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From: Helen P. <par...@eb...> - 2009-11-05 16:42:25
|
Hi http://magetabutils.sourceforge.net MAGE-TAB Perl module "The MAGE-TAB Utilities project has been created with the aim of providing an easy-to-use API for the parsing, manipulation, visualization and output of data in MAGE-TAB format. Early versions of the API are initially being developed in Perl, although contributions in other languages are welcomed." code from Tim Rayner, ex-EBI, ArrayExpress will be using this in our production code soon, just in case anyone else is interested cheers Helen -- Helen Parkinson, PhD ArrayExpress Production Coordinator, Microarray Informatics Team, EBI EBI 01223 494672 Skype: helen.parkinson.ebi |
From: Junmin L. <ju...@pc...> - 2008-11-17 19:35:49
|
FYI: MAGE-TAB Annotation Tools Workshop (12/15 - 12/16,contact Chris for this) http://www.cbil.upenn.edu/meetings/MAGE-TAB/ MAGE-TAB programmer meeting (Dec. 14) https://www.cbil.upenn.edu/magewiki/index.php/12-14-2008 Thanks, ---junmin |
From: Gavin S. <she...@ge...> - 2008-08-22 00:37:41
|
Hi Leandro, Sorry for the delayed reply. There will not be a programming jamboree at the meeting, nor a meeting about programming efforts. Cheers, Gavin On Aug 15, 2008, at 1:39 AM, Hermida, Leandro wrote: > Hello, > > Just wondering if there will be a programming jamboree or even just > a meeting about programming efforts at MGED 11? > > Sincerely, > Leandro > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 |
From: Hermida, L. <Lea...@fm...> - 2008-08-15 08:40:02
|
Hello, Just wondering if there will be a programming jamboree or even just a meeting about programming efforts at MGED 11? Sincerely, Leandro |
From: Junmin L. <ju...@pc...> - 2008-08-03 19:39:37
|
For many of you: http://www.infoq.com/news/2008/07/8-reasons-md-fails The title may be misleading, but discussions are more interesting. ---junmin |
From: Gavin S. <she...@ge...> - 2008-08-01 13:00:18
|
Hi Adam, No - we didn't perceive sufficient interest to hold a jamboree at the Italy meeting, so there won't be one this year. Cheers, Gavin On Aug 1, 2008, at 5:57 AM, Adam Witney wrote: > > are there any plans for a Jamboree at the upcoming MGED meeting? > > thanks > > adam > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Adam W. <aw...@sg...> - 2008-08-01 12:58:12
|
are there any plans for a Jamboree at the upcoming MGED meeting? thanks adam |
From: Don M. <dM...@ge...> - 2008-05-05 22:03:18
|
Hi all, For some personal (and personnel) news from SMD, please skip to the end of this message. We would like to share with you our canonical Java parser and object model for MAGE-TAB -- in their current, work-in-progress state. Although the work to make the MAGE-TAB parser create and populate MAGE-TAB objects is not yet complete, we think that what we already have is of considerable value. We're sending it out now because it would benefit from your consideration and feedback. All files referenced below are available on the SMD ftp site: ftp://smd-ftp.stanford.edu/smd/transfers/magetab. ------------------------------------------- A MAGE-TAB syntactic validator ------------------------------------------- This: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/MAGE-TAB.jar is a MAGE-TAB parser generated from the ANTLR formal grammars ftp://smd-ftp.stanford.edu/smd/transfers/magetab/IDF.g ftp://smd-ftp.stanford.edu/smd/transfers/magetab/SDRF.g ftp://smd-ftp.stanford.edu/smd/transfers/magetab/ADF.g We believe that these grammars precisely embody the MAGE-TAB specification. It incorporates the MAGE-TAB community's latest thinking on the MAGE-TAB 1.1 specification from our January meeting in Rockville. It also implements the proposals expressed in ftp://smd-ftp.stanford.edu/smd/transfers/magetab/MAGE-TAB%20Residual% 20Problems%20and%20Proposals%20-%20rev.doc for some residual issues. We invite you to test your IDF, ADF, and SDRF files for validity using the parser. You may run the jar from a command line such as: java -jar MAGE-TAB.jar Invoked with that command, the jar will emit a brief description of its syntax and semantics. One caution: It may not yet work on very large ADF files. The buffer management for that is yet to be done. Here are some small (positive) test files: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/e-mexp-428_v1.1.idf ftp://smd-ftp.stanford.edu/smd/transfers/magetab/e-mexp-428sdrf_v1.1.txt ftp://smd-ftp.stanford.edu/smd/transfers/magetab/test1.adf ftp://smd-ftp.stanford.edu/smd/transfers/magetab/test2.adf The idf and the sdrf are from the online version of the MAGE-TAB v 1.1 specification. I made up the adf files myself. --------------------------------------------------------------- A MAGE-TAB object model, expressed in UML --------------------------------------------------------------- This is a UML description of MAGE-TAB: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/magetab.xml You can open and view this UML with MagicDraw. We have used MagicDraw 12.1 and it's likely that more recent versions of MagicDraw work equally well. We have no experience with other UML visualizers. This object model (we believe) reflects a precise and isomorphic representation of the contents of MAGE-TAB. We are generating very clean Java classes from it using a hand-crafted Velocity template: ftp://smd-ftp.stanford.edu/smd/transfers/magetab/ValueObject.vsl (There is also a Java class mapping file that maps Collections to a typed Vector subclass that knows its type and deals intelligently with Dates and some other basic data types.) We believe that the UML satisfies these properties: 1) It is complete. That is, it is capable of representing any information that can be expressed in MAGE-TAB. Please try to verify this. See if you can find all the MAGE-TAB constructs in the UML. If you think that something is missing, look more closely; if you still can't find it, let us know. 2) It is concise. That is, it does not represent any information other than what is required for MAGE-TAB. Please try to verify this, too. If you notice something in the UML and can't understand how it relates to MAGE-TAB, then once again, let us know. 3 MAGE-TAB keywords are almost always used for the names of classes, attributes, and associations. The principal exceptions are the MAGE-TAB Comment[] construct, which conveys a UserDefinedAttritbute; and the MAGE-TAB ProtocolREF construct which is ambiguous between an externally defined protocol and the application of a protocol. In the UML, protocolREF is a possibly defining attribute of a Protocol object, and there is a separate, ProtocolApplication object. Also, some names for classes that are super classes (particularly the abstract ones) don't correspond to MAGE-TAB keywords, but are drawn directly from the descriptive text of the specification. 4) The diagram is visually clear. That is, no lines cross, no lines have more than one "break", and whenever possible, related elements (for example, subclasses of a common super class) are grouped together and aligned as space permits. 5) It is well-commented and our code generation template (above) transfers the comments as Javadoc comments to the generated Java classes. Because the object model is (we claim) isomorphic with the information conveyed by MAGE-TAB, it offers a kind of feedback tool for the specification. We would suggest that, if you don't like something in the object model -- for example, it seems to you overly complex -- then this may well be a dissatisfaction with MAGE-TAB itself -- perhaps meriting a reexamination of it. ------------------- Personal Note ------------------- Finally, I'm sad to report that I am taking my leave of SMD and of you-all. I will no longer be working on MAGE-TAB after Tuesday, May 6. The good news is that MAGE-TAB efforts at SMD will be in the very capable hands of Maria Mao (mar...@st...). Please welcome her to our group! I apologize for not getting this message out last week. I sent it last Wednesday with attachments that apparently made it too big to squeeze through the MAGE mailing lists. Regards, Don Maier Sr. Software Designer/Research Dept. of Biochemistry Stanford University School of Medicine |
From: Joe W. <jw...@ji...> - 2008-04-10 16:47:00
|
Hi Gerald, I think you can still have your picnic--but you may have to guess the source of your mustard. The 'Term Source REF' column describes the source of the term used in each row in the Characteristics column. In the absense of the Term Source REF column, the ontology is assumed to be the MO, and the data values are either drawn from MO or are user defined. If Term Source REF is used, it is applied to the rows and not the column heading, so your cell line database would be the term source. The bracketted term is the category of the annotation supplied in the BMC column, and is assumed to be drawn from the MO. There is no good way to specify the source of the category at the present time. There is another way to do this without Term Source REF: use a [Comment] column. In the column specify the data source for the BMC cell lines. Since Term Source REF is not provided, the Characteristic[cellLine] will be assumed to be a MO term, and the individual data values will be user defined. The Comment column is treated as an NVT--a local property--and is not guarentteed to be processed by the MAGE-TAB parser. So this method has this drawback. An alternate syntax has been discussed in past sessions, but I cannot find my notes on this; does anyone else have notes describing a syntax similar to this: Characteristic [term: term source] ? Cheers, Joe Gerald Fontenay wrote: >Hi, > >I have a simple question and apologies if this is in the MAGE-TAB 1.1 doc.. >Please consider the column header: Characteristics[CellLine]. >If I assume that the value in the subsequent Term Source REF column >defines the term source of the value in the previous Characteristics row, >where should I state that "CellLine" comes from the MO, for example? >I suppose a cellline database should also contain the term "CellLine". >Is that implied or am I a sandwich short of a picnic? > >TIA, >-g > > >------------------------------------------------------------------------- >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >Don't miss this year's exciting event. There's still time to save $100. >Use priority code J8TL2D2. >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >_______________________________________________ >Mged-mage mailing list >Mge...@li... >https://lists.sourceforge.net/lists/listinfo/mged-mage > > |
From: Gerald F. <gvf...@lb...> - 2008-04-09 23:46:54
|
Hi, I have a simple question and apologies if this is in the MAGE-TAB 1.1 doc.. Please consider the column header: Characteristics[CellLine]. If I assume that the value in the subsequent Term Source REF column defines the term source of the value in the previous Characteristics row, where should I state that "CellLine" comes from the MO, for example? I suppose a cellline database should also contain the term "CellLine". Is that implied or am I a sandwich short of a picnic? TIA, -g |
From: Jason S. <jas...@gm...> - 2008-03-19 08:09:45
|
Hey, Lately the cvs commit mailing list from SF has been getting spammed. Since there is no actual commit traffic (it was never enabled for SVN when we switched) I unsubscribed everyone that was on the list. If we want to we can reactivate it in the future. Cheers, jas. |
From: Susanna <sa...@eb...> - 2008-03-11 12:02:23
|
- Apologies for cross posting - Dear All, We* are in the process of developing ISA-TAB, a simple format to submit or exchange studies employing omics technologies along with more conventional methodologies. This proposal builds on the successful uptake of the MAGE TAB format and employs its syntax to: - ensure backward compatibility with existing MAGE-TAB files - facilitate the future adoption of one common format. However, ISA-TAB has a number of additional features making it a more general framework that can capture the complexity of studies employing a combination of technologies. If you wish to know more or get involved, please go to the website to view the ISA-TAB v0.2 spec (under Documents) and/or register to the mailing list: http://isatab.sf.net ISA-TAB in a nutshell and the rationale behind the initial proposal is summarized below. This is an extract from the first ISA-TAB workshop report, that will come out in summer/june as part of the 2nd open issue on data standard, dedicated to the activities of the Genomics Standards Consortium (GSC). Best regards, Susanna (* See list of contributors at http://isatab.sf.net) %%%%%%%%%%%%%%%%%%%%% ISA-TAB in a nutshell %%%%%%%%%%%%%%%%%%%%% Investigation, Study and Assay are the three key entities (Sansone et al., 2006) around which the ISA-TAB framework is built; these assist in structuring metadata and describing the relationship of samples to data (Figure 1). The ISA-TAB proposal builds on the successful uptake of the MicroArray Gene Expression (MAGE) TAB format, which supports the management, exchange and submission of microarray-based experiment data and metadata (Rayner et al., 2006). MAGE-TAB was designed for use by laboratories with little or no bioinformatics support, rendering them unable to deal with the complexity of MAGE Markup Language (ML) formatted files (Spellman et al., 2002), which often are also exceptionally large - too large to be easily read by most people, and often too large to be read by most software programs (Maier et al., 2008). ISA-TAB can be viewed as an extended version of the MAGE-TAB paradigm, sharing its motivation for the use of tab-delimited text files; i.e., that they can be created programmatically or by using spreadsheet software such as Microsoft Excel, where they can easily be viewed and edited by researchers. Like MAGE-TAB before it, ISA-TAB is simply a format with which to communicate information. Neither minimum requirements, nor the use of controlled terminologies are within the scope of this proposal. Therefore, the decision on how to regulate its use (e.g., by enforcing MIBBI minimum requirements, or mandating the use of OBO Foundry terminologies) is solely a matter for those who will implement the format in their system. The ISA-TAB actually employs MAGE-TAB syntax to ensure backward compatibility with existing MAGE-TAB files, to facilitate the future adoption of one common format. However, ISA-TAB has a number of additional features making it a more general framework that can capture the complexity of studies employing a combination of technologies. For example, where omics-based technologies are being used in clinical or non-clinical studies, ISA-TAB can complement existing biomedical formats such as the SDTM by formally capturing information about the interrelationship of the various parts. It is important to maintain an alignment between the concepts in ISA-TAB and (some of) the objects in the FuGE model, partly as that model is integral to the development of MAGE-ML v2. The ISA-TAB format could be seen as competing with XML-based formats, whether existing or under development, such as the FuGE-ML. However, ISA-TAB addresses an immediate need, whereas a complete set of FuGE-based modules or other interoperable XML is still some way off. Once such formats do become available, ISA-TAB can continue to serve those with little or no bioinformatics support, as well as finding utility as a user-friendly presentation layer for XML-based formats (via an XSL transformation); i.e., in the manner of the HTML rendering of MAGE-ML documents (http://www.ebi.ac.uk/~rocca/MAGE-XSLT/HTML%20rendering%20of%20MAGE.htm). For the development of this format, openness and due process must apply. To ensure that all groups have access to information, a public website has been created at SourceForge (http://isatab.sourceforge.net). It contains the latest ISA-TAB v0.2 specification, an alignment with MAGE-TAB, the list of participants and their systems and a link to a mailing list to which interested parties can subscribe. Several example ISA-TAB 'instance' files are being created from published biological, biomedical and environmental studies, to be posted on the website. For example, the first was created by members of the Genomics Standards Consortium (GSC) (Field et al., 2008, this issue) using a dataset published by Gilbert et al. (in review) originating from a joint metagenomics and metatranscriptomics study looking at the effect of ocean acidification on phytoplankton and bacterioplankton. %%%%%%%%%% Rationale %%%%%%%%% The initial motivation for creating the ISA-TAB straw man proposal was to meet the needs of the BioMAP system at EBI (www.ebi.ac.uk/net-project). BioMAP aims to create a common structured representation of the metadata and the sample-data relationship for biological, biomedical and environmental studies employing omics-based technologies along with more conventional methodologies. The ISA-TAB format is being developed to assist users make combined submissions to EBI public archives; for example, to ArrayExpress, PRIDE and a metabolomics repository to be developed in the near future. It has been clear from the outset that the ISA-TAB framework could also serve as a common cross-platform format, thereby greatly benefiting other collaborators; to pipeline omics-based experimental data into EBI public repositories, to enable their users to import data from EBI repositories into their local systems, or simply to exchange data among themselves. Therefore, in a collaborative spirit the development of the ISA-TAB has been opened up and shared with a wider community........... -- Susanna-Assunta Sansone, PhD www.ebi.ac.uk/net-project |
From: Jason S. <jas...@gm...> - 2008-02-29 05:35:04
|
Hey All, MAGE can be a huge producer of *BIG* XML files... In case you haven't seen this before, here are some pointers to the VTD-XML project - it really looks like a big improvement over both the SAX and DOM API's for certain XML handling tasks, usually where you need to modify a persistent XML document. Cheers, jas. ---------- Forwarded message ---------- From: jimmy Zhang <cra...@co...> Date: 26 Feb 2008 04:53 Subject: [Soaplite-devel] VTD-XML 2.3 released To: soaplite-devel <soa...@li...> VTD-XML 2.3 is now released. To download the latest version please visit http://sourceforge.net/project/showfiles.php?group_id=110612&package_id=120172. Below is a list of new features and enhancements in this version. a.. VTDException is now introduced as the root class for all other VTD-XML's exception classes (per suggestion of Max Rahder). b.. Transcoding capability is now added for inter-document cut and paste. You can cut a chuck of bytes in a UTF-8 encoded document and paste it into a UTF-16 encoded document and the output document is still well-formed. c.. ISO-8859-10, ISO-8859-11, ISO-8859-12, ISO-8859-13, ISO-8859-14 and ISO-8859-15 support has now been added d.. Zero length Text node is now possible. e.. Ability to dump in-memory copy of text is added. f.. Various code cleanup, enhancement and bug fixes. Below are some new articles related to VTD-XML a.. Index XML documents with VTD-XML http://xml.sys-con.com/read/453082.htm b.. Manipulate XML content the Ximple Way http://www.devx.com/xml/Article/36379 c.. VTD-XML: A new vision of XML http://www.developer.com/xml/article.php/3714051 d.. VTD-XML: XML Processing for the future http://www.codeproject.com/KB/cs/vtd-xml_examples.aspx If you (or someone you know) like the concept of VTD-XML, think that it can help solve enterprises' XML processing related issues (particularly those related to SOA), and would like to directly influence and contribute to the development of the future of Internet, please email me cra...@co...). We are looking for open source software developers and project management people to take VTD-XML to the next level. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Soaplite-devel mailing list Soa...@li... https://lists.sourceforge.net/lists/listinfo/soaplite-devel |
From: Helen P. <par...@eb...> - 2008-02-25 15:11:09
|
I can help do this if someone will find it useful, shouldn't take too long, best regards Helen Chris Stoeckert wrote: > Dear All, > Has anyone attempted to map MIAME-Plant onto MAGE-ML? > Do you know who might know? > Am passing this question on from Richard Bruskiewich and his group at > CGIAR (cc'd). > Thanks. > Chris > > Chris Stoeckert, Ph.D. > > Research Professor, Dept. of Genetics > > 1415 Blockley Hall, Center for Bioinformatics > > 423 Guardian Dr., University of Pennsylvania > > Philadelphia, PA 19104 > > Ph: 215-573-4409 FAX: 215-573-3111 > > http://www.cbil.upenn.edu > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > ------------------------------------------------------------------------ > > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > -- Helen Parkinson, PhD ArrayExpress Production Coordinator, Microarray Informatics Team, EBI EBI 01223 494672 Skype: helen.parkinson.ebi |
From: Chris S. <sto...@pc...> - 2008-02-25 15:06:28
|
Dear All, Has anyone attempted to map MIAME-Plant onto MAGE-ML? Do you know who might know? Am passing this question on from Richard Bruskiewich and his group at CGIAR (cc'd). Thanks. Chris Chris Stoeckert, Ph.D. Research Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 http://www.cbil.upenn.edu |
From: Tim R. <ra...@eb...> - 2008-01-15 09:58:23
|
Hi Don, Thanks for reminding me; you are of course correct. I guess we should also add these to the ADF: Technology Type Term Accession Number Surface Type Term Accession Number Substrate Type Term Accession Number Sequence Polymer Type Term Accession Number Cheers, Tim On Mon, 14 Jan 2008, Don Maier wrote: > Hi again, Tim, > > With your proposal, there would be Term Accession Numbers in the IDF and SDRF > -- but still not in the ADF (header). Is there a reason to omit term > accession numbers in the ADF header, but to include them in the other two > kinds of MAGE-TAB file? > > Regards, > Don M. > > > On Jan 14, 2008, at 10:40 AM, Don Maier wrote: > >> Hi Tim, >> >> Ok, Tim, I'll fold this into the compiled document, which I'll send out >> again just before next week's meeting. >> >> Thanks! >> >> Regards, >> Don M. >> >> On Jan 14, 2008, at 6:39 AM, Tim Rayner wrote: >> >>> Hi, >>> >>> Thanks for putting this together, Don. I only have one small addition to >>> suggest. When we discussed adding the "Term Accession Number" column to >>> SDRF we neglected the IDF, and a couple of groups have asked me in the >>> meantime whether we could rectify this. I'd therefore suggest the addition >>> of these (optional!) IDF tags, one for each "* Term Source REF" tag: >>> >>> Experimental Design Term Accession Number >>> Experimental Factor Term Accession Number >>> Person Roles Term Accession Number >>> Quality Control Term Accession Number >>> Replicate Term Accession Number >>> Normalization Term Accession Number >>> Publication Status Term Accession Number >>> Protocol Term Accession Number >>> >>> I think we probably omitted these tags because we didn't see any immediate >>> need for them, but both the ISA-TAB and modENCODE projects are keen to >>> fully annotate with OBI terms with accessions. >>> >>> Cheers, >>> >>> Tim >>> >>> >>> On Thu, 20 Dec 2007, Don Maier wrote: >>> >>>> Hi all, >>>> >>>> To ease the chore of reading and comparing comments on MAGE-TAB v. 1.1, >>>> I've incorporated into my original feedback document all other published >>>> comments to date -- those of Michael, Junmin, Helen, and Alvis: >>>> >>>> >>>> >>>> Those people should check to make sure that I've transcribed their >>>> remarks correctly and completely. If anyone else sends out comments, >>>> I'll incorporate those in a final version of the document before we meet >>>> in January. >>>> >>>> Have a great holiday! >>>> >>>> Regards, >>>> Don M. >>>> >>>> >>>> On Dec 7, 2007, at 11:36 AM, Don Maier wrote: >>>> >>>>> Hi all, >>>>> Here is a set of problems and proposed solutions for MAGE-TAB that we at >>>>> Stanford would like to discuss at the MAGE-TAB workshop in January: >>>>> >>>>> <MAGE-TAB Proposals.doc> >>>>> We would greatly appreciate your contribution of creative energy to help >>>>> with this! >>>>> Regards, >>>>> Don Maier >>>>> Sr. Software Designer/Research >>>>> Dept. of Biochemistry >>>>> Stanford University School of Medicine >>>>> On Nov 26, 2007, at 2:34 AM, Tim Rayner wrote: >>>>>> Hi, >>>>>> My apologies if you receive this email more than once. At the last >>>>>> couple >>>>>> of jamborees a set of requested changes to the MAGE-TAB specification >>>>>> emerged, and the least contentious of these changes have been >>>>>> incorporated >>>>>> into the ArrayExpress MAGE-TAB parser. We've also created a new draft >>>>>> MAGE-TAB v1.1 specification, and the document is now available for >>>>>> download here: >>>>>> http://www.ebi.ac.uk/systems-srv/mp/file-exchange/MAGE-TABv1.1.tar.gz >>>>>> Changes were made as discussed at the Stanford and Brisbane jamborees >>>>>> (2007): >>>>>> >>>>>> * Added "Experimental Design Term Source REF" to IDF. >>>>>> >>>>>> * Added "Term Accession Number" to SDRF. >>>>>> >>>>>> * Added "Assay Name" and "Technology Type" to SDRF. >>>>>> >>>>>> * Added notes indicating that lines starting with the # character are >>>>>> to be treated as ignorable comments. >>>>>> >>>>>> * Added free-text "Protocol REF" heading prefixes (e.g. "Growth >>>>>> Protocol REF"). >>>>>> Note that in each case a document compliant with the v1.0 specification >>>>>> remains compliant with this updated version. The following changes were >>>>>> made to clarify the specification where it seemed necessary: >>>>>> >>>>>> * Sections were added providing notes on all the IDF and SDRF fields >>>>>> and columns. >>>>>> >>>>>> * Table 7 (SDRF columns) was modified to remove the data file columns >>>>>> as attributes of Hybridization, Scan and Normalization name, in an >>>>>> attempt >>>>>> to disambiguate the grammar needed to parse SDRF column headings. >>>>>> >>>>>> * Added a note (section 3.3.7, point 8) regarding what to do with SDRF >>>>>> attribute columns when applied to empty node or edge column values >>>>>> (i.e., >>>>>> ignore the attributes in such cases). >>>>>> >>>>>> * Other minor clarifications were added to the text where necessary. >>>>>> Don Maier at Stanford has also proposed disambiguating the behaviour of >>>>>> Comment[] columns by restricting their use such that they always >>>>>> immediately follow the column to which they apply. This change has not >>>>>> yet >>>>>> been included as it is likely to break compatibility with older >>>>>> documents; >>>>>> I think that this proposal needs to be circulated more widely before >>>>>> inclusion. >>>>>> We would appreciate your feedback on this new draft specification. >>>>>> Best regards, >>>>>> Tim >>>>>> -- >>>>>> Tim Rayner, Ph.D. >>>>>> Scientific Database Curator >>>>>> Microarray Informatics Team >>>>>> European Bioinformatics Institute >>>>>> ------------------------------------------------------------------------- >>>>>> This SF.net email is sponsored by: Microsoft >>>>>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>>> _______________________________________________ >>>>>> Mged-mage mailing list >>>>>> Mge...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>>>> ------------------------------------------------------------------------- >>>>> SF.Net email is sponsored by: >>>>> Check out the new SourceForge.net Marketplace. >>>>> It's the best place to buy or sell services for >>>>> just about anything Open Source. >>>>> http://sourceforge.net/services/buy/index.php_______________________________________________ >>>>> Mged-MAGE2 mailing list >>>>> Mge...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>>> >> >> Don Maier >> Sr. Software Designer/Research >> Dept. of Biochemistry >> Stanford University School of Medicine >> >> > |
From: Don M. <dM...@ge...> - 2008-01-14 21:06:44
|
Hi again, Tim, With your proposal, there would be Term Accession Numbers in the IDF and SDRF -- but still not in the ADF (header). Is there a reason to omit term accession numbers in the ADF header, but to include them in the other two kinds of MAGE-TAB file? Regards, Don M. On Jan 14, 2008, at 10:40 AM, Don Maier wrote: > Hi Tim, > > Ok, Tim, I'll fold this into the compiled document, which I'll send > out again just before next week's meeting. > > Thanks! > > Regards, > Don M. > > On Jan 14, 2008, at 6:39 AM, Tim Rayner wrote: > >> Hi, >> >> Thanks for putting this together, Don. I only have one small >> addition to suggest. When we discussed adding the "Term Accession >> Number" column to SDRF we neglected the IDF, and a couple of >> groups have asked me in the meantime whether we could rectify >> this. I'd therefore suggest the addition of these (optional!) IDF >> tags, one for each "* Term Source REF" tag: >> >> Experimental Design Term Accession Number >> Experimental Factor Term Accession Number >> Person Roles Term Accession Number >> Quality Control Term Accession Number >> Replicate Term Accession Number >> Normalization Term Accession Number >> Publication Status Term Accession Number >> Protocol Term Accession Number >> >> I think we probably omitted these tags because we didn't see any >> immediate need for them, but both the ISA-TAB and modENCODE >> projects are keen to fully annotate with OBI terms with accessions. >> >> Cheers, >> >> Tim >> >> >> On Thu, 20 Dec 2007, Don Maier wrote: >> >>> Hi all, >>> >>> To ease the chore of reading and comparing comments on MAGE-TAB >>> v. 1.1, I've incorporated into my original feedback document all >>> other published comments to date -- those of Michael, Junmin, >>> Helen, and Alvis: >>> >>> >>> >>> Those people should check to make sure that I've transcribed >>> their remarks correctly and completely. If anyone else sends out >>> comments, I'll incorporate those in a final version of the >>> document before we meet in January. >>> >>> Have a great holiday! >>> >>> Regards, >>> Don M. >>> >>> >>> On Dec 7, 2007, at 11:36 AM, Don Maier wrote: >>> >>>> Hi all, >>>> Here is a set of problems and proposed solutions for MAGE-TAB >>>> that we at Stanford would like to discuss at the MAGE-TAB >>>> workshop in January: >>>> >>>> <MAGE-TAB Proposals.doc> >>>> We would greatly appreciate your contribution of creative energy >>>> to help with this! >>>> Regards, >>>> Don Maier >>>> Sr. Software Designer/Research >>>> Dept. of Biochemistry >>>> Stanford University School of Medicine >>>> On Nov 26, 2007, at 2:34 AM, Tim Rayner wrote: >>>>> Hi, >>>>> My apologies if you receive this email more than once. At the >>>>> last couple >>>>> of jamborees a set of requested changes to the MAGE-TAB >>>>> specification >>>>> emerged, and the least contentious of these changes have been >>>>> incorporated >>>>> into the ArrayExpress MAGE-TAB parser. We've also created a new >>>>> draft >>>>> MAGE-TAB v1.1 specification, and the document is now available for >>>>> download here: >>>>> http://www.ebi.ac.uk/systems-srv/mp/file-exchange/MAGE- >>>>> TABv1.1.tar.gz >>>>> Changes were made as discussed at the Stanford and Brisbane >>>>> jamborees >>>>> (2007): >>>>> >>>>> * Added "Experimental Design Term Source REF" to IDF. >>>>> >>>>> * Added "Term Accession Number" to SDRF. >>>>> >>>>> * Added "Assay Name" and "Technology Type" to SDRF. >>>>> >>>>> * Added notes indicating that lines starting with the # >>>>> character are >>>>> to be treated as ignorable comments. >>>>> >>>>> * Added free-text "Protocol REF" heading prefixes (e.g. "Growth >>>>> Protocol REF"). >>>>> Note that in each case a document compliant with the v1.0 >>>>> specification >>>>> remains compliant with this updated version. The following >>>>> changes were >>>>> made to clarify the specification where it seemed necessary: >>>>> >>>>> * Sections were added providing notes on all the IDF and SDRF >>>>> fields >>>>> and columns. >>>>> >>>>> * Table 7 (SDRF columns) was modified to remove the data file >>>>> columns >>>>> as attributes of Hybridization, Scan and Normalization name, in >>>>> an attempt >>>>> to disambiguate the grammar needed to parse SDRF column headings. >>>>> >>>>> * Added a note (section 3.3.7, point 8) regarding what to do >>>>> with SDRF >>>>> attribute columns when applied to empty node or edge column >>>>> values (i.e., >>>>> ignore the attributes in such cases). >>>>> >>>>> * Other minor clarifications were added to the text where >>>>> necessary. >>>>> Don Maier at Stanford has also proposed disambiguating the >>>>> behaviour of >>>>> Comment[] columns by restricting their use such that they always >>>>> immediately follow the column to which they apply. This change >>>>> has not yet >>>>> been included as it is likely to break compatibility with older >>>>> documents; >>>>> I think that this proposal needs to be circulated more widely >>>>> before >>>>> inclusion. >>>>> We would appreciate your feedback on this new draft specification. >>>>> Best regards, >>>>> Tim >>>>> -- >>>>> Tim Rayner, Ph.D. >>>>> Scientific Database Curator >>>>> Microarray Informatics Team >>>>> European Bioinformatics Institute >>>>> ------------------------------------------------------------------ >>>>> ------- >>>>> This SF.net email is sponsored by: Microsoft >>>>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>> _______________________________________________ >>>>> Mged-mage mailing list >>>>> Mge...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>>> ------------------------------------------------------------------- >>>> ------ >>>> SF.Net email is sponsored by: >>>> Check out the new SourceForge.net Marketplace. >>>> It's the best place to buy or sell services for >>>> just about anything Open Source. >>>> http://sourceforge.net/services/buy/ >>>> index.php_______________________________________________ >>>> Mged-MAGE2 mailing list >>>> Mge...@li... >>>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>> > > Don Maier > Sr. Software Designer/Research > Dept. of Biochemistry > Stanford University School of Medicine > > |
From: Don M. <dM...@ge...> - 2008-01-14 18:41:08
|
Hi Tim, Ok, Tim, I'll fold this into the compiled document, which I'll send out again just before next week's meeting. Thanks! Regards, Don M. On Jan 14, 2008, at 6:39 AM, Tim Rayner wrote: > Hi, > > Thanks for putting this together, Don. I only have one small > addition to suggest. When we discussed adding the "Term Accession > Number" column to SDRF we neglected the IDF, and a couple of groups > have asked me in the meantime whether we could rectify this. I'd > therefore suggest the addition of these (optional!) IDF tags, one > for each "* Term Source REF" tag: > > Experimental Design Term Accession Number > Experimental Factor Term Accession Number > Person Roles Term Accession Number > Quality Control Term Accession Number > Replicate Term Accession Number > Normalization Term Accession Number > Publication Status Term Accession Number > Protocol Term Accession Number > > I think we probably omitted these tags because we didn't see any > immediate need for them, but both the ISA-TAB and modENCODE > projects are keen to fully annotate with OBI terms with accessions. > > Cheers, > > Tim > > > On Thu, 20 Dec 2007, Don Maier wrote: > >> Hi all, >> >> To ease the chore of reading and comparing comments on MAGE-TAB v. >> 1.1, I've incorporated into my original feedback document all >> other published comments to date -- those of Michael, Junmin, >> Helen, and Alvis: >> >> >> >> Those people should check to make sure that I've transcribed their >> remarks correctly and completely. If anyone else sends out >> comments, I'll incorporate those in a final version of the >> document before we meet in January. >> >> Have a great holiday! >> >> Regards, >> Don M. >> >> >> On Dec 7, 2007, at 11:36 AM, Don Maier wrote: >> >>> Hi all, >>> Here is a set of problems and proposed solutions for MAGE-TAB >>> that we at Stanford would like to discuss at the MAGE-TAB >>> workshop in January: >>> >>> <MAGE-TAB Proposals.doc> >>> We would greatly appreciate your contribution of creative energy >>> to help with this! >>> Regards, >>> Don Maier >>> Sr. Software Designer/Research >>> Dept. of Biochemistry >>> Stanford University School of Medicine >>> On Nov 26, 2007, at 2:34 AM, Tim Rayner wrote: >>>> Hi, >>>> My apologies if you receive this email more than once. At the >>>> last couple >>>> of jamborees a set of requested changes to the MAGE-TAB >>>> specification >>>> emerged, and the least contentious of these changes have been >>>> incorporated >>>> into the ArrayExpress MAGE-TAB parser. We've also created a new >>>> draft >>>> MAGE-TAB v1.1 specification, and the document is now available for >>>> download here: >>>> http://www.ebi.ac.uk/systems-srv/mp/file-exchange/MAGE- >>>> TABv1.1.tar.gz >>>> Changes were made as discussed at the Stanford and Brisbane >>>> jamborees >>>> (2007): >>>> >>>> * Added "Experimental Design Term Source REF" to IDF. >>>> >>>> * Added "Term Accession Number" to SDRF. >>>> >>>> * Added "Assay Name" and "Technology Type" to SDRF. >>>> >>>> * Added notes indicating that lines starting with the # >>>> character are >>>> to be treated as ignorable comments. >>>> >>>> * Added free-text "Protocol REF" heading prefixes (e.g. "Growth >>>> Protocol REF"). >>>> Note that in each case a document compliant with the v1.0 >>>> specification >>>> remains compliant with this updated version. The following >>>> changes were >>>> made to clarify the specification where it seemed necessary: >>>> >>>> * Sections were added providing notes on all the IDF and SDRF >>>> fields >>>> and columns. >>>> >>>> * Table 7 (SDRF columns) was modified to remove the data file >>>> columns >>>> as attributes of Hybridization, Scan and Normalization name, in >>>> an attempt >>>> to disambiguate the grammar needed to parse SDRF column headings. >>>> >>>> * Added a note (section 3.3.7, point 8) regarding what to do >>>> with SDRF >>>> attribute columns when applied to empty node or edge column >>>> values (i.e., >>>> ignore the attributes in such cases). >>>> >>>> * Other minor clarifications were added to the text where >>>> necessary. >>>> Don Maier at Stanford has also proposed disambiguating the >>>> behaviour of >>>> Comment[] columns by restricting their use such that they always >>>> immediately follow the column to which they apply. This change >>>> has not yet >>>> been included as it is likely to break compatibility with older >>>> documents; >>>> I think that this proposal needs to be circulated more widely >>>> before >>>> inclusion. >>>> We would appreciate your feedback on this new draft specification. >>>> Best regards, >>>> Tim >>>> -- >>>> Tim Rayner, Ph.D. >>>> Scientific Database Curator >>>> Microarray Informatics Team >>>> European Bioinformatics Institute >>>> ------------------------------------------------------------------- >>>> ------ >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> _______________________________________________ >>>> Mged-mage mailing list >>>> Mge...@li... >>>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>> -------------------------------------------------------------------- >>> ----- >>> SF.Net email is sponsored by: >>> Check out the new SourceForge.net Marketplace. >>> It's the best place to buy or sell services for >>> just about anything Open Source. >>> http://sourceforge.net/services/buy/ >>> index.php_______________________________________________ >>> Mged-MAGE2 mailing list >>> Mge...@li... >>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >> Don Maier Sr. Software Designer/Research Dept. of Biochemistry Stanford University School of Medicine |
From: Tim R. <ra...@eb...> - 2008-01-14 14:39:50
|
Hi, Thanks for putting this together, Don. I only have one small addition to suggest. When we discussed adding the "Term Accession Number" column to SDRF we neglected the IDF, and a couple of groups have asked me in the meantime whether we could rectify this. I'd therefore suggest the addition of these (optional!) IDF tags, one for each "* Term Source REF" tag: Experimental Design Term Accession Number Experimental Factor Term Accession Number Person Roles Term Accession Number Quality Control Term Accession Number Replicate Term Accession Number Normalization Term Accession Number Publication Status Term Accession Number Protocol Term Accession Number I think we probably omitted these tags because we didn't see any immediate need for them, but both the ISA-TAB and modENCODE projects are keen to fully annotate with OBI terms with accessions. Cheers, Tim On Thu, 20 Dec 2007, Don Maier wrote: > Hi all, > > To ease the chore of reading and comparing comments on MAGE-TAB v. 1.1, I've > incorporated into my original feedback document all other published comments > to date -- those of Michael, Junmin, Helen, and Alvis: > > > > Those people should check to make sure that I've transcribed their remarks > correctly and completely. If anyone else sends out comments, I'll > incorporate those in a final version of the document before we meet in > January. > > Have a great holiday! > > Regards, > Don M. > > > On Dec 7, 2007, at 11:36 AM, Don Maier wrote: > >> Hi all, >> >> Here is a set of problems and proposed solutions for MAGE-TAB that we at >> Stanford would like to discuss at the MAGE-TAB workshop in January: >> >> <MAGE-TAB Proposals.doc> >> >> We would greatly appreciate your contribution of creative energy to help >> with this! >> >> Regards, >> Don Maier >> Sr. Software Designer/Research >> Dept. of Biochemistry >> Stanford University School of Medicine >> >> >> On Nov 26, 2007, at 2:34 AM, Tim Rayner wrote: >> >>> Hi, >>> >>> My apologies if you receive this email more than once. At the last couple >>> of jamborees a set of requested changes to the MAGE-TAB specification >>> emerged, and the least contentious of these changes have been incorporated >>> into the ArrayExpress MAGE-TAB parser. We've also created a new draft >>> MAGE-TAB v1.1 specification, and the document is now available for >>> download here: >>> >>> http://www.ebi.ac.uk/systems-srv/mp/file-exchange/MAGE-TABv1.1.tar.gz >>> >>> Changes were made as discussed at the Stanford and Brisbane jamborees >>> (2007): >>> >>> * Added "Experimental Design Term Source REF" to IDF. >>> >>> * Added "Term Accession Number" to SDRF. >>> >>> * Added "Assay Name" and "Technology Type" to SDRF. >>> >>> * Added notes indicating that lines starting with the # character are >>> to be treated as ignorable comments. >>> >>> * Added free-text "Protocol REF" heading prefixes (e.g. "Growth >>> Protocol REF"). >>> >>> Note that in each case a document compliant with the v1.0 specification >>> remains compliant with this updated version. The following changes were >>> made to clarify the specification where it seemed necessary: >>> >>> * Sections were added providing notes on all the IDF and SDRF fields >>> and columns. >>> >>> * Table 7 (SDRF columns) was modified to remove the data file columns >>> as attributes of Hybridization, Scan and Normalization name, in an attempt >>> to disambiguate the grammar needed to parse SDRF column headings. >>> >>> * Added a note (section 3.3.7, point 8) regarding what to do with SDRF >>> attribute columns when applied to empty node or edge column values (i.e., >>> ignore the attributes in such cases). >>> >>> * Other minor clarifications were added to the text where necessary. >>> >>> Don Maier at Stanford has also proposed disambiguating the behaviour of >>> Comment[] columns by restricting their use such that they always >>> immediately follow the column to which they apply. This change has not yet >>> been included as it is likely to break compatibility with older documents; >>> I think that this proposal needs to be circulated more widely before >>> inclusion. >>> >>> We would appreciate your feedback on this new draft specification. >>> >>> Best regards, >>> >>> Tim >>> >>> >>> -- >>> Tim Rayner, Ph.D. >>> Scientific Database Curator >>> Microarray Informatics Team >>> European Bioinformatics Institute >>> >>> >>> ------------------------------------------------------------------------- >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Mged-mage mailing list >>> Mge...@li... >>> https://lists.sourceforge.net/lists/listinfo/mged-mage >> >> >> >> >> ------------------------------------------------------------------------- >> SF.Net email is sponsored by: >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://sourceforge.net/services/buy/index.php_______________________________________________ >> Mged-MAGE2 mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage2 > |
From: Tim R. <ra...@eb...> - 2007-11-30 10:56:09
|
Hi, So far we have not received any comments or suggestions regarding the proposed MAGE-TAB v1.1 specification document which I circulated on Monday. We would like to set Saturday Dec. 15 as a deadline for comments, after which time we will assume that the proposed changes are generally accepted. Best regards, Tim -- Tim Rayner ArrayExpress ---------- Forwarded message ---------- Date: Mon, 26 Nov 2007 10:34:40 +0000 (GMT) From: Tim Rayner <ra...@eb...> To: mge...@li..., mge...@li... Subject: Draft MAGE-TAB 1.1 specification Hi, My apologies if you receive this email more than once. At the last couple of jamborees a set of requested changes to the MAGE-TAB specification emerged, and the least contentious of these changes have been incorporated into the ArrayExpress MAGE-TAB parser. We've also created a new draft MAGE-TAB v1.1 specification, and the document is now available for download here: http://www.ebi.ac.uk/systems-srv/mp/file-exchange/MAGE-TABv1.1.tar.gz Changes were made as discussed at the Stanford and Brisbane jamborees (2007): * Added "Experimental Design Term Source REF" to IDF. * Added "Term Accession Number" to SDRF. * Added "Assay Name" and "Technology Type" to SDRF. * Added notes indicating that lines starting with the # character are to be treated as ignorable comments. * Added free-text "Protocol REF" heading prefixes (e.g. "Growth Protocol REF"). Note that in each case a document compliant with the v1.0 specification remains compliant with this updated version. The following changes were made to clarify the specification where it seemed necessary: * Sections were added providing notes on all the IDF and SDRF fields and columns. * Table 7 (SDRF columns) was modified to remove the data file columns as attributes of Hybridization, Scan and Normalization name, in an attempt to disambiguate the grammar needed to parse SDRF column headings. * Added a note (section 3.3.7, point 8) regarding what to do with SDRF attribute columns when applied to empty node or edge column values (i.e., ignore the attributes in such cases). * Other minor clarifications were added to the text where necessary. Don Maier at Stanford has also proposed disambiguating the behaviour of Comment[] columns by restricting their use such that they always immediately follow the column to which they apply. This change has not yet been included as it is likely to break compatibility with older documents; I think that this proposal needs to be circulated more widely before inclusion. We would appreciate your feedback on this new draft specification. Best regards, Tim -- Tim Rayner, Ph.D. Scientific Database Curator Microarray Informatics Team European Bioinformatics Institute |
From: Tim R. <ra...@eb...> - 2007-11-26 10:34:50
|
Hi, My apologies if you receive this email more than once. At the last couple of jamborees a set of requested changes to the MAGE-TAB specification emerged, and the least contentious of these changes have been incorporated into the ArrayExpress MAGE-TAB parser. We've also created a new draft MAGE-TAB v1.1 specification, and the document is now available for download here: http://www.ebi.ac.uk/systems-srv/mp/file-exchange/MAGE-TABv1.1.tar.gz Changes were made as discussed at the Stanford and Brisbane jamborees (2007): * Added "Experimental Design Term Source REF" to IDF. * Added "Term Accession Number" to SDRF. * Added "Assay Name" and "Technology Type" to SDRF. * Added notes indicating that lines starting with the # character are to be treated as ignorable comments. * Added free-text "Protocol REF" heading prefixes (e.g. "Growth Protocol REF"). Note that in each case a document compliant with the v1.0 specification remains compliant with this updated version. The following changes were made to clarify the specification where it seemed necessary: * Sections were added providing notes on all the IDF and SDRF fields and columns. * Table 7 (SDRF columns) was modified to remove the data file columns as attributes of Hybridization, Scan and Normalization name, in an attempt to disambiguate the grammar needed to parse SDRF column headings. * Added a note (section 3.3.7, point 8) regarding what to do with SDRF attribute columns when applied to empty node or edge column values (i.e., ignore the attributes in such cases). * Other minor clarifications were added to the text where necessary. Don Maier at Stanford has also proposed disambiguating the behaviour of Comment[] columns by restricting their use such that they always immediately follow the column to which they apply. This change has not yet been included as it is likely to break compatibility with older documents; I think that this proposal needs to be circulated more widely before inclusion. We would appreciate your feedback on this new draft specification. Best regards, Tim -- Tim Rayner, Ph.D. Scientific Database Curator Microarray Informatics Team European Bioinformatics Institute |
From: Ari K. <ar...@ma...> - 2007-08-27 03:38:30
|
I was thinking of something similar to that. I thought if a tab- delimited document could be turned into an XML document, then validating the form and value domains would simply be a matter of validating the XML against the XSD. I thought surely someone would have tackled the issue before. Check out this page http://www.infoloom.com/gcaconfs/WEB/philadelphia99/lyons.HTM It has a more general approach I think. Ari Kahn, PhD Contractor, SRA NCICB/DCC 703-930-9939 The Cancer Genome Atlas (TCGA) http://tcga-data.nci.nih.gov http://cancergenome.nih.gov On Aug 26, 2007, at 10:40 PM, mge...@li... wrote: > Date: Tue, 17 Apr 2007 11:29:17 -0700 > From: Gerald Fontenay <gv...@me...> > Subject: [Mged-mage] Simple idea wrt MAGE-TAB parsing/validation > To: MGED-mage <mge...@li...> > Message-ID: <462...@me...> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Hi everyone, > > I sent the following to the mage2 list but I actually don't see it in > the archive, so I'm sending it to this list as well. > Thanks. > > Cheers, > -g > > > ---- > > As I've mentioned, I'm parsing datasets in a format derived from > MAGE-TAB. The approach I'm using to encapsulating validation and > parsing > is dirt simple. I wanted to float this idea to this group to see what > others may think. It's really just a trivial way of encapsulating the > validation. > > There could be two modules, module1 and module2. > > The result of validation of an SDRF set of headers, e.g., by > module1 > is a trivial XML document that encapsulates, in the XML tree > structure, the implicit heirarchy structure of information in the > MAGE-TAB nodes or edges. Column numbers are listed as attributes in > the > elements. The heirarchy comes naturally from how production > methods in > the grammar get called. Column indexing is simple. This is useful > information and could be wrapped up nicely along with a list of > referenced files, e.g., and so on... > > A simple example is below. > > The XML may not look like much ( and terms are abbreviated), but basic > validation and parsing has occurred and a heirarchy was derived > according to the spec.. More validation ( e.g., terms ) could be > incorporated optionally into module1. > > Object graph and/or code generation gets offloaded to another module, > module2. Module2 would use the XML document in reading the actual > data in the file. Module2 could be in any language suitable to the > user. A module2 writer would provide for use of code tailored to > their > targeted application/data store. It seems much simpler to start > with a > set of possibly valid XML docs.. for this, at least to me. > > The problem I see with incorporating object graph generation in the > parsing/validation module is that the user may not want a particular > object graph and so some translational system would need to be set up > anyway. A module2 writer could use XSLT or xml parsing to generate > their particular objects or events accordingly, hopefully avoiding > efficiency issues and potentially tricky inter-language calls. > > Sorry if this idea has come up already on the list or meetings or > if in > fact, object generation was not planned to be incorporated into the > parser, but that was what I gathered. Perhaps specific object graph > generation is a desired requirement for the "community parser". If > those > are true, sorry you've had to read this far. > > > Cheers, > -g > > P.S. Also, if anyone is interested in my JavaCC grammar for "RPLA- > TAB" > data sets, I'd be more than glad to talk about it, perhaps offline. > > ------------------------ > > Source Name Comment Characteristics[AB-_ACAB] Term Source > REF Characteristics[ABACAB] Term Source REF Unit[CAB] Term > Source REF Sample Name Characteristics[ABACAB] Term Source > REF Characteristics[ABACAB] Term Source REF Unit[CAB] Term > Source REF Protocol REF Performer Parameter Value[ABB] > Unit[BB] Term Source REF Sample Name > > would generate: > > <SourceName col="1"> > <Comment col="2"/> > <BsChar col="3"><CT>AB-_ACAB</CT><Tsr col="4"/></BsChar> > <BsChar col="5"><CT>ABACAB</CT><Tsr col="6"/><Unit > col="7"><UnitTypeTerm>CAB</UnitTypeTerm><Tsr col="8"/> </Unit></ > BsChar> > </SourceName> > > <SampleName col="9"> > <BSampleChar col="10"> > <CT>ABACAB</CT> > <Tsr col="11"/> > </BSampleChar> > <BSampleChar col="12"> > <CT>ABACAB</CT> > <Tsr col="13"/> > <Unit col="14"> > <UnitTypeTerm>CAB</UnitTypeTerm> > <Tsr col="15"/> > </Unit> > </BSampleChar> > </SampleName> > > <Protocol col="16" type=""> > <Performer col="17"/> > <ParameterValue col="18"> > <ParameterValueTerm>ABB</ParameterValueTerm> > <Unit col="19"> > <UnitTypeTerm>BB</UnitTypeTerm> > <Tsr col="20"/> > </Unit></ParameterValue> > </Protocol> > <SampleName col="21"></SampleName> > |
From: Joe W. <jw...@ji...> - 2007-08-27 02:40:29
|
Hi Folks, So far I have 5 respondents for the mage jam. Although this workshop doesn't have a 'last call', we would like to get a reasonable head count for the people who are helping us set up network connections and space arrangements. If you are interested in participating in the mage jam, please send email to me by Tuesday. The proposed agenda for discussions is below: 1) roadmap for the stk (where are we going and how do we expect to get there) 2) with the work on MAGE-TAB at EBI, Stanford, Dana Farber, etc, is there a way to gather that as a resource available maintained one place 3) status and direction for development of MAGEv2 4) evaluation of incorporation of MO into MAGEstk (from Jason's work) 5) continue discussion on tools for MAGE-TAB/MAGEstk, e.g. that loads a MAGE-ML file and creates a (or maybe several) graphical view(s) of the data? I think Tim has the basis of something like this with Graphviz... Cheers, Joe White DFCI |
From: Junmin L. <ju...@pc...> - 2007-08-13 18:22:30
|
Hi,Joe I am in contact with Ugis regarding using the web service to share queries across different microarray sites. Currently our database RAD is starting to expose couple web queries as web services to beta cell biology consortium site (www.betacell.org). Thanks to latest j2ee technologies like xfire, jsr181, those things at least look easily for us. Also one kind of web service protocol I am particular interested in is the RESTFul type web service. Unfortunately I cann't attend the MGED10 meeting, but I am just tossing around the idea to the mailing list to see if it can generate some interest. Thanks, ---junmin On Fri, 10 Aug 2007, Joe White wrote: > Hi Everyone, > > If you are interested in attending the MAGE programming jam on Sept. 6-7 > during the MGED10 meeting, please contact me. We have several items on > a preliminary agenda; if you have other items that we should include, > please send them to me. > > Proposed Agenda: > > 1) roadmap for the stk (where are we going and how do we expect to get > there) > 2) with the work on MAGE-TAB at EBI, Stanford, Dana Farber, etc, is > there a way to gather that as a resource available maintained one place > 3) status and direction for development of MAGEv2 > 4) evaluation of incorporation of MO into MAGEstk (from Jason's work) > 5) continue discussion on tools for MAGE-TAB/MAGEstk, e.g. that loads a > MAGE-ML file and creates a (or maybe several) graphical view(s) of the > data? I think Tim has the basis of something like this with Graphviz... > > Cheers, > Joe White > DFCI > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Joe W. <jw...@ji...> - 2007-08-10 14:11:14
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Hi Everyone, If you are interested in attending the MAGE programming jam on Sept. 6-7 during the MGED10 meeting, please contact me. We have several items on a preliminary agenda; if you have other items that we should include, please send them to me. Proposed Agenda: 1) roadmap for the stk (where are we going and how do we expect to get there) 2) with the work on MAGE-TAB at EBI, Stanford, Dana Farber, etc, is there a way to gather that as a resource available maintained one place 3) status and direction for development of MAGEv2 4) evaluation of incorporation of MO into MAGEstk (from Jason's work) 5) continue discussion on tools for MAGE-TAB/MAGEstk, e.g. that loads a MAGE-ML file and creates a (or maybe several) graphical view(s) of the data? I think Tim has the basis of something like this with Graphviz... Cheers, Joe White DFCI |