[Fostel, J. (NIH/NIEHS) <fo...@ni...>]

in case you are interested, a description of the CEBS data dictionary has
just been published:
Abstract:
http://toxsci.oxfordjournals.org/cgi/content/abstract/kfi315?ijkey=vIMtRVY0p
pgdAA6&keytype=ref

PDF:
http://toxsci.oxfordjournals.org/cgi/reprint/kfi315?ijkey=vIMtRVY0ppgdAA6&ke
ytype=ref

CEBS is a public toxicogenomics knowledgebase, under development at the
NIEHS-NCT.  Becasue CEBS accepts data from the public, it must be able to
accept "any" study design / tox data, hence the need to create a method for
describing studies and data, which we have termed the CEBS-DD.  We would be
very interested in sharing novel study designs so that we can test the
CEBS-DD model.  Data in CEBS can be either private or public.

[Mged-toxico] Re: Mged-toxico digest, Vol 1 #36 - 1 msg

[Yasuo O. M. P. F. <os...@ji...>]

Thank you, Dr. Fostel for your reply,

We also study to find early predictor genes for renal toxicity, which 
change their expression at close to clinical dose or sub-clinical dose 
(serum/plasma concentration).
I will search clinical pharmacokinetics parameters, such as Cmax or AUC 
that may be useful to estimate clinical concentration.

Yasuo Oshima

On 2005/07/19, at 12:21, mge...@li... 
wrote:

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> Today's Topics:
>
>    1. RE: exposure conditions (Fostel, Jennifer (NIH/NIEHS))
>
> --__--__--
>
> Message: 1
> From: "Fostel, Jennifer (NIH/NIEHS)" <fo...@ni...>
> To: 'yasuo oshima' <osh...@ya...>,
> 	mge...@li...
> Subject: RE: [Mged-toxico] exposure conditions
> Date: Mon, 18 Jul 2005 12:07:52 -0400
>
> this depends on the question you ar trying to answer!
>
> we study early predictors of toxicity, or predictors present at 
> sub-toxic
> doses.
>
> for in vivo studies we tend to use one dose that is guaranteed to 
> provide an
> effect and a lower "sub-toxic" dose.  We tend to take time points 
> earlier
> than overt toxicity can be detected, however it is useful to have an
> exposure at which one is confident that all the exposed subjects will
> experience toxicity.
>
> so, to answer your question, i would say that having an endpoint 
> (induction
> of a gene, loss of viability, change in phenotype) is very helpful, 
> and i
> would include a dose that will produce this change and than use a 
> second
> dose at one fifth or one tenth of this one as well.  you could take 
> time
> points prior to the onset of toxicity, but knowing that all cultures 
> will
> eventually experience toxicity will help ensure that the changes in 
> gene
> expression that you see are related to toxicity rather than just 
> adaptation.
>
> -----Original Message-----
> From: yasuo oshima [mailto:osh...@ya...]
> Sent: Monday, July 11, 2005 4:03 AM
> To: mge...@li...
> Subject: [Mged-toxico] exposure conditions
>
>
> Dear Mged-toxic Members,
>
> We are now initiating gene expression analyses after drug exposure in
> vitro. In that project, we expose cultured cells to approximately two
> hundred drugs and compare gene expressions. We want to avoid a very
> high concentration that cells in ones body is never exposed in clinical
> use. However, the drug can stimulate the cells.
>
> How do people working in toxicogenomics project in vito judge exposure
> dose and term?
>
> Thank you for your consideration.
> Best Regards,
>
> _/ _/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/ _/ _/ _/
> Yasuo Oshima, MD, PhD, FACP
>     Division of Clinical Pharmacology,
>       Jichi Medical School
> 3311 Yakushiji Minamikawachimachi
>     Kawachigun Tochigiken 3290498 Japan
> tel +81-285-58-7388 fax +81-285-44-7562
> e-mail oshima@ji..
> _/ _/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/ _/ _/ _/
>
> __________________________________
> Save the earth
> http://pr.mail.yahoo.co.jp/ondanka/
>
>
>
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> _______________________________________________
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RE: [Mged-toxico] exposure conditions

[Fostel, J. (NIH/NIEHS) <fo...@ni...>]

this depends on the question you ar trying to answer!

we study early predictors of toxicity, or predictors present at sub-toxic
doses.

for in vivo studies we tend to use one dose that is guaranteed to provide an
effect and a lower "sub-toxic" dose.  We tend to take time points earlier
than overt toxicity can be detected, however it is useful to have an
exposure at which one is confident that all the exposed subjects will
experience toxicity.

so, to answer your question, i would say that having an endpoint (induction
of a gene, loss of viability, change in phenotype) is very helpful, and i
would include a dose that will produce this change and than use a second
dose at one fifth or one tenth of this one as well.  you could take time
points prior to the onset of toxicity, but knowing that all cultures will
eventually experience toxicity will help ensure that the changes in gene
expression that you see are related to toxicity rather than just adaptation.

-----Original Message-----
From: yasuo oshima [mailto:osh...@ya...] 
Sent: Monday, July 11, 2005 4:03 AM
To: mge...@li...
Subject: [Mged-toxico] exposure conditions


Dear Mged-toxic Members,

We are now initiating gene expression analyses after drug exposure in 
vitro. In that project, we expose cultured cells to approximately two 
hundred drugs and compare gene expressions. We want to avoid a very 
high concentration that cells in ones body is never exposed in clinical 
use. However, the drug can stimulate the cells.

How do people working in toxicogenomics project in vito judge exposure 
dose and term?

Thank you for your consideration.
Best Regards,

_/ _/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/ _/ _/ _/
Yasuo Oshima, MD, PhD, FACP
    Division of Clinical Pharmacology,
      Jichi Medical School
3311 Yakushiji Minamikawachimachi
    Kawachigun Tochigiken 3290498 Japan
tel +81-285-58-7388 fax +81-285-44-7562
e-mail oshima@ji..
_/ _/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/ _/ _/ _/

__________________________________
Save the earth
http://pr.mail.yahoo.co.jp/ondanka/



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This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening
July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual
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_______________________________________________
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Mge...@li...
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[Mged-toxico] exposure conditions

[yasuo o. <osh...@ya...>]

Dear Mged-toxic Members,

We are now initiating gene expression analyses after drug exposure in 
vitro. In that project, we expose cultured cells to approximately two 
hundred drugs and compare gene expressions. We want to avoid a very 
high concentration that cells in ones body is never exposed in clinical 
use. However, the drug can stimulate the cells.

How do people working in toxicogenomics project in vito judge exposure 
dose and term?

Thank you for your consideration.
Best Regards,

_/ _/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/ _/ _/ _/
Yasuo Oshima, MD, PhD, FACP
    Division of Clinical Pharmacology,
      Jichi Medical School
3311 Yakushiji Minamikawachimachi
    Kawachigun Tochigiken 3290498 Japan
tel +81-285-58-7388 fax +81-285-44-7562
e-mail oshima@ji..
_/ _/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/ _/ _/ _/

__________________________________
Save the earth
http://pr.mail.yahoo.co.jp/ondanka/

[Mged-toxico] MetaboMeeting: Data Standards - Metabolic Study

[Susanna S. <sa...@eb...>]

This is a meeting announcement.  SORRY about multiple posting

------------------------------------------------------

Dear Colleague,

http://smrsgroup.sourceforge.net/metabomeeting.html

The generation of standard file formats with which to exchange data and 
submit to repositories has brought great benefits to the fields of 
transcriptomics and proteomics, through the work of MGED (www.mged.org) 
and PSI (psidev.sf.net) respectively. Similarly the propagation of 
agreed standards by those same bodies is raising the level of 
experimental description across the board.

It is now time to extend this standardisation process to the study of 
metabolism, and in this age of functional genomics, to then play an 
active role in the existing formal collaboration between the standards 
movements in proteomics and transcriptomics.

I wish to draw your attention to the next 'MetaboMeeting' to be staged 
in Cambridge, UK on the 18th and 19th of July. This free-to-attend 
meeting will attract a wide range of researchers from both the public 
and private sectors; representatives of funding agencies and publishers; 
delegates from MGED and PSI; and vendors of lab instrumentation and 
analysis/databasing/LIMS software.

It is crucial that both the generators of data (who must ultimately use 
these formats and guidelines) and the developers of such formats and 
guidelines are firmly at the core of this process. This meeting will 
afford an excellent opportunity to ensure that that is the case. This 
will be a lively and interesting meeting, in an historic and beautiful 
city; we the organisers look forward to welcoming you.

Kind regards, the organising committee.

All correspondence to Chris Taylor <ch...@eb...>

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Chris Taylor (ch...@eb...)
HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-- 
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html                  

  

RE: [Mged-toxico] Differences between MAGE and MAGE/Tox

[Fostel, J. (NIH/NIEHS) <fo...@ni...>]

MAGE = microarray gene expression.  there is a MAGE ontology (MO), a MAGE
Object model (OM) and an exchange format (MAGE-ML)  MAGE was originally
designed to describe a microarray experiment.

the current MAGE OM has a BioMaterials Package which describes many of the
biological characteristics of the material in the experiment.  There is an
effort underway to move this information to a different part of the OM so
that other technologies, such as proteomics, can access it as well.

a new MGED WG, the RSBI WG, (Reporting Standards for Biological
Investigations) is working to define terms associated with the descritpion
of a complex biological investigation.  
RSBI consists of representatives from the MO, from the ToxWG, from the
EnvWG, and from NutWG (Nutrigenomics).  

It is the aim of the discussion to incorporate the modifications to the
Biomaterials Package and the RSBI terms into the second version of MAGE OM /
MO.  This will be discussed at the MGED meeting in Bergen in September, or
by joining working groups via the MGED site.

At the moment the strcuture is still under discussion, and changing as new
concepts and ue cases are identified.  The RSBI work will be reported in the
ToxWG as it is made public, at which time comments and suggestions from
toxicologists will be eagerly solicited.


-----Original Message-----
From: Khan, Ari (NIH/NCI) 
Sent: Thursday, May 26, 2005 6:38 PM
To: mge...@li...
Subject: [Mged-toxico] Differences between MIAME and MIAME/Tox


Where are the main differences between MIAME and MIAME/Tox?
OR
Where are the main differences between MAGE and MAGE/Tox?
Is there a MIAME/Tox to MAGE-OM/Tox document?

Thanks,
Ari



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RE: [Mged-toxico] Differences between MIAME and MIAME/Tox

[Fostel, J. (NIH/NIEHS) <fo...@ni...>]

MIAME = Minimal information about a microarray experiment; it describes the
information deemed necessary to interpret someone else's microarray data

MIAME/Tox was an effort to create a "MIAME" for toxicogenomics.  It merged a
large description of toxicology information with the then-current MIAME for
microarray.  you can find more information here:
www.mged.org/MIAME1.1-DenverDraft.DOC

this is distinct from defining the minimal information needed for a
toxicogenomics experiment.  The minimal info needed is, in essence, the
MIAME for the technology and a description of what the subject experienced /
what phenotype the subject showed.  In the case of an experiment of the
effects of a hepatocarcinogen, the minimal tox info would be the dose /
dosing regimen / time elapsed following the last dose and a relevant
phenotype such as the presence of liver enzymes in the blood, or the
observation of pathological changes in the liver.

the information would be different for a tox model of diabetes using a
genetic construct.  in this case the genotype and measures of pancreatic
function would be needed to interpret the toxicogenomics experiment.

there is a consortium trying to define, in the context of CEBS, the minimal
information to collect about a toxicogenomics experiment.  CEBS is the
Chemical Effects in Biological Systems.  after we submit the paper we plan
to post it on the CEBS Development Forum site, and will announce it here as
well.

I'll split your question into two threads


-----Original Message-----
From: Khan, Ari (NIH/NCI) 
Sent: Thursday, May 26, 2005 6:38 PM
To: mge...@li...
Subject: [Mged-toxico] Differences between MIAME and MIAME/Tox


Where are the main differences between MIAME and MIAME/Tox?
OR
Where are the main differences between MAGE and MAGE/Tox?
Is there a MIAME/Tox to MAGE-OM/Tox document?

Thanks,
Ari



-------------------------------------------------------
This SF.Net email is sponsored by Yahoo.
Introducing Yahoo! Search Developer Network - Create apps using Yahoo!
Search APIs Find out how you can build Yahoo! directly into your own
Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005
_______________________________________________
Mged-toxico mailing list
Mge...@li...
https://lists.sourceforge.net/lists/listinfo/mged-toxico

[Mged-toxico] Differences between MIAME and MIAME/Tox

[Ari K. <ar...@ma...>]

Where are the main differences between MIAME and MIAME/Tox?
OR
Where are the main differences between MAGE and MAGE/Tox?
Is there a MIAME/Tox to MAGE-OM/Tox document?

Thanks,
Ari

[Mged-toxico] (no subject)

[<sha...@sy...>]

-------------------------
Sharon Potter Lewis
Bioinformatics
Syngenta Biotechnology, Inc.
3054 Cornwallis Road
PO Box 12257
Research Triangle Park, North Carolina 27709

phone: 919 541-8613
fax:  919 541-8557
email:  sha...@sy...

[Mged-toxico] Carcinogen study use case

[Fostel, J. (NIH/NIEHS) <fo...@ni...>]

We are looking for examples of study designs that can be used to test models
being developed in several database and academic groups.  One example is
shown below.  We need a brief description of the study purpose and method.
If you could contribute others, especially study formats you use yourself,
it would be very helpful

Investigation: Study of long and short-term responses to Carcinogen X 
Purpose:  To understand the effect of carcinogen under a variety of exposure
regimens

Study design 1 = parallel, acute
Study design 2 = parallel, chronic
Study design 3 = parallel, acute
Microarray design = two-channel, hybridize treated vs untreated
Contact info:  Dr. ABCD

Study 1:
	Stressor  = Carcinogen X at 0, 100, 500 mg/kg
	Subjects = Fisher 344 rats, 14 weeks old, male
House the rats under standard conditions
	21 degrees, 50% humidity, 12 hour light-dark, NTP 2000 diet, two /
cage

Treat 40 rats with vehicle, 20 rats with 100 mg/kg and 25 rats with 500
mg/kg by gavage
Sacrifice 5 rats from each group at times 3, 6, 24, 48 hours.
For vehicle-treated rats, make two groups for each time point
Remove section of liver and blood from each animal at sacrifice
Send liver section to (1) microarray lab and (2) histopath lab
Send blood specimen to clin chem lab

Microarray experiment:
Extract RNA from each liver specimen
Pool the RNAs from 5 rats treated with vehicle only, sacrificed at 3 hours.
Also pool from vehicle-treated, 24 hours, and vehicle-treated, 48 hours.  Do
this twice, so there are a total of two 3 hour pools, two 6 hour pools, etc.
Label each with Cy3 and with Cy5.
Extract RNA from the three rats in each of the treated groups with the most
significant pathology findings.
Label each with Cy3 and Cy5.
Hybridize 3 hour 150 mg/kg treated RNAs with opposite color-labeled 3 hour
pool #1
Hybridize 3 hour 1500 mg/kg treated RNAs with opposite color labeled 3 hour
pool #2
Ditto for 6, 24 and 48 hours


Study 2:
	Stressor = Carcinogen X at 0, 10, 50 mg/kg
	Same Subject type, characteristics as Study 1

Treat 40 rats with vehicle, 20 rats with 10 mg/kg and 25 rats with 50 mg/kg
by gavage daily for 10 days.

Sacrifice 5 rats from each group on day 2 and 11, and after 3 and 6 months.
The sacrifice on day 2 and 11 occurs 24 hours after the previous dose.
For vehicle-treated rats, make two groups for each time point
Remove section of liver and blood from each animal at sacrifice
Send liver section to (1) microarray lab and (2) histopath lab
Send blood specimen to clin chem lab

Microarray experiment:
Extract RNA from each liver specimen
Pool the RNAs from 5 rats treated with vehicle only, sacrificed at 2 days.
Also pool from vehicle-treated, 11 days, 3 months and 6 months.  Do this
twice, so there are a total of two 2 day pools, two 11 day pools, etc.
Label each with Cy3 and with Cy5
Extract RNA from the three rats in each of the treated groups with the most
significant pathology findings.
Label each with Cy3 and Cy5.
Hybridize 2-day 10 mg/kg treated RNAs with opposite color-labeled 2-day pool
#1
Hybridize 2-day 50 mg/kg treated RNAs with opposite color-labeled 2-day pool
#2
Ditto for 11 day, 3 month and 6 month.


Study 3
	Stressor = Carcinogen X at 0, 1, 5 ppm in the food
	Same Subject type, characteristics as Study 1, except rat mash used
in place of 
NTP2000 diet, and singly house in place of two per cage

Treat 40 rats with vehicle, 20 rats with 1 ppm and 25 rats with 5 ppm in the
food for a period of 10 days.
Sacrifice 5 rats from each group on day 2 and 11, and after 3 and 6 months.
The sacrifice on day 2 and 11 occurs 24 hours after the previous dose.
For vehicle-treated rats, make two groups for each time point
Remove section of liver and blood from each animal at sacrifice
Send liver section to (1) microarray lab and (2) histopath lab
Send blood specimen to clin chem lab

Microarray experiment:
Extract RNA from each liver specimen
Pool the RNAs from 5 rats treated with vehicle only, sacrificed at 2 days.
Also pool from vehicle-treated, 11 days, 3 months and 6 months.  Do this
twice, so there are a total of two 2 day pools, two 11 day pools, etc.
Label each with Cy3 and with Cy5
Extract RNA from the three rats in each of the treated groups which consumed
the amount of Carcinogen closest to 100 mg/kg and 500 mg/kg total.
Label each with Cy3 and Cy5.
Hybridize 2-day 10 mg/kg treated RNAs with opposite color-labeled 2-day pool
#1
Hybridize 2-day 50 mg/kg treated RNAs with opposite color-labeled 2-day pool
#2
Ditto for 11 day, 3 month and 6 month.


cheers!


Jennifer Fostel, Ph.D.
CEBS Scientific Administrator
NIEHS ITSS contractor

National Center for Toxicogenomics
PO Box 12233 Mail Drop F1-05
111 Alexander Drive
Research Triangle Park NC 27709-2233

phone 919 541 5055
fax 919 541 1460

[Mged-toxico] Axel Klenk/Actelion is out of the office.

[Axel.Klenk@Actelion.Com]

I will be out of the office starting  12.02.2005 and will not return until
28.02.2005.

I am out of my office until Monday, 2005-02-28, and will respond to your
message when I return.
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[Mged-toxico] DNA Micro-array and image analysis market data

[Carlos M. <mec...@ya...>]

Hello,

 

I would interested to find some data on the current state of the market of DNA chips (total sales, past, present and expected evolution, major companies and their shares) and specially on DNA chips image analysis.

 

I am a Master’s Degree student in Technology Management at the University of Dauphine in Paris and I am currently working on a prospective study on DNA chips image analysis software.

 

Is it possible to find some of this information on the net on a free (or not very expensive) basis? Reports from Frost & Sullivan and the like are too expensive to a student’s wage. Thank you very much,

 

Carlos C. Meca


		
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[Mged-toxico] ToxWG, RSBI and toxicology terms

[Fostel, J. (NIH/NIEHS) <fo...@ni...>]

Recently the ToxWG is joined with other MGED working groups to give rise to
RSBI WG (Reporting Structure for Biological Investigations).

RSBI has proposed a tiered checklist format (extending MIAME and MIAME/Tox).
The first tier is the IDD (Investigation Design Description).  Tier II
consists of biology-specific checklists, Tier III consists of
technology-specific checklists.

The IDD is envisioned to describe the structure of a biological
investigation (groups, animal characteristics, treatment protocols, etc.).
We anticipate that domain-independent definitions should be possible, and
plan to keep the ToxWG and other WGs engaged in the discussion as the IDD
develops.

It is also clear that there are tox-specific terms and definitions, for
instance clinical tests, histopathology etc., which we could identify and
define so that (1) public databases are aligned with toxicology if they
contain toxicology information and (2) exchange of data between groups is
facilitated. 

Since it makes sense not to re-invent the wheel, if you have terms and
concepts already in use for toxicology data capture, this would be a good
forum to share them if you are able to do so.

CEBS (Chemical Effects in Biological Systems) at the NCT has begun the
process of aligning public data exchange formats, including SEND, Xybion,
ToxML, TDMS, and will make this available as it is finalized.

cheers!

Jennifer Fostel, Ph.D.
NIEHS ITSS contractor
CEBS Knowledgebase 

National Center for Toxicogenomics
111 Alexander Drive
PO Box 12233 MD F1-05
Research Triangle Park, NC 27709-2233

phone 919 541 5055
fax 919 541 1460

[Mged-toxico] MIAME/Tox-version 2 and the RSBI WGs

[Fostel, J. (NIH/NIEHS) <fo...@ni...>]

> This summer has seen significant change in the Toxicogenomics WG.  We
> began by trying to improve the current MIAME/Tox Checklist to produce a
> document that said, in essence, "at the minimum, a toxicogenomics study
> should identify the treatment (dose and time) group and comparator group
> for each subject, and a relevant measure of effect, such as histopathology
> or clinical chemistry."
> 
> However, the concept of "minimal" information has different definitions in
> different study types.  Thus is it not straightforward to know what to
> suggest to be captured without knowledge of the stressor type (chemical or
> genetic?), subject type (animal or culture?), and discipline (acute
> toxicology or reprotox or...?)
> 
> Additionally, other information can be recorded, which permits more
> faithful replication / understanding of the study, and so we also began an
> effort towards building a toxicology ontology, aimed to capture pertinent
> information beyond the minimum.
> 
> At the same time, we met other communities working on parallel efforts,
> and so have joined forces to produce the "RSBI Working Groups" (Reporting
> Structure for Biological Investigations), a collaboration of individuals
> working from both a biology-centric and microarray-centric view of 'omics
> studies.   This group produced the following proposal.
> 
> 
> 
> MGED Reporting Structure for Biological Investigations (RSBI)
> RSBI Working Groups (RSBI WGs)
> ~.~
> RSBI Tiered Checklist (RSBI TC)
> A proposed framework structure for reporting biological investigations
> ~.~
> MGED RSBI Working Groups: <http://www.mged.org> Mailing list:
> mge...@li... <mailto:mge...@li...>
> Toxicogenomics Working Group: mge...@li...
> <mailto:mge...@li...>
> Environmental Genomics Working Group: mge...@li...
> <mailto:mge...@li...>
> Nutrigenomics Working Group: mge...@li...
> <mailto:mge...@li...>
> 
> BACKGROUND
> MIAME/Tox - The first child
> Following the favorable response that the MIAME Checklist received, the
> MGED TWG has developed MIAME/Tox16, an extension of MIAME as applied to
> array-based toxicogenomic experiments. MIAME/Tox provides a structured
> annotation and framework that includes the conventional toxicology
> component of the experiment found to be missing in MIAME, which was
> designed to capture only the experimental microarray component.
> MIAME/Tox was been developed by the MGED TWG as part of a collaborative
> undertaking with the ILSI Health and Environmental Sciences Institute's
> (HESI) 'Technical Committee on the Application of Genomics to Mechanism
> Based Risk Assessment', the EMBL-EBI, the NIEHS-NCT and the NCTR-FDA.
> MIAME/Tox has initiated several discussions in the academic settings as
> well as in the industrial and regulatory arenas (including FDA and ECVAM).
> The MGED TWG has also established links with other inter-related
> initiatives2, including a Pharmacogenomics Standards Group, a joint
> project of HL7, CDISC and I3C, aiming to define the requirements for
> submission of microarray experiments to the FDA.
> 
> MIAME/Env and MIAME/Nut 
> As microarrays are incorporated into other complex biological
> investigations (e.g. Nutrigenomics, Environmental Genomics), it has become
> apparent that analogous minimal descriptors should be identified for these
> applications. MIAME/Env Checklists have been developed to fulfill the
> specific requirements of array-based Environmental Genomics applications
> and a MIAME/Nut is in preparation for Nutrigenomics applications.
> Discipline-specific initiatives are important, because they target 'real
> world' data capture requirements. A consequence of this however is that
> the knowledge can become fragmented, resulting in unnecessary
> duplications, problematic data exchange and ultimately incompatible
> databases. 
> 
> Furthermore, as other -omics technologies will be used in combination with
> microarrays, technology-specific Checklists will soon be insufficient to
> serve the scope of experimenters' needs! 
> MGED RSBI WORKING GROUPS
> Following plans of the MGED Society to extend its mission to other
> functional genomics, proteomics and metabolomics / metabonomics high
> throughput technologies, the MGED Toxicogenomics Working Group is likewise
> revisiting its mission statement. The Working Group is enlarging
> objectives and restructuring activities to include other communities,
> where efforts are already underway to promote standardization and develop
> databases to facilitate data exchange.
> The group recognizes the need for a 'single point of focus' for these
> domains and recommends the formation of a new working group to include
> Toxicogenomics, Nutrigenomics and Environmental Genomics domains of
> application. The proposed name is the Reporting Structure for Biological
> Investigations (RSBI) Working Groups.
> 
> The RSBI Working Groups have three main objectives, detailed in the
> sections below.
> 
> -Objective 1 - Collecting use cases
> RSBI Working Groups will act as a hub for use cases in these different
> communities, contributing to the activities of other MGED Working Groups,
> as they move toward a model to support exchange of multiple functional
> genomics experiments.
> 
> Objective 2 - Optimizing interactions
> RSBI Working Groups will aim to maintain collaboration between
> technology-driven standardization efforts and activities that relate to
> biological investigations in specific domains of application. It is a
> generally accepted view that duplication and incompatibility should be
> avoided where possible, maximizing the synergy and optimizing
> harmonization.
> Currently, the Human Proteomic Organization (HUPO)-Proteomics
> Standardization Initiative (PSI)24 is working to define community
> standards for data representation in proteomics to facilitate data
> comparison, exchange and verification, whilst the Standard Metabolomics
> Reporting Structure (SMRS)25 initiative aims to define community standards
> for metabolomics data representation establishing the foundation that will
> facilitate future regulatory acceptance. The activities of RSBI Working
> Groups will not constrain these needs. However, all have in common the
> need to accurately describe the design of an investigation, the
> characteristics and the treatments applied to the biomaterial, and to link
> these to any test results produced, for example, omics data or
> domain-specific data.  RSBI Working Groups will address the common need to
> unambiguously describe an investigation, as described in its third
> objective.
> 
> Objective 3 - Facilitating description
> RSBI Working Groups have initiated the development of a reporting
> structure for describing information intensive investigations
> unambiguously. The proposed reporting structure utilizes components of
> different MIAME-based Checklists into a 'tiered structure' concept. In
> trying to do this, we encountered the need to split the design module of
> the investigations (Tier I) from both the data requirements of a specific
> application (toxicological, environmental and nutritional endpoints) (Tier
> II) and the -omics data descriptions (Tier III). The resulting RSBI Tiered
> Checklist (RSBI TC) is a modular context depended structure, described in
> details below.
> 
> RSBI Tiered Checklist (RSBI TC) Objectives
> 
> RSBI TC should provide a mechanism for the participant members of
> Toxicogenomics, Nutrigenomics and Environmental Genomics communities to:
> 	(1) organize the information in a structured manner to promote
> harmonization across high throughput technologies and their domains of
> application (where a clear overlap exists), but retaining the specifics of
> each discipline;
> 	(2) identify minimal requirements of data to be recorded and
> exchanged in order to allow interpretation and validation of a biological
> investigation;
> 	(3) identify steps or processes currently considered quality metrics
> to validate the technology used and/or as checkpoints for performance
> assessment;
> 	(4) identify a common terminology for an unambiguous description, so
> that the same concept is described unambiguously within and across the
> different communities;
> Ultimately, this will enable structured queries to be made of such
> information-intensive, intricate investigations as well as the facile and
> meaningful interchange of information.
> 
> 
> THE PROPOSED REPORTING STRUCTURE
> From a checklist to a tiered structured checklist:  RSBI Tiered Checklist
> (RSBI TC)
> RSBI TC is a modular context depended structure, composed as it follows: 
> *	Tier I:  An Investigation Design Description (IDD) checklist, which
> is a high level description including an overview of the design of the
> study structure and components and the description of one or multiple
> in-life, clinical or in vitro investigations;
> *	Tier II:  Several 'discipline-specific' checklists, describing the
> information needed to interpret different applications  (e.g.
> toxicological, environmental, nutritional measures)
> 
> 	Currently, the existing modules under development include:
> 		o	Toxicogenomics Checklist:  The Minimal Information
> Needed for a Toxicology Experiment (MINTox) Checklist;
> 
> 		o	Environmental Genomics Checklist: The Minimal
> Information Needed for an Environmental Experiment (????) Checklist;
> 
> 		o	Nutrigenomics Checklist: The Minimal Information
> Needed for a Nutrition Experiment (???) Checklist.
> 
> *	Tier III:  Several 'test' checklists, describing the information
> needed to interpret the technology domains (microarray, proteomics
> measures and metabon/lomics measures)
> 
> 	Currently, the existing modules under development include:
> 
> 		o	The Minimal Information About a Microarray
> Experiment (MIAME) Checklist;
> 		o	The Minimal Information About a Proteomics
> Experiment (MIAPE) Checklist.
> 
> Proposed checklists will be developed in concordance with MGED OWG
> (Ontology Working Group) and other MGED efforts.
> 
> If you would like more information please ask -- we have some examples of
> the different tiers and are looking for additional use cases.
> 
> ...jennifer
> 
> Jennifer Fostel, Ph.D.
> NIEHS ITSS contractor
> CEBS Knowledgebase 
> 
> National Center for Toxicogenomics
> 111 Alexander Drive
> PO Box 12233 MD F1-05
> Research Triangle Park, NC 27709-2233
> 
> phone 919 541 5055
> fax 919 541 1460
> 

RE: [Mged-toxico] Open letter to microarray community

[Susanna-Assunta S. <sa...@eb...>]

Dear Erik,

sorry if I keep cc my reply to the list. I reckon would be beneficial
sharing our thoughts with the others, stimulating further discussion if
required.

I can see your concern to 'provide only partial data' to the reviews,
expecting to be asked for the remaining lot. This is an issue that has
been touched several time and requires a separate discussion.

However, this letter does not aim to address this issue. Further, it has
not been addressed to the journal editors, just to the manufacturers of
oligo sets for arrays, including:

a. QIAGEN Operon
b. Nimblegen Systems Inc
c. Illumina Inc
d. Affymetrix
e. Agilent
f. MWG
g. Sigma-Genosys
h. Stanford Functional Genomics Facility

Hope it helps.

Regards,
Susanna

ca...@en... (Eric Carlson) said:
> Susanna, You are correct in that we will sequence and verify "interesting
> genes", but we will not determine the identity of every clone used in the
> screening process. My concern was that this could be used by reviewers and
> editors to possibly force researchers to validate "every" clone used on a
> microarray before making a submisson viable for review, that is, if the
> standards are not written in such a way as to allow experiments similar to
> what i am doing.
>
> Thanks
>
> Erik
>
> -----Original Message-----
> From: Susanna-Assunta Sansone [mailto:sa...@eb...]
> Sent: Friday, April 09, 2004 10:42 AM
> To: Eric Carlson
> Cc: mge...@li...
> Subject: RE: [Mged-toxico] Open letter to microarray community
>
>
> Dear Erik,
>
> thanks for your comment. Please, see my replies below.
>
> ca...@en... (Eric Carlson) said:
>> I think that this depends upon your application. It could be dangerous
>> to
>> force researchers into set experimental designs. We are using
>> microarrays
>> to
>> identify novel genes. These are shotgun experiments using clones of
>> unkown
>> identities.
>
> I agree with you and indeed MIAME does not want to enforce standard exp
> design, penalizing novel applications like profiling unknow clones.
>
> MIAME addresses the issue of reporting data in an open scientific
> publication and aims to support full and independent analysis and
> verification of the data.
> In your case, I assume that once you identify 'interesting' clones, before
> publishing your data, you sequence them. What MIAME asks is to provide the
> relevant annotations for such clones: an accession number for a public
> record and any relevant coordinate (e.g. if only a subsection of a clone
> is amplified by PCR), not just a clone number with no link to any public
> resources.
>
> So in this specific case then, the message in the letter below would be
> addressed to the researcher (not the array manufacturer).
>
> Best regards,
> Susanna
>
>> I do believe that rules for reporting exactly what was done
>> (such as MIAME) are necessary, but exceptions must be allowed.
>
>
>
>>
>> Thanks
>>
>> Erik
>>
>> Erik A. Carlson, Ph.D.
>> Nelson Institute of Environmental Medicine
>> New York University School of Medicine
>> 57 Old Forge Rd
>> Tuxedo, NY 10987
>> (845)731-3545
>> ca...@en...
>>
>> -----Original Message-----
>> From: mge...@li...
>> [mailto:mge...@li...]On Behalf Of Susanna
>> Sansone
>> Sent: Thursday, April 08, 2004 10:36 AM
>> To: mge...@li...
>> Subject: [Mged-toxico] Open letter to microarray community
>>
>>
>> Dear Colleagues,
>>
>> The following open letter has been recently sent to many of the major
>> microarray and oligonucleotide manufacturers and users (please, text is
>> below). Essentially it states that the MGED board feels that the exact
>> reporter (probe) sequences, such as oligonucleotides should be given
>> when publishing microarray based data.
>>
>> I would like to ask your opinions on this matter, and if you feel that
>> we should change the MIAME requirements appropriately. Would you support
>> this requirement yourself?
>>
>> Regards, - Susanna Sansone
>>
>>
>> ----------------------------------------------------------------------
>> Dear Colleagues,
>>
>> The Microarray Gene Expression Data society (MGED, www.mged.org) is a
>> non-profit organization comprised of representatives of a broad
>> cross-section of the functional genomics community, from both the public
>> and private sectors and includes both producers and users of microarray
>> technology, who came together to facilitate the sharing and analysis of
>> microarray data. To address this scientific need, we developed
>> guidelines for reporting the results of microarray experiments known as
>> the Minimal Information About a Microarray Experiment (MIAME [Nature
>> Genetics, 29, 365-71]), which has been widely adopted by both the major
>> scientific journals as a requirement for publication and the broader
>> research community.
>>
>> The goal of MIAME is to describe the information that an open scientific
>> publication should provide, so that full and independent analysis and
>> verification of the data can be performed. This includes annotation of
>> the experimental conditions, the format of the array platform used and
>> the composition of the reporter sequences (or probes) on the array.
>> Information on the sequence represented at each spot is particularly
>> important for biological interpretation of the data, mapping the
>> information onto the genome, combining information from different arrays
>> and evaluating the significance of the results obtained.
>>
>> Many microarray manufacturers and suppliers of oligonucleotides that can
>> be spotted onto arrays provide information about the sequence
>> represented at each spot without restriction. However, others have
>> instead released information on only the DDBJ/EMBL/GenBank Accession
>> Number representing the region from which each reporter sequence was
>> designed. This significantly limits the extent to which the data can be
>> verified or interpreted, and is of paramount concern to the scientific
>> community at large.
>>
>> For these reasons, the MGED society believes that for data to be fully
>> MIAME-compliant, the sequence represented at each feature of the array
>> should be provided as best known in accordance with the array
>> manufacture technology:
>>
>> -For synthesized oligonucleotides, the full sequence should be provided
>>
>> -For samples physically derived from cloned DNA, an accession number for
>> a public record of the sequence should be provided, and if relevant, the
>> relative coordinates of the reporter (for example, if only a subsection
>> of a clone is amplified by PCR)
>>
>> We hope that you see the value in joining our efforts to create open
>> array platforms and that your organization will accordingly make
>> oligonucleotide sequences available to the community. We would be happy
>> to work with you to create appropriate platform submissions to public
>> databases, allowing your customers to simply supply a reference for the
>> array used, instead of having to submit the information themselves.
>>
>> If you have any questions about this process or if we can provide any
>> further information, please do not hesitate to contact us.
>>
>> On the behalf of MGED Board of Directors:
>>
>> Catherine Ball, Stanford University School of Medicine
>> Virginia Barbour, Public Library of Science
>> Alvis Brazma, European Bioinformatics Institute
>> Helen Causton, Imperial College London
>> Steve Chervitz, Affymetrix, Inc.
>> Terry Gaasterland, The Rockefeller University and University of
>> California, San Diego
>> Pascal Hingamp, INSERM ERM 206
>> Frank Holstege, UMC Utrecht
>> John Matese, Princeton University
>> John Quackenbush, The Institute for Genomic Research
>> Gavin Sherlock, Stanford University School of Medicine
>> Paul Spellman, Lawrence Berkeley Laboratory
>> Christian Stoeckert, University of Pennsylvania
>> Ronald Taylor, MGED Secretary
>> Joseph White, The Institute for Genomic Research
>>
>> --
>> Susanna-Assunta Sansone, PhD
>>
>> Nutri/Toxicogenomics Project Coordinator, EBI
>>
>> The European Bioinformatics Institute   email:  sa...@eb...
>> EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
>> Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
>> Cambridge CB10 1SD, UK
>>
>> Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html
>>
>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IBM Linux Tutorials
>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>> GenToo technologies. Learn everything from fundamentals to system
>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>> _______________________________________________
>> Mged-toxico mailing list
>> Mge...@li...
>> https://lists.sourceforge.net/lists/listinfo/mged-toxico
>>
>>
>
>

RE: [Mged-toxico] Open letter to microarray community

[Susanna-Assunta S. <sa...@eb...>]

Dear Erik,

thanks for your comment. Please, see my replies below.

ca...@en... (Eric Carlson) said:
> I think that this depends upon your application. It could be dangerous to
> force researchers into set experimental designs. We are using microarrays
> to
> identify novel genes. These are shotgun experiments using clones of unkown
> identities.

I agree with you and indeed MIAME does not want to enforce standard exp
design, penalizing novel applications like profiling unknow clones.

MIAME addresses the issue of reporting data in an open scientific
publication and aims to support full and independent analysis and
verification of the data.
In your case, I assume that once you identify 'interesting' clones, before
publishing your data, you sequence them. What MIAME asks is to provide the
relevant annotations for such clones: an accession number for a public
record and any relevant coordinate (e.g. if only a subsection of a clone
is amplified by PCR), not just a clone number with no link to any public
resources.

So in this specific case then, the message in the letter below would be
addressed to the researcher (not the array manufacturer).

Best regards,
Susanna

> I do believe that rules for reporting exactly what was done
> (such as MIAME) are necessary, but exceptions must be allowed.



>
> Thanks
>
> Erik
>
> Erik A. Carlson, Ph.D.
> Nelson Institute of Environmental Medicine
> New York University School of Medicine
> 57 Old Forge Rd
> Tuxedo, NY 10987
> (845)731-3545
> ca...@en...
>
> -----Original Message-----
> From: mge...@li...
> [mailto:mge...@li...]On Behalf Of Susanna
> Sansone
> Sent: Thursday, April 08, 2004 10:36 AM
> To: mge...@li...
> Subject: [Mged-toxico] Open letter to microarray community
>
>
> Dear Colleagues,
>
> The following open letter has been recently sent to many of the major
> microarray and oligonucleotide manufacturers and users (please, text is
> below). Essentially it states that the MGED board feels that the exact
> reporter (probe) sequences, such as oligonucleotides should be given
> when publishing microarray based data.
>
> I would like to ask your opinions on this matter, and if you feel that
> we should change the MIAME requirements appropriately. Would you support
> this requirement yourself?
>
> Regards, - Susanna Sansone
>
>
> ----------------------------------------------------------------------
> Dear Colleagues,
>
> The Microarray Gene Expression Data society (MGED, www.mged.org) is a
> non-profit organization comprised of representatives of a broad
> cross-section of the functional genomics community, from both the public
> and private sectors and includes both producers and users of microarray
> technology, who came together to facilitate the sharing and analysis of
> microarray data. To address this scientific need, we developed
> guidelines for reporting the results of microarray experiments known as
> the Minimal Information About a Microarray Experiment (MIAME [Nature
> Genetics, 29, 365-71]), which has been widely adopted by both the major
> scientific journals as a requirement for publication and the broader
> research community.
>
> The goal of MIAME is to describe the information that an open scientific
> publication should provide, so that full and independent analysis and
> verification of the data can be performed. This includes annotation of
> the experimental conditions, the format of the array platform used and
> the composition of the reporter sequences (or probes) on the array.
> Information on the sequence represented at each spot is particularly
> important for biological interpretation of the data, mapping the
> information onto the genome, combining information from different arrays
> and evaluating the significance of the results obtained.
>
> Many microarray manufacturers and suppliers of oligonucleotides that can
> be spotted onto arrays provide information about the sequence
> represented at each spot without restriction. However, others have
> instead released information on only the DDBJ/EMBL/GenBank Accession
> Number representing the region from which each reporter sequence was
> designed. This significantly limits the extent to which the data can be
> verified or interpreted, and is of paramount concern to the scientific
> community at large.
>
> For these reasons, the MGED society believes that for data to be fully
> MIAME-compliant, the sequence represented at each feature of the array
> should be provided as best known in accordance with the array
> manufacture technology:
>
> -For synthesized oligonucleotides, the full sequence should be provided
>
> -For samples physically derived from cloned DNA, an accession number for
> a public record of the sequence should be provided, and if relevant, the
> relative coordinates of the reporter (for example, if only a subsection
> of a clone is amplified by PCR)
>
> We hope that you see the value in joining our efforts to create open
> array platforms and that your organization will accordingly make
> oligonucleotide sequences available to the community. We would be happy
> to work with you to create appropriate platform submissions to public
> databases, allowing your customers to simply supply a reference for the
> array used, instead of having to submit the information themselves.
>
> If you have any questions about this process or if we can provide any
> further information, please do not hesitate to contact us.
>
> On the behalf of MGED Board of Directors:
>
> Catherine Ball, Stanford University School of Medicine
> Virginia Barbour, Public Library of Science
> Alvis Brazma, European Bioinformatics Institute
> Helen Causton, Imperial College London
> Steve Chervitz, Affymetrix, Inc.
> Terry Gaasterland, The Rockefeller University and University of
> California, San Diego
> Pascal Hingamp, INSERM ERM 206
> Frank Holstege, UMC Utrecht
> John Matese, Princeton University
> John Quackenbush, The Institute for Genomic Research
> Gavin Sherlock, Stanford University School of Medicine
> Paul Spellman, Lawrence Berkeley Laboratory
> Christian Stoeckert, University of Pennsylvania
> Ronald Taylor, MGED Secretary
> Joseph White, The Institute for Genomic Research
>
> --
> Susanna-Assunta Sansone, PhD
>
> Nutri/Toxicogenomics Project Coordinator, EBI
>
> The European Bioinformatics Institute   email:  sa...@eb...
> EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
> Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK
>
> Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html
>
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Mged-toxico mailing list
> Mge...@li...
> https://lists.sourceforge.net/lists/listinfo/mged-toxico
>
>

[Mged-toxico] Open letter to microarray community

[Susanna S. <sa...@eb...>]

Dear Colleagues,

The following open letter has been recently sent to many of the major 
microarray and oligonucleotide manufacturers and users (please, text is 
below). Essentially it states that the MGED board feels that the exact 
reporter (probe) sequences, such as oligonucleotides should be given 
when publishing microarray based data.

I would like to ask your opinions on this matter, and if you feel that 
we should change the MIAME requirements appropriately. Would you support 
this requirement yourself?

Regards, - Susanna Sansone


----------------------------------------------------------------------
Dear Colleagues,

The Microarray Gene Expression Data society (MGED, www.mged.org) is a 
non-profit organization comprised of representatives of a broad 
cross-section of the functional genomics community, from both the public 
and private sectors and includes both producers and users of microarray 
technology, who came together to facilitate the sharing and analysis of 
microarray data. To address this scientific need, we developed 
guidelines for reporting the results of microarray experiments known as 
the Minimal Information About a Microarray Experiment (MIAME [Nature 
Genetics, 29, 365-71]), which has been widely adopted by both the major 
scientific journals as a requirement for publication and the broader 
research community.

The goal of MIAME is to describe the information that an open scientific 
publication should provide, so that full and independent analysis and 
verification of the data can be performed. This includes annotation of 
the experimental conditions, the format of the array platform used and 
the composition of the reporter sequences (or probes) on the array. 
Information on the sequence represented at each spot is particularly 
important for biological interpretation of the data, mapping the 
information onto the genome, combining information from different arrays 
and evaluating the significance of the results obtained.

Many microarray manufacturers and suppliers of oligonucleotides that can 
be spotted onto arrays provide information about the sequence 
represented at each spot without restriction. However, others have 
instead released information on only the DDBJ/EMBL/GenBank Accession 
Number representing the region from which each reporter sequence was 
designed. This significantly limits the extent to which the data can be 
verified or interpreted, and is of paramount concern to the scientific 
community at large.

For these reasons, the MGED society believes that for data to be fully 
MIAME-compliant, the sequence represented at each feature of the array 
should be provided as best known in accordance with the array 
manufacture technology:

-For synthesized oligonucleotides, the full sequence should be provided

-For samples physically derived from cloned DNA, an accession number for 
a public record of the sequence should be provided, and if relevant, the 
relative coordinates of the reporter (for example, if only a subsection 
of a clone is amplified by PCR)

We hope that you see the value in joining our efforts to create open 
array platforms and that your organization will accordingly make 
oligonucleotide sequences available to the community. We would be happy 
to work with you to create appropriate platform submissions to public 
databases, allowing your customers to simply supply a reference for the 
array used, instead of having to submit the information themselves.

If you have any questions about this process or if we can provide any 
further information, please do not hesitate to contact us.

On the behalf of MGED Board of Directors:

Catherine Ball, Stanford University School of Medicine
Virginia Barbour, Public Library of Science
Alvis Brazma, European Bioinformatics Institute
Helen Causton, Imperial College London
Steve Chervitz, Affymetrix, Inc.
Terry Gaasterland, The Rockefeller University and University of 
California, San Diego
Pascal Hingamp, INSERM ERM 206
Frank Holstege, UMC Utrecht
John Matese, Princeton University
John Quackenbush, The Institute for Genomic Research
Gavin Sherlock, Stanford University School of Medicine
Paul Spellman, Lawrence Berkeley Laboratory
Christian Stoeckert, University of Pennsylvania
Ronald Taylor, MGED Secretary
Joseph White, The Institute for Genomic Research

-- 
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html                  

  

[Mged-toxico] [Fwd: First Announcement for MGED7 Meeting]

[Susanna S. <sa...@eb...>]

  Dear all,

this is the First Announcement for MGED7 Meeting.

Please see below.

Regards,
Susanna

-------- Original Message --------
Subject: First Announcement for MGED7 Meeting
Date: Fri, 2 Apr 2004 12:13:42 -0800 (PST)
From: Gavin Sherlock <she...@ge...>
To: Gavin Sherlock <she...@ge...>
CC: mge...@li..., 
mge...@li..., mic...@eb..., 
mic...@eb..., GENE-ARRAYS@ITSSRV1.UCSF.EDU, 
uk...@ar...



Dear Colleagues,

Apologies if you receive this more than once.

	It is the pleasure of the Microarray Gene Expression Data (MGED)  
society to announce its 7th International meeting, MGED7, to be held in
Toronto, Canada, Wednesday September 8 -> Friday September 10th, 2004.  
Further information is available at http://www.microarrays.ca/MGED7.html.  
Registration is now open, and early registration, before August 18th 2004,
confers an early bird discount.

	The scientific focus of the meeting will be high throughput
screening methods - in particular microarrays - and associated data
handling issues and analysis techniques.  With the maturation of
microarray annotation standards and tools, this year's meeting will offer
more 'hands-on' tutorials to tackle specific practical applications of
these concepts.  Tutorials will cover the full process from experimental
design to data normalization of both two-color and Affymetrix data, to
data analysis, all the way to submission to public databanks.

	Parallel workshops will cover MIAME compliant experiment
annotation (Brazma et al, 2001), the MAGE object model and MAGE-ML
(Spellman et al 2002), the MGED Core Ontology, as well as standards for
normalization, and the adoption of MIAME-like standards for
toxicogenomics.

	We have lined up some outstanding speakers, who are leaders in
their respective fields, and in addition, this year we will be selecting
half of the plenary speakers from submitted abstracts, to encourage
greater participation in the MGED community.  Continuing from last year,
we will again be running a poster competition, with prizes of $1000, $750
and $500 for the best three posters presented by students.

	Immediately following MGED 7 will be the 7th MGED Programming
Jamboree, to be held on September 11th and 12th.  The Programming Jamboree
is an opportunity for programmers to come together to work on problems
relating to MAGE, MIAME, and the MGED Ontology in an interactive
environment with leading experts in these areas.

We look forward to seeing you all in Toronto,

Sincerely,

The Microarray Gene Expression Data (MGED) Society


----------------------------------------------------------------------
Preliminary Program:

This year's three day meeting is triple action: parallel tutorials and 
workshops the first day, and plenary talks on the second and third 
days.  Note that this year's MGED7 meeting will be directly followed by 
MGED's seventh Programming Jamboree (see below).

Tuesday 7th Sept

17:00-20:00 Registration



Wednesday 8th September

08:00-18:00 Registration

08:30-09:00 Welcome - Neil Winegarden / Catherine Ball
09:00-10:00 An Introductory Guide to MIAME - Helen Parkinson (EBI)

10:30-12:30

Track I : Tutorial I : Experimental Design

		Richard Simon (National Cancer Institute)
		Jenny Bryan   (University of British Columbia)

Track II: Workshop I : MIAME

		Alvis Brazma (European Bioinformatics Institute)

12:30-13:30 Lunch

13:30-15:30

Track I : Tutorial II : Normalization

		Catherine Ball  (Stanford University)
		Jason Goncalves (Iobion Informatics)
		Helen Causton   (Medical Research Council)

Track II: Workshop II : MAGE

		Paul Spellman (Lawrence Berkeley Livermore Labs)

		Workshop III: Transformations/ERRC

		Marc Salit (National Institute of Standards and Technology)

15:30-16:00 : Break

16:00-17:00 : Keynote 1 : Jeremy Nicholson (Imperial College, London)

17:00-17:30 : Break

17:30-19:30

Track I : Tutorial III : Hands On Analysis

		John Quackenbush (TIGR)
		Sandrine Dudoit  (UC Berkeley)

Track II: Workshop IV : Ontologies

		Chris Stoeckert (University of Pennsylvania)

	Workshop V : Toxicogenomics

		Susanna Sansone (European Bioinformatics Institute)




Thursday 9th September

08:30-10:30 Session I : Microarrays and Disease I

Therese Tsorlie   (Norwegian Radium Hospital)
Michael Whitfield (Dartmouth Medical School)

plus 2 speakers to be chosen from submitted abstracts

10:30-11:00 Break

11:00-13:00 Session II : Applications to Model Organisms I

Karine Le Roch (Scripps Research Institute)
Jurg Bahler    (The Sanger Centre)

plus 2 speakers to be chosen from submitted abstracts

13:00-14:00 Lunch

14:00-16:00 Session III : Applications to Model Organisms II

Scott Peterson (TIGR)
Josh Stuart    (UC Santa Cruz)

plus 2 speakers to be chosen from submitted abstracts

16:00-18:00 Posters and Wine

18:00-19:00 Keynote II : Timothy Hughes (University of Toronto)

Friday 10th September

08:30-10:30 Session IV : Microarrays and Disease II

Charles Whitfield (University of Illinois)
TBA

plus 2 speakers to be chosen from submitted abstracts

10:30-11:00 Break

11:00-13:00 Session V : Beyond Expression

George Stephanopoulos (MIT)
Peggy Farnham         (University of Wisonsin)

plus 2 speakers to be chosen from submitted abstracts

13:00-14:00 Lunch

14:00-16:00 Session VI : Bioinformatics

Trey Ideker      (UC San Diego)
Olga Troyanskaya (Princeton)

plus 2 speakers to be chosen from submitted abstracts

16:00-16:30 Break

16:30-17:30 Keynote III : Eric Schadt (Rosetta Inpharmatics)

17:30-18:30 Wrap Up - Catherine Ball/Chris Stoeckert

Saturday 11th September

10:00-19:00 Programming Jamboree

Sunday 12th September

10:00-19:00 Programming Jamboree




-- 
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html                  

  

[Mged-toxico] article of interest

[Willy Valdivia-G. <wil...@or...>]

Hello

Perhaps of interest

Tailored gene array databases: applications in mechanistic toxicology

       Tatiana V. Karpinets, Brent D. Foy, and John M. Frazier
       Bioinformatics 2004 20: 507-517.
       http://bioinformatics.oupjournals.org/cgi/content/abstract/20/4/507?etoc

[Mged-toxico] MGED Tox WG- webpage and related initiatives

[Susanna S. <sa...@eb...>]

  Dear Tox Working Group Members,

the MGED TWG webpage is now live on MGED Society web site 
(http://www.mged.org) at:
http://www.mged.org/Workgroups/tox/tox.html

- At the end of the page you can find a section on 'Inter-related 
initiatives:' as result of the discussion started between Dr. Thomas 
Papoian of FDA and some Tox WG members (see first email communication 
below). As the discussion moves forward, I will post further information 
and links on the MGED TWG website.

- The 'TWG participants' section lists database systems aiming to 
implement MGED-standards.

- If you wish to become a MGED Sponsor, please do not hesitate to 
contact me.

Best regards,
Susanna


-------- Original Message --------
Subject: Re: [Mged-toxico] Nonclinical Data Standards
Date: Tue, 27 Jan 2004 15:22:27 +0000
From: Susanna Sansone <sa...@eb...>
To: "Papoian, Thomas" <PAP...@cd...>
CC: "'mge...@li...'" 
<mge...@li...>
References: <D59...@cd...>



Dear Tom,

thanks for your email and accept my apologies for this late reply.

I am the moderator of this mailing list and currently leading this Tox 
Working Group within the MGED Society. We will be very happy to start a 
discussion and see what can be done to harmonize efforts.

Please find here some background information and references.

****
The MGED Society and data standardization
****
The MGED Society is an international organization of biologists, 
computer scientists, and data analysts. The Board includes 
representatives from academia (incl. Stanford Un., Un of Penn., TIGR, 
EBI), government (incl.DDBJ, NCBI, NCICB) and industry (incl.Agilent, 
Silicon Genetics, Affymetrix) across the globe. The current focus of the 
MGED Society is on establishing standards for microarray data annotation 
and exchange, facilitating the creation of microarray databases and 
related software implementing these standards, and promoting the sharing 
of high quality, well annotated data within the life sciences community. 
A long-term goal for the future is to extend the mission to other 
functional genomics and proteomics high throughput technologies.

The MGED Society has to develop a set of open source 'standards' needed 
for microarray data sharing infrastructure.
- Data content
The Minimum Information About Microarray Experiments (MIAME) [1], 
defines the minimum descriptors that must be reported about array based 
gene expression monitoring experiments, in order to ensure the 
interpretability of the results, as well as potential verification by 
third parties. By providing a structured framework for capturing 
information, MIAME is a data content standard, not a format standard.
- Software interoperability
The MicroArray Gene Expression (MAGE) standards [2] refer to the MAGE 
Object Model (MAGE-OM) and MAGE Markup Language (MAGE-ML). MAGE provides 
the formal standard that specifies the communication protocols, ensuring 
software interoperability and encoding all MIAME required information. 
MAGE is a stable, formal specification (Gene Expression, v1.1) [3] of 
the Object Management Group (OMG).
- Data annotation
The MGED ontology [4] defines sets of common terms and annotation rules 
for microarray experiments, enabling unambiguous annotation and 
efficient queries and data analysis.


****
The MGED Tox Working Group
****
As part of a collaborative undertaking with the ILSI Health and 
Environmental Sciences Institute's (HESI) 'Technical Committee on the 
Application of Genomics to Mechanism Based Risk Assessment [5] the 
EMBL-EBI [6], the NIEHS-NCT [7] and the NCTR-FDA [8] have worked 
closely. We aim to develop internationally compatible and public 
infrastructure for reporting array-based toxicogenomics data in our 
database systems (ArrayExpress at EBI, CEBS at NCTand ArrayTrack at 
NCTR) and be able to exchange datasets using common descriptors, 
standard data storage and exchange format (the MGED standards mentioned 
above) and harmonized nomenclature.

Recently this collaboration has developed in the establishment of a 
Toxicogenomics Working Group under the Microarray Gene Expression Data 
society (MGED www.mged.org) umbrella, focusing on the informatics 
challenges that this marriage of toxicology and genomics has created.

Please, see below the MGED Tox Working Group - position statement. I 
will soon set up a page for this Working Group at www.mged.org

[1] Brazma, A., et al. (2001). Minimum information about a microarray 
experiment (MIAME)-toward standards for microarray data. Nat Genet 
29:365-71.
[2] Spellman, P.T., et al. (2002). Design and implementation of 
microarray gene expression markup language (MAGE-ML). Genome Biol 3(9), 
research0046.1-0046.9.
[3] Gene Expression, v1.1 formal specification 
http://www.omg.org/technology/documents/formal/gene_expression.htm
[4] MGED ontology: http://mged.sourceforge.net/ontologies
[5] ILSI-HESI http://hesi.ilsi.org/publications/pubslist.cfm?pubentityid=120
[6] ArrayExpress database and the Toxicogenomics project at EBI: 
http://www.ebi.ac.uk/microarray/Projects/tox-nutri/
[7] Chemical Effects in Biological Systems (CEBS) Knowledge Base at 
NIEHS NCT: http://www.niehs.nih.gov/nct/
[8] ArrayTrack at NCTR-FDA: 
http://www.fda.gov/nctr/science/centers/toxicoinformatics/tools.htm#ArrayTrack
************************

The ILSI-HESI Genomics Committee jointly with others will held a 
symposia on 'Toxicogenomic Databases and Their Role in the Toxicology 
Community' at the upcoming SOT Annual Meeting in Baltimore, on March 
23rd. If you plan to attend the meeting it would be an opportunity to 
discuss this further with the representatives from ILSI-HESI Genomics 
Committee, NCT and NCTR attending and presenting at the symposia.

Furthermore the ILSI-HESI Genomics Committee has been talking with Karol 
Thompson and John Leighton re: opportunities for FDA/HESI collaboration 
on these types of issues. Representatives of the ILSI-HESI Genomics 
Committee are members of this mailing list, and I am sure that they will 
join this discussion.

With reference to the SEND and the SDS it would be helpful if developers 
of the MAGE model could view these models. Perhaps they could get in 
touch with Dr. Seema Handu. Please, let me know if this is possible and 
how you want to precede.

Lastly, I will report our email communication to the MGED Board that 
meets in a teleconference today.

I look forward to the future progress.

My best regards,
Susanna

-- 
Susanna-Assunta Sansone, PhD

Toxicogenomics Project Coordinator, Microarray Informatics @ EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html                  

  

**************************************************
Tox Working Group - position statement
****************************************************

The MGED Tox Working Group provides a public forum for developing 
internationally compatible and public infrastructure for reporting 
array-based toxicogenomics data (and similarly ecotox, phama, ) data.

Ultimately the creation of an internationally compatible informatics 
platform will
- Enhance the impact of the individual datasets;
- Provide the scientific and regulatory community with easy access to 
integrated data in a structured standard format;
- Facilitate data exchange comparison and data analysis.

Initially, this Working Group will focus on array-based toxicogenomics 
experiments, by leveraging the MGED accomplishments. As the MGED Society 
extends its mission to other functional genomics and proteomics high 
throughput technologies, this working group will contribute accordingly.

This Working Group seeks to address technical, informatics, and team 
science challenges, including:

1. Standard data representation:
1.1. Reach a consensus on the minimal information descriptors for 
array-based toxicogenomics experiments (extending MIAME).
1.2. Prepare a checklist, including those descriptors (MIAME/Tox checklist)
1.3. Include guidelines on experimental design and statistical analysis 
(working closely with Data Transformation and Normalization Working Group)

2. Data harmonization for conventional toxicology terms:
2.1. Promote use of ontologies (preferably), databased controlled 
vocabularies or at least terms available with with IDs or codes
2.2. Add a tox-specific arm/layer to the MGED Core Ontology (working 
closely with Ontology Working Group)

3. Data storage and data sharing:
3.1. Implement the use MAGE-OM and/or MAGE-ML standards (in our 
individual repositories)
3.2. Gain support from the scientific community, end users and softwares 
developers companies.

4. Outreach:
4.1. Give critical mass to the effort
4.2. Dissemination and joint communication to keep stakeholders informed

Please join the discussion list of the MGED Toxicogenomics Working Group 
( https://lists.sourceforge.net/lists/listinfo/mged-toxico ) and
contribute with your ideas and comments.


Papoian, Thomas wrote:

>Dear Mged-toxico Members,
>
>I have just subscribed to the Mged-toxico discussion group. The reason for
>doing so is that I have been involved in efforts at the U.S. Food and Drug
>Administration (FDA) to help define data standards for submission of animal
>toxicity data to the agency. As part of these efforts, a consortium has been
>formed among the pharmaceutical industry, contract labs, software
>developers, and the FDA Centers to develop a common and open data standard,
>termed SEND (Standard for Exchange of Nonclinical Data). The SEND model is
>similar to the SDS (Submissions Data Standards) model developed by CDISC
>(http://www.cdisc.org/) for submission of clinical data from drug trials.
>The SEND model has defined metadata for all aspects of a typical animal
>toxicity study, such as body weights, food consumption, organ weights,
>clinical pathology (lab tests), macroscopic/microscopic findings,
>reproductive toxicity parameters, and tumor findings, among others.
>Information regarding the SEND data model can be found at:
>http://www.pharmquest.com/default.html. 
>
>As part of this process we have initiated a pilot project (published in the
>U.S. Federal Register; Jan 27, 2003) among several pharmaceutical companies
>in which datasets from single-dose and repeat-dose toxicity studies are
>being submitted using the SEND format. The next phases of the pilot will
>include datasets for carcinogenicity and reproductive toxicity studies.
>These data are being used to help validate the model, as well as help us
>develop customized software tools for viewing the data. The SEND data model
>has recently gone through the initial HL7 (http://www.hl7.org/) balloting
>process.
>
>Since the recent publication of a draft Guidance for Industry on
>Pharmacogenomic Data Submissions from the Center for Drug Evaluation and
>Research (CDER) of the FDA (http://www.fda.gov/cder/guidance/5900dft.pdf),
>efforts have begun by data standards organizations (I3C/CDISC/HL7) to help
>develop data standards for pharmacogenomic data as well. Given that the
>Mged-toxico group is working on developing similar standards for animal
>toxicity data as part of a microarray experiment, I felt the time was
>appropriate to contact this group to see what can be done to harmonize
>efforts to develop data submission standards for all types of animal
>toxicity data, including microarray studies.
>
>I hope I can contribute to the discussions in a meaningful way.
>
>Tom
>
>Thomas Papoian, Ph.D., D.A.B.T. 
>Senior Pharmacologist 
>Cardio-Renal Drug Products (HFD-110) 
>Center for Drug Evaluation and Research 
>Food and Drug Administration 
>5600 Fishers Lane 
>Rockville, MD  20857
>U.S.A. 
>Tel: 301-594-5383 
>Email: pap...@cd... 
>
>
>
>
>
>
>
>-------------------------------------------------------
>The SF.Net email is sponsored by EclipseCon 2004
>Premiere Conference on Open Tools Development and Integration
>See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
>http://www.eclipsecon.org/osdn
>_______________________________________________
>Mged-toxico mailing list
>Mge...@li...
>https://lists.sourceforge.net/lists/listinfo/mged-toxico
>
     

  





-------------------------------------------------------
The SF.Net email is sponsored by EclipseCon 2004
Premiere Conference on Open Tools Development and Integration
See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
http://www.eclipsecon.org/osdn
_______________________________________________
Mged-toxico mailing list
Mge...@li...
https://lists.sourceforge.net/lists/listinfo/mged-toxico


-- 
Susanna-Assunta Sansone, PhD

Toxicogenomics Project Coordinator, Microarray Informatics @ EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html                  

  

Re: [Mged-toxico] Nonclinical Data Standards

[Susanna S. <sa...@eb...>]

Dear Tom,

thanks for your email and accept my apologies for this late reply.

I am the moderator of this mailing list and currently leading this Tox 
Working Group within the MGED Society. We will be very happy to start a 
discussion and see what can be done to harmonize efforts.

Please find here some background information and references.

****
The MGED Society and data standardization
****
The MGED Society is an international organization of biologists, 
computer scientists, and data analysts. The Board includes 
representatives from academia (incl. Stanford Un., Un of Penn., TIGR, 
EBI), government (incl.DDBJ, NCBI, NCICB) and industry (incl.Agilent, 
Silicon Genetics, Affymetrix) across the globe. The current focus of the 
MGED Society is on establishing standards for microarray data annotation 
and exchange, facilitating the creation of microarray databases and 
related software implementing these standards, and promoting the sharing 
of high quality, well annotated data within the life sciences community. 
A long-term goal for the future is to extend the mission to other 
functional genomics and proteomics high throughput technologies.

The MGED Society has to develop a set of open source 'standards' needed 
for microarray data sharing infrastructure.
- Data content
The Minimum Information About Microarray Experiments (MIAME) [1], 
defines the minimum descriptors that must be reported about array based 
gene expression monitoring experiments, in order to ensure the 
interpretability of the results, as well as potential verification by 
third parties. By providing a structured framework for capturing 
information, MIAME is a data content standard, not a format standard.
- Software interoperability
The MicroArray Gene Expression (MAGE) standards [2] refer to the MAGE 
Object Model (MAGE-OM) and MAGE Markup Language (MAGE-ML). MAGE provides 
the formal standard that specifies the communication protocols, ensuring 
software interoperability and encoding all MIAME required information. 
MAGE is a stable, formal specification (Gene Expression, v1.1) [3] of 
the Object Management Group (OMG).
- Data annotation
The MGED ontology [4] defines sets of common terms and annotation rules 
for microarray experiments, enabling unambiguous annotation and 
efficient queries and data analysis.


****
The MGED Tox Working Group
****
As part of a collaborative undertaking with the ILSI Health and 
Environmental Sciences Institute's (HESI) 'Technical Committee on the 
Application of Genomics to Mechanism Based Risk Assessment [5] the 
EMBL-EBI [6], the NIEHS-NCT [7] and the NCTR-FDA [8] have worked 
closely. We aim to develop internationally compatible and public 
infrastructure for reporting array-based toxicogenomics data in our 
database systems (ArrayExpress at EBI, CEBS at NCTand ArrayTrack at 
NCTR) and be able to exchange datasets using common descriptors, 
standard data storage and exchange format (the MGED standards mentioned 
above) and harmonized nomenclature.

Recently this collaboration has developed in the establishment of a 
Toxicogenomics Working Group under the Microarray Gene Expression Data 
society (MGED www.mged.org) umbrella, focusing on the informatics 
challenges that this marriage of toxicology and genomics has created.

Please, see below the MGED Tox Working Group - position statement. I 
will soon set up a page for this Working Group at www.mged.org

[1] Brazma, A., et al. (2001). Minimum information about a microarray 
experiment (MIAME)-toward standards for microarray data. Nat Genet 
29:365-71.
[2] Spellman, P.T., et al. (2002). Design and implementation of 
microarray gene expression markup language (MAGE-ML). Genome Biol 3(9), 
research0046.1-0046.9.
[3] Gene Expression, v1.1 formal specification 
http://www.omg.org/technology/documents/formal/gene_expression.htm
[4] MGED ontology: http://mged.sourceforge.net/ontologies
[5] ILSI-HESI http://hesi.ilsi.org/publications/pubslist.cfm?pubentityid=120
[6] ArrayExpress database and the Toxicogenomics project at EBI: 
http://www.ebi.ac.uk/microarray/Projects/tox-nutri/
[7] Chemical Effects in Biological Systems (CEBS) Knowledge Base at 
NIEHS NCT: http://www.niehs.nih.gov/nct/
[8] ArrayTrack at NCTR-FDA: 
http://www.fda.gov/nctr/science/centers/toxicoinformatics/tools.htm#ArrayTrack
************************

The ILSI-HESI Genomics Committee jointly with others will held a 
symposia on 'Toxicogenomic Databases and Their Role in the Toxicology 
Community' at the upcoming SOT Annual Meeting in Baltimore, on March 
23rd. If you plan to attend the meeting it would be an opportunity to 
discuss this further with the representatives from ILSI-HESI Genomics 
Committee, NCT and NCTR attending and presenting at the symposia.

Furthermore the ILSI-HESI Genomics Committee has been talking with Karol 
Thompson and John Leighton re: opportunities for FDA/HESI collaboration 
on these types of issues. Representatives of the ILSI-HESI Genomics 
Committee are members of this mailing list, and I am sure that they will 
join this discussion.

With reference to the SEND and the SDS it would be helpful if developers 
of the MAGE model could view these models. Perhaps they could get in 
touch with Dr. Seema Handu. Please, let me know if this is possible and 
how you want to precede.

Lastly, I will report our email communication to the MGED Board that 
meets in a teleconference today.

I look forward to the future progress.

My best regards,
Susanna

-- 
Susanna-Assunta Sansone, PhD

Toxicogenomics Project Coordinator, Microarray Informatics @ EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html                  

  

**************************************************
Tox Working Group - position statement
****************************************************

The MGED Tox Working Group provides a public forum for developing 
internationally compatible and public infrastructure for reporting 
array-based toxicogenomics data (and similarly ecotox, phama, ) data.

Ultimately the creation of an internationally compatible informatics 
platform will
- Enhance the impact of the individual datasets;
- Provide the scientific and regulatory community with easy access to 
integrated data in a structured standard format;
- Facilitate data exchange comparison and data analysis.

Initially, this Working Group will focus on array-based toxicogenomics 
experiments, by leveraging the MGED accomplishments. As the MGED Society 
extends its mission to other functional genomics and proteomics high 
throughput technologies, this working group will contribute accordingly.

This Working Group seeks to address technical, informatics, and team 
science challenges, including:

1. Standard data representation:
1.1. Reach a consensus on the minimal information descriptors for 
array-based toxicogenomics experiments (extending MIAME).
1.2. Prepare a checklist, including those descriptors (MIAME/Tox checklist)
1.3. Include guidelines on experimental design and statistical analysis 
(working closely with Data Transformation and Normalization Working Group)

2. Data harmonization for conventional toxicology terms:
2.1. Promote use of ontologies (preferably), databased controlled 
vocabularies or at least terms available with with IDs or codes
2.2. Add a tox-specific arm/layer to the MGED Core Ontology (working 
closely with Ontology Working Group)

3. Data storage and data sharing:
3.1. Implement the use MAGE-OM and/or MAGE-ML standards (in our 
individual repositories)
3.2. Gain support from the scientific community, end users and softwares 
developers companies.

4. Outreach:
4.1. Give critical mass to the effort
4.2. Dissemination and joint communication to keep stakeholders informed

Please join the discussion list of the MGED Toxicogenomics Working Group 
( https://lists.sourceforge.net/lists/listinfo/mged-toxico ) and
contribute with your ideas and comments.


Papoian, Thomas wrote:

>Dear Mged-toxico Members,
>
>I have just subscribed to the Mged-toxico discussion group. The reason for
>doing so is that I have been involved in efforts at the U.S. Food and Drug
>Administration (FDA) to help define data standards for submission of animal
>toxicity data to the agency. As part of these efforts, a consortium has been
>formed among the pharmaceutical industry, contract labs, software
>developers, and the FDA Centers to develop a common and open data standard,
>termed SEND (Standard for Exchange of Nonclinical Data). The SEND model is
>similar to the SDS (Submissions Data Standards) model developed by CDISC
>(http://www.cdisc.org/) for submission of clinical data from drug trials.
>The SEND model has defined metadata for all aspects of a typical animal
>toxicity study, such as body weights, food consumption, organ weights,
>clinical pathology (lab tests), macroscopic/microscopic findings,
>reproductive toxicity parameters, and tumor findings, among others.
>Information regarding the SEND data model can be found at:
>http://www.pharmquest.com/default.html. 
>
>As part of this process we have initiated a pilot project (published in the
>U.S. Federal Register; Jan 27, 2003) among several pharmaceutical companies
>in which datasets from single-dose and repeat-dose toxicity studies are
>being submitted using the SEND format. The next phases of the pilot will
>include datasets for carcinogenicity and reproductive toxicity studies.
>These data are being used to help validate the model, as well as help us
>develop customized software tools for viewing the data. The SEND data model
>has recently gone through the initial HL7 (http://www.hl7.org/) balloting
>process.
>
>Since the recent publication of a draft Guidance for Industry on
>Pharmacogenomic Data Submissions from the Center for Drug Evaluation and
>Research (CDER) of the FDA (http://www.fda.gov/cder/guidance/5900dft.pdf),
>efforts have begun by data standards organizations (I3C/CDISC/HL7) to help
>develop data standards for pharmacogenomic data as well. Given that the
>Mged-toxico group is working on developing similar standards for animal
>toxicity data as part of a microarray experiment, I felt the time was
>appropriate to contact this group to see what can be done to harmonize
>efforts to develop data submission standards for all types of animal
>toxicity data, including microarray studies.
>
>I hope I can contribute to the discussions in a meaningful way.
>
>Tom
>
>Thomas Papoian, Ph.D., D.A.B.T. 
>Senior Pharmacologist 
>Cardio-Renal Drug Products (HFD-110) 
>Center for Drug Evaluation and Research 
>Food and Drug Administration 
>5600 Fishers Lane 
>Rockville, MD  20857
>U.S.A. 
>Tel: 301-594-5383 
>Email: pap...@cd... 
>
>
>
>
>
>
>
>-------------------------------------------------------
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>_______________________________________________
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>
     

  

[Mged-toxico] Nonclinical Data Standards

[Papoian, T. <PAP...@cd...>]

Dear Mged-toxico Members,

I have just subscribed to the Mged-toxico discussion group. The reason for
doing so is that I have been involved in efforts at the U.S. Food and Drug
Administration (FDA) to help define data standards for submission of animal
toxicity data to the agency. As part of these efforts, a consortium has been
formed among the pharmaceutical industry, contract labs, software
developers, and the FDA Centers to develop a common and open data standard,
termed SEND (Standard for Exchange of Nonclinical Data). The SEND model is
similar to the SDS (Submissions Data Standards) model developed by CDISC
(http://www.cdisc.org/) for submission of clinical data from drug trials.
The SEND model has defined metadata for all aspects of a typical animal
toxicity study, such as body weights, food consumption, organ weights,
clinical pathology (lab tests), macroscopic/microscopic findings,
reproductive toxicity parameters, and tumor findings, among others.
Information regarding the SEND data model can be found at:
http://www.pharmquest.com/default.html. 

As part of this process we have initiated a pilot project (published in the
U.S. Federal Register; Jan 27, 2003) among several pharmaceutical companies
in which datasets from single-dose and repeat-dose toxicity studies are
being submitted using the SEND format. The next phases of the pilot will
include datasets for carcinogenicity and reproductive toxicity studies.
These data are being used to help validate the model, as well as help us
develop customized software tools for viewing the data. The SEND data model
has recently gone through the initial HL7 (http://www.hl7.org/) balloting
process.

Since the recent publication of a draft Guidance for Industry on
Pharmacogenomic Data Submissions from the Center for Drug Evaluation and
Research (CDER) of the FDA (http://www.fda.gov/cder/guidance/5900dft.pdf),
efforts have begun by data standards organizations (I3C/CDISC/HL7) to help
develop data standards for pharmacogenomic data as well. Given that the
Mged-toxico group is working on developing similar standards for animal
toxicity data as part of a microarray experiment, I felt the time was
appropriate to contact this group to see what can be done to harmonize
efforts to develop data submission standards for all types of animal
toxicity data, including microarray studies.

I hope I can contribute to the discussions in a meaningful way.

Tom

Thomas Papoian, Ph.D., D.A.B.T. 
Senior Pharmacologist 
Cardio-Renal Drug Products (HFD-110) 
Center for Drug Evaluation and Research 
Food and Drug Administration 
5600 Fishers Lane 
Rockville, MD  20857
U.S.A. 
Tel: 301-594-5383 
Email: pap...@cd...