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msi-workgroups-bio-metadata — This is the list for the msi biological context metadata WG
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From: Susanna-Assunta S. <sa...@eb...> - 2008-08-08 16:06:20
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Dear colleagues, We would like to inform you that the paper describing the Minimum Information for Biological and Biomedical Investigations (MIBBI) project -- http://www.mibbi.org/ -- has been published this month in Nature Biotechnology. This represents a significant step towards a comprehensive set complementary reporting guidelines for the biosciences; both by describing our work to date, and by acting as a beacon for new participants. A PDF of the paper is freely-available for download: http://www.nature.com/nbt/journal/v26/n8/pdf/nbt.1411.pdf This paper: 1. Describes the foundational work performed by the ever-growing list of participants in this project. 2. Provides analysis of the various MI specifications registered at the site (scope, conflicts, etc.), including the MSI's CIMR 3. Addresses the view of funders and publishers on the enforcement of consensual reporting guidelines. 4. Outlines our plans for future work, which all are strongly encouraged to monitor, and in which all are invited to participate. Any questions can be directed to: Chris Taylor Susanna-Assunta Sansone Dawn Field Yours Sincerely, Susanna, Chris and Dawn, on behalf of all authors. -- |
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From: Abma, T.W. <T.W...@um...> - 2008-04-24 14:38:18
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Hello all, Let me first introduce myself. I am a scientific programmer from the Utrecht University (The Netherlands) and work for the Netherlands Metabolomics Centre. We are setting up a metabolomics platform and are looking into existing standards like MSI and we are already working together with other universities in The Netherlands to do that. We also plan to include/add clinical studies to our database. I see that the latest draft proposal is from 2005. Have there been any updates on the proposals/drafts in the meanwhile or is everything put on non-active? Thanks in advance and kind regards, Tjeerd Abma Scientific programmer/Bioinformatician UMCU Metabolomics Centre Dept. Metabolic and Endocrine Diseases Wilhelmina Childrens Hospital, UMC Utrecht T: 088-7554330 E: t.w...@um... http://www.metabolomics-utrecht.nl |
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From: Sumner, L. <lws...@no...> - 2007-09-14 02:18:07
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I thought you might be interested in the recent update notice from the plant ontology db. Lloyd =20 Plant Ontology Consortium is happy to announce the release #0907 of PO database! http://www.plantontology.org <http://www.plantontology.org/>=20 =20 * Ontology update - 1109 PO terms - 32104 annotations visit http://www.plantontology.org/docs/release_notes/index.html for more details =20 * New version of PO browser (http://www.plantontology.org/amigo/go.cgi) - New interface - New users guide - New tutorials - New feature: added "GO" (Gene Ontology) associations link to Arabidopsis genes =20 * POC Website updates (http://www.plantontology.org/) - added "Request PO terms" feature on navigation menu - added "POC Outreach Activities" link in "Documentation" page - Updated "Mail Archives" - Updated "PO website usage statistics" - Updated "Tutorials" =20 * POC and plant community - Welcome experts from Medicago, Populus, Rosaceae, Solanaceae, Vitis fields to join plant ontology development Please email to po...@pl... or subscribe po-dev mailing list =20 - Phenote (a phenotype annotation tool using ontologies http:// www.phenote.org/) has added "plant" configuration, plus PO and other plant related ontologies for curation. Contact Nicole Washington ( NLW...@lb... ) for more information about downloading and using Phenote tool =20 - Meet POC members in international conferences @ 8th Agricultural Ontology Service (AOS) workshop, Rome, Italy =20 Sep 21-22 @ 5th International Symposium of Rice Functional Genomics, Tsukuba, Japan Oct 15-17 @ 2nd International Biocuration meeting, San Jose, CA Oct 25-28 =20 =20 =20 The Plant Ontology Consortium web: http:www.plantontology.org e-mail: po...@pl... submit requests at: http://sourceforge.net/tracker/?func=3Dadd&group_id=3D76834&atid=3D835555= =20 =20 =20 =20 |
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From: Basil N. <di...@ia...> - 2007-06-01 14:08:47
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di...@ia... > >From popserve Fri Jun 1 05:59:29 2007 >From: msi...@li... >To: msi...@li... >X-No-Archive: yes >Date: Fri, 01 Jun 2007 03:54:00 -0700 >X-BeenThere: msi...@li... >Subject: [Msi-workgroups-board] Welcome to the "Msi-workgroups-feedback" > mailing list >X-BeenThere: msi...@li... >List-Id: <msi-workgroups-board.lists.sourceforge.net> >List-Unsubscribe: ><https://lists.sourceforge.net/lists/listinfo/msi-workgroups-board>, > > <mailto:msi...@li...?subject=unsubscribe> >List-Archive: ><http://sourceforge.net/mailarchive/forum.php?forum=msi-workgroups-board> >List-Post: <mailto:msi...@li...> >List-Help: ><mailto:msi...@li...?subject=help> >List-Subscribe: ><https://lists.sourceforge.net/lists/listinfo/msi-workgroups-board>, > > <mailto:msi...@li...?subject=subscribe> >Sender: msi...@li... > >Welcome to the Msi...@li... mailing >list! Dear msi-workgroups list admins. Please confirm this request for >subscription of your list to the msi-feedback umbrella list. Best >regards, Daniel Schober. > > > >To post to this list, send your email to: > > msi...@li... > >General information about the mailing list is at: > > https://lists.sourceforge.net/lists/listinfo/msi-workgroups-feedback > >If you ever want to unsubscribe or change your options (eg, switch to >or from digest mode, change your password, etc.), visit your >subscription page at: > > >https://lists.sourceforge.net/lists/options/msi-workgroups-feedback/msi-workgroups-board%40lists.sourceforge.net > > >You can also make such adjustments via email by sending a message to: > > Msi...@li... > >with the word `help' in the subject or body (don't include the >quotes), and you will get back a message with instructions. > >You must know your password to change your options (including changing >the password, itself) or to unsubscribe. It is: > > axoxovov > >Normally, Mailman will remind you of your lists.sourceforge.net >mailing list passwords once every month, although you can disable this >if you prefer. This reminder will also include instructions on how to >unsubscribe or change your account options. There is also a button on >your options page that will email your current password to you. > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Msi-workgroups-board mailing list >Msi...@li... >https://lists.sourceforge.net/lists/listinfo/msi-workgroups-board -- Basil J. Nikolau Professor of Biochemistry, Director, Center for Designer Crops, Director, W.M. Keck Metabolomics Research Laboratory Iowa State University Phone: 515-294-9423 Fax: 515-294-0453 http://www.bb.iastate.edu/FacultyResearchFolder/Nikolau/index.html ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Msi-workgroups-feedback mailing list Msi...@li... https://lists.sourceforge.net/lists/listinfo/msi-workgroups-feedback |
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From: Susanna <sa...@eb...> - 2006-11-24 17:31:05
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Dear Stys, I am fw your reply to me to the lists - in particular the Ontology and Data Processing WGs- so they are e able to comment on this. Thanks, Susanna Dalibor Stys wrote: > Dear All, > > I believe that simple definitions of data transformation are > dangerous. These methods are developing, we, for example, in our > Expertomica software for chromatography-mass spectrometry use adaptive > noise filtration and subtraction of backgroun in each data point. That > means that we analyse the information content of the data and subtract > the random noise, spikes and the background contributions separately. > This is principially impossible to describe by simple terms but it is > quite similar to what a qualified operator is doing, i.e. considering > how good are the data surrounding each peak and assessing the baseline > and the precision by which data may be integrated. We have > algoritmised the operator knowledge, added mathematical description of > noise and do it automatically. > Other programs, i.e. Hyperchem, ask you to introduce couple of > parameter defined precisely only as mathematical equations inside the > program, which are then used for data transformation. > This is true for MS, NMR, but in principle for any dataset. > I, actually, suggested some terms but the more I think about it, the > more I do not like it. The only absolutely correct way would be the > reference to place where the original data may be downloaded, the > reference to the software and to all parameters which were used in > data analysis. > > Best regards > > Dalibor Stys > > Susanna-A Sansone wrote: > >> Dear Ontology and Data WGs, >> >> We are collecting these terms for MSI and then feed these in >> FuGO/OBI, here is more info for you: >> >> *Definition for Data Transformation* (up for discussion): The >> process of redefining data based on some predefined rules. The values >> are redefined based on a specific formula or technique. This >> includes mapping data elements from from a source data format into >> destination data. >> >> *An example:* >> NAME: low_intensity_filter DEF: A transformation method that >> involves removal of low intensity values in a data set. For >> microarrays and gels the threshold for exclusion is usually based on >> some estimation of local or global background intensity; for mass >> spectrometry and NMR, it is usually based on the signal-to-noise >> ratio in the spectrum. >> >> Can you please send Daniel your tems, as a tab-delimited file with >> the following information in the file: >> >> Person Submitting: >> NAME: DEF: >> NAME: DEF: >> NAME: DEF: >> etc. >> >> Thanks, >> Susanna >> >> >> Susanna-A Sansone wrote: >> >>> ***sorry for cross-posting*** >>> >>> Dear Ontology and Data WGs, >>> (cc to Exchange, Chemical, Biology WGs fyi) >>> >>> We are in the process of collecting terms for **data >>> transformation** terms. >>> >>> Please, send your list of terms and definitions (if you have these) >>> to Daniel Schober -here cc- in an excel sheet. >>> >>> Thanks, >>> Susanna >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------------------- >>> >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys - and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> msi-ontology-devel mailing list >>> msi...@li... >>> https://lists.sourceforge.net/lists/listinfo/msi-ontology-devel >>> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Msi-workgroups-data-processing mailing list >> Msi...@li... >> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-data-processing >> >> > -- Susanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project 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 room: A229 |
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From: Susanna-A S. <sa...@eb...> - 2006-11-22 10:30:53
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***sorry for cross-posting*** Dear Ontology and Data WGs, (cc to Exchange, Chemical, Biology WGs fyi) We are in the process of collecting terms for *data transformation* terms. Please, send your list of terms and definitions (if you have these) to Daniel Schober -here cc- in an excel sheet. Thanks, Susanna |
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From: Susanna <sa...@eb...> - 2006-08-29 13:41:21
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**** Sorry for the multiple postings ***** Dear All, This is just a note to flag the *special issue of OMICS journal on data standards*. The online version is *free* and available at the following URL: http://www.liebertonline.com/toc/omi/10/2;jsessionid=nWAx67n0VoVdcUfY8Z It containts 20 invited articles, including a piece on MSI, MGED and PSI. Best regards, Susanna -- Susanna-Assunta Sansone, PhD Project Coordinator The European Bioinformatics Institute (EBI) EMBL Outstation - Hinxton Wellcome Trust Genome Campus Cambridge CB10 1SD, UK |
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From: Oliver J. <oa...@mo...> - 2006-07-11 11:08:50
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To whom it may concern, I would like to get involved in the Metabolomics Standards Initiative. My areas of interest/expertise is in Environmental Metabolomics and so I would like to be involved in helping developing standards for the environmental working group if possible. Yours sincerely Oliver Jones ******************************** Dr. Oliver Jones Hopkins Building Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1QW UK Tel: +44 (0) 1223 764 948 Fax: +44 (0) 1223 333 345 E-mail - oa...@mo... ******************************** |
