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From: Fostel, J. \(NIH/NIEHS\) [C] <fo...@ni...> - 2007-01-22 17:33:55
|
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 |
From: <wil...@or...> - 2005-10-26 12:22:11
|
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 |
From: <ann...@vi...> - 2005-09-22 08:30:56
|
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 |
From: Fostel, J. (NIH/NIEHS) <fo...@ni...> - 2005-09-15 20:43:47
|
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. |
From: Yasuo O. M. P. F. <os...@ji...> - 2005-07-22 00:12:04
|
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: > Send Mged-toxico mailing list submissions to > mge...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/mged-toxico > or, via email, send a message with subject or body 'help' to > mge...@li... > > You can reach the person managing the list at > mge...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Mged-toxico digest..." > > > 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/ > > > > ------------------------------------------------------- > 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 > core and dual graphics technology at this free one hour event hosted > by HP, > AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar > _______________________________________________ > Mged-toxico mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-toxico > > > > --__--__-- > > _______________________________________________ > Mged-toxico mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-toxico > > > End of Mged-toxico Digest > |
From: Fostel, J. (NIH/NIEHS) <fo...@ni...> - 2005-07-18 16:08:15
|
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/ ------------------------------------------------------- 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 core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar _______________________________________________ Mged-toxico mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-toxico |
From: yasuo o. <osh...@ya...> - 2005-07-11 08:05:03
|
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/ |
From: Susanna S. <sa...@eb...> - 2005-06-14 13:08:36
|
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 |
From: Fostel, J. (NIH/NIEHS) <fo...@ni...> - 2005-05-31 16:32:36
|
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 ------------------------------------------------------- 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 |
From: Fostel, J. (NIH/NIEHS) <fo...@ni...> - 2005-05-31 15:51:07
|
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 |
From: Ari K. <ar...@ma...> - 2005-05-26 22:37:49
|
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 |
From: <sha...@sy...> - 2005-04-28 19:21:16
|
------------------------- 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... |
From: Fostel, J. (NIH/NIEHS) <fo...@ni...> - 2005-04-08 14:38:11
|
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 |
From: Axel.Klenk@Actelion.Com - 2005-02-15 04:47:02
|
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. ************************************************************************* The information of this e-mail and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this e-mail is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this e-mail. The content of this e-mail is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com. ************************************************************************** |
From: Carlos M. <mec...@ya...> - 2005-02-14 18:23:57
|
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 Masters 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 students wage. Thank you very much, Carlos C. Meca --------------------------------- Découvrez le nouveau Yahoo! Mail : 250 Mo d'espace de stockage pour vos mails ! Créez votre Yahoo! Mail |
From: Fostel, J. (NIH/NIEHS) <fo...@ni...> - 2004-12-21 16:27:31
|
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 |
From: Fostel, J. (NIH/NIEHS) <fo...@ni...> - 2004-09-13 15:27:07
|
> 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 > |
From: Susanna-Assunta S. <sa...@eb...> - 2004-04-09 15:19:59
|
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 >> >> > > |
From: Susanna-Assunta S. <sa...@eb...> - 2004-04-09 14:42:01
|
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 > > |
From: Susanna S. <sa...@eb...> - 2004-04-08 14:39:27
|
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 |
From: Susanna S. <sa...@eb...> - 2004-04-02 20:38:20
|
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 |
From: Willy Valdivia-G. <wil...@or...> - 2004-03-02 15:10:03
|
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 |
From: Susanna S. <sa...@eb...> - 2004-02-18 19:44:39
|
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 |
From: Susanna S. <sa...@eb...> - 2004-01-27 15:25:12
|
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 > |
From: Papoian, T. <PAP...@cd...> - 2004-01-22 16:23:21
|
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... |