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From: Jason S. <jas...@gm...> - 2006-08-22 11:54:48
|
Hey all, Sorry for the cross-posting. I am in the process of doing a number of things with the MAGEv1.0 for Perl and Java. First, the Perl MAGEstk has been overhauled and renewed - including full support for ENUM values in attributes (and yes that includes type checking). There is a verion that is ready to be tested - it would be great if people could help test it for me. Let me know if you'd like to run it thru your tests at your org, and I'll tell you where to grab the tarball. Second, I'm working on unifying the Ontology API's for both Java and Perl. The current Perl ontology tests all run with the new version of the Perl MAGEstk, but I need to finish adding the features - unfortunately, I don't have a good idea *how* this API is intended to be used. Kjell has given me some idea, but if others could help give me a clue how you would use it in your code, that would be much appreciated. So for example my current task is adding the path based search feature. I'm assuming people would be: 1) parsing an XML file into an in-mem data structure 2) finding a specific node of interest - say a BioSource 3) want to query the BioSource for the presence of some Ontology term... how would that look like in the code? Help me flesh out this use-case so I can design the API. Thanks again for your help, jas. |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-08-10 16:05:07
|
Hi All, Just a reminder to please register for the programming jamboree in Seattle, 9/10-12, if you plan to attend. A link is provided on the MGED9 web-site. A more complete agenda will be posted early next week but likely areas of work will be MAGEv2, MAGE-TAB and further work on the MAGEstk (likely on ontology support and general robustness) When registering, please include your areas of expertise and the areas you would like to work on. cheers, Michael Michael Miller Lead Software Developer Rosetta Biosoftware Business Unit www.rosettabio.com |
From: Stephen H. <s.h...@uc...> - 2006-08-03 07:44:02
|
Thursday is good for me. ________________________________ From: mge...@li... on behalf of mged-mage-reques= t...@li... Sent: Wed 02/08/2006 20:13 To: mge...@li... Subject: Mged-mage Digest, Vol 3, Issue 1 Send Mged-mage mailing list submissions to mge...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/mged-mage 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-mage digest..." Today's Topics: 1. mage v2 model (Junmin Liu) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Aug 2006 12:06:01 -0400 (EDT) From: Junmin Liu <ju...@pc...> Subject: [Mged-mage] mage v2 model To: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com> Cc: mged-mage2 <mge...@li...>, mge...@li... Message-ID: <Pin...@he...> Content-Type: TEXT/PLAIN; charset=3DUS-ASCII; format=3Dflowed Hi, Michael and others, I am going to take the latest mage v2 model from helen dated on 7/13/06 to modify it. As you know, there are couple validation error output from AndroMDA, I need to fix them. Also when I open up the model in MagicDraw, Besides MAGE package, there is a separate "Relations" item on the menu, it contains a dozen of associations which should belong to MAGE package under it, not directly under the root. I think their ownerships are just wrong. I will change them also. cheers, ---junmin ------------------------------ ------------------------------------------------------------------------- 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=3Djoin.php&p=3Dsourceforge&CID=3DDE= VDEV ------------------------------ _______________________________________________ Mged-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage End of Mged-mage Digest, Vol 3, Issue 1 *************************************** ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (it....@wi...). All files are scanned for v= iruses. ********************************************************************** |
From: Junmin L. <ju...@pc...> - 2006-08-02 16:06:08
|
Hi, Michael and others, I am going to take the latest mage v2 model from helen dated on 7/13/06 to modify it. As you know, there are couple validation error output from AndroMDA, I need to fix them. Also when I open up the model in MagicDraw, Besides MAGE package, there is a separate "Relations" item on the menu, it contains a dozen of associations which should belong to MAGE package under it, not directly under the root. I think their ownerships are just wrong. I will change them also. cheers, ---junmin |
From: Junmin L. <ju...@pc...> - 2006-07-28 20:19:48
|
I will try to make it. ---junmin On Mon, 24 Jul 2006, Helen Parkinson wrote: > Michael, > > that works for me, Ugis is probably away though, anyone else? > > cheers > > Helen > > Miller, Michael D (Rosetta) wrote: >> Hi All, >> >> This was what I was hoping to put out as part of an agenda early next >> month--in fact I would love if there were a teleconference around August >> 21st to do a presorting out of issues for MAGEv2. I'm off for vacation >> next week and a half but when I return I'll start gathering other >> potential agenda items for MAGEstk and MAGE-TAB and any other items >> people are interested in. >> >> cheers, >> Michael >> >> >>> -----Original Message----- >>> From: mge...@li... >>> [mailto:mge...@li...] On Behalf >>> Of Helen Parkinson >>> Sent: Monday, July 24, 2006 12:59 AM >>> To: Ugis Sarkans >>> Cc: mged-mage2 >>> Subject: Re: [Mged-mage2] Meeting Report for MAGEModelling Meeting >>> >>> >>> Hi all, >>> >>> can we use these and Michael's comments on Array etc as an agenda for >>> the next meeting - I assume this will be at the MGED Jamboree >>> in Seattle? >>> >>> cheers >>> >>> Helen >>> >>> Ugis Sarkans wrote: >>> >>>> Hi all, >>>> >>>> Following up on what I promised to do in the meeting: >>>> >>>> 1) A cleaned-up version of the model has been posted on >>>> http://www.mged.org/Workgroups/MAGE/magev2.html >>>> >>>> a) Associations from ArrayManufacture, Hybridization, >>>> >>> ImageAcquisition >>> >>>> and MeasuredDataExtraction to >>>> GenericProtocol have been added, derived from >>>> ProtocolApplication->Protocol. Data Transformation already >>>> had that, and I didn't touch HLA. >>>> >>>> b) general cleanup of diagrams in Array and Data packages - >>>> >>> again didn't >>> >>>> touch HLA. QPCR is not finished. >>>> >>>> c) Michael enquired about some unnamed assoications in the >>>> >>> Array diagram >>> >>>> - I think this is not quite finished >>>> either, especially in the light of changes to >>>> >>> DesignElements. I still >>> >>>> think that a concept of MaterialReporter would >>>> make sense, and ArrayFeatureMaterial should go. >>>> >>>> d) Some small issues I found: >>>> - ArrayImage - needs format, since it derives directly >>>> >>> from Data, >>> >>>> not ExternalData >>>> - If we want to support post-ImageAcquisition manipulations of >>>> HybridizedArray (e.g. another >>>> ImageAcquisition) like in MAGEv1, then ImageAcquisition should have >>>> outputMaterial HybridizedArray, not >>>> just outputData. >>>> >>>> 2) Mapping v1 to v2. >>>> >>>> I'm trying to describe mapping as a series of diagrams that >>>> >>> show how >>> >>>> various structures of MAGEv1 (objects+links+ >>>> attribute values) should be translated into MAGEv2 structures. 6 >>>> diagrams are in >>>> >>>> http://www.ebi.ac.uk/~ugis/MAGEmapping/ >>>> >>>> This is not finished, I haven't >>>> done any explaining text, but I hope that this way the >>>> >>> explanation might >>> >>>> be easier than when there are only bits >>>> of object models to look at. Feedback welcome on both the >>>> >>> approach and >>> >>>> details of the mapping - there are some >>>> hard bits when dealing with BioAssays. I'll not be able to >>>> >>> do anything >>> >>>> else with this now till September though. >>>> >>>> Cheers, >>>> Ugis >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Helen Parkinson wrote: >>>> >>>> >>>> >>>>> Hi >>>>> >>>>> a draft version of the meeting report with action items >>>>> >>> and comments >>> >>>>> >>>>> >>>>> from Ugis and Andy Jones has now been posted: >>>> >>>> >>>>> www.ebi.ac.uk/~parkinso/MAGE2_modelling_Meeting_Report2_aj.doc >>>>> >>>>> MAGE2_modelling_Meeting_Report2_aj.doc >>>>> >>> <http://www.ebi.ac.uk/%7Eparkinso/MAGE2_modelling_Meeting_Repo >>> rt2_aj.doc> >>> >>>>> >>>>> Final version UML model edited by Ugis is also posted: >>>>> >>>>> www.ebi.ac.uk/~parkinso/MAGEv2_uml20_2006_07_13.zip >>>>> >>>>> MAGEv2_uml20_2006_07_13.zip >>>>> >>> <http://www.ebi.ac.uk/%7Eparkinso/MAGEv2_uml20_2006_07_13.zip> >>> >>>>> >>>>> cheers >>>>> >>>>> Helen >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> -------------------------------------------------------------- >>> ----------- >>> >>>> 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 >> >>> _______________________________________________ >>> Mged-MAGE2 mailing list >>> Mge...@li... >>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>> >>> >> >> > > -- > Helen Parkinson, PhD > Curation Coordinator > Microarray Informatics Team, > EBI > > and > > Seconded Scientific Programme Manager > NCRI Cancer Informatics Initiative > www.cancerinformatics.org.uk > > Tel: > EBI 01223 494672 > Skype: helen.parkinson.ebi > > > ------------------------------------------------------------------------- > 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 > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > |
From: Joe W. <jw...@ji...> - 2006-07-25 08:28:52
|
Hi, August 21st is ok for me. Joe Helen Parkinson wrote: >Michael, > >that works for me, Ugis is probably away though, anyone else? > >cheers > >Helen > >Miller, Michael D (Rosetta) wrote: > > >>Hi All, >> >>This was what I was hoping to put out as part of an agenda early next >>month--in fact I would love if there were a teleconference around August >>21st to do a presorting out of issues for MAGEv2. I'm off for vacation >>next week and a half but when I return I'll start gathering other >>potential agenda items for MAGEstk and MAGE-TAB and any other items >>people are interested in. >> >>cheers, >>Michael >> >> >> >> >>>-----Original Message----- >>>From: mge...@li... >>>[mailto:mge...@li...] On Behalf >>>Of Helen Parkinson >>>Sent: Monday, July 24, 2006 12:59 AM >>>To: Ugis Sarkans >>>Cc: mged-mage2 >>>Subject: Re: [Mged-mage2] Meeting Report for MAGEModelling Meeting >>> >>> >>>Hi all, >>> >>>can we use these and Michael's comments on Array etc as an agenda for >>>the next meeting - I assume this will be at the MGED Jamboree >>>in Seattle? >>> >>>cheers >>> >>>Helen >>> >>>Ugis Sarkans wrote: >>> >>> >>> >>>>Hi all, >>>> >>>>Following up on what I promised to do in the meeting: >>>> >>>>1) A cleaned-up version of the model has been posted on >>>>http://www.mged.org/Workgroups/MAGE/magev2.html >>>> >>>>a) Associations from ArrayManufacture, Hybridization, >>>> >>>> >>>> >>>ImageAcquisition >>> >>> >>> >>>>and MeasuredDataExtraction to >>>>GenericProtocol have been added, derived from >>>>ProtocolApplication->Protocol. Data Transformation already >>>>had that, and I didn't touch HLA. >>>> >>>>b) general cleanup of diagrams in Array and Data packages - >>>> >>>> >>>> >>>again didn't >>> >>> >>> >>>>touch HLA. QPCR is not finished. >>>> >>>>c) Michael enquired about some unnamed assoications in the >>>> >>>> >>>> >>>Array diagram >>> >>> >>> >>>>- I think this is not quite finished >>>>either, especially in the light of changes to >>>> >>>> >>>> >>>DesignElements. I still >>> >>> >>> >>>>think that a concept of MaterialReporter would >>>>make sense, and ArrayFeatureMaterial should go. >>>> >>>>d) Some small issues I found: >>>> - ArrayImage - needs format, since it derives directly >>>> >>>> >>>> >>>from Data, >>> >>> >>> >>>>not ExternalData >>>> - If we want to support post-ImageAcquisition manipulations of >>>>HybridizedArray (e.g. another >>>>ImageAcquisition) like in MAGEv1, then ImageAcquisition should have >>>>outputMaterial HybridizedArray, not >>>>just outputData. >>>> >>>>2) Mapping v1 to v2. >>>> >>>>I'm trying to describe mapping as a series of diagrams that >>>> >>>> >>>> >>>show how >>> >>> >>> >>>>various structures of MAGEv1 (objects+links+ >>>>attribute values) should be translated into MAGEv2 structures. 6 >>>>diagrams are in >>>> >>>>http://www.ebi.ac.uk/~ugis/MAGEmapping/ >>>> >>>>This is not finished, I haven't >>>>done any explaining text, but I hope that this way the >>>> >>>> >>>> >>>explanation might >>> >>> >>> >>>>be easier than when there are only bits >>>>of object models to look at. Feedback welcome on both the >>>> >>>> >>>> >>>approach and >>> >>> >>> >>>>details of the mapping - there are some >>>>hard bits when dealing with BioAssays. I'll not be able to >>>> >>>> >>>> >>>do anything >>> >>> >>> >>>>else with this now till September though. >>>> >>>>Cheers, >>>>Ugis >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>Helen Parkinson wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Hi >>>>> >>>>>a draft version of the meeting report with action items >>>>> >>>>> >>>>> >>>and comments >>> >>> >>> >>>>> >>>>> >>>>> >>>>> >>>>>from Ugis and Andy Jones has now been posted: >>>> >>>> >>>> >>>> >>>>>www.ebi.ac.uk/~parkinso/MAGE2_modelling_Meeting_Report2_aj.doc >>>>> >>>>>MAGE2_modelling_Meeting_Report2_aj.doc >>>>> >>>>> >>>>> >>><http://www.ebi.ac.uk/%7Eparkinso/MAGE2_modelling_Meeting_Repo >>>rt2_aj.doc> >>> >>> >>> >>>>>Final version UML model edited by Ugis is also posted: >>>>> >>>>>www.ebi.ac.uk/~parkinso/MAGEv2_uml20_2006_07_13.zip >>>>> >>>>>MAGEv2_uml20_2006_07_13.zip >>>>> >>>>> >>>>> >>><http://www.ebi.ac.uk/%7Eparkinso/MAGEv2_uml20_2006_07_13.zip> >>> >>> >>> >>>>>cheers >>>>> >>>>>Helen >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>-------------------------------------------------------------- >>>----------- >>> >>> >>> >>>>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 >> >> >> >>>_______________________________________________ >>>Mged-MAGE2 mailing list >>>Mge...@li... >>>https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>> >>> >>> >>> >> >> >> > > > |
From: <ro...@eb...> - 2006-07-24 15:49:25
|
Hi Michael, I should be able to join in Thanks Philippe > Michael, > > that works for me, Ugis is probably away though, anyone else? > > cheers > > Helen > > Miller, Michael D (Rosetta) wrote: >> Hi All, >> >> This was what I was hoping to put out as part of an agenda early next >> month--in fact I would love if there were a teleconference around August >> 21st to do a presorting out of issues for MAGEv2. I'm off for vacation >> next week and a half but when I return I'll start gathering other >> potential agenda items for MAGEstk and MAGE-TAB and any other items >> people are interested in. >> >> cheers, >> Michael >> >> >>> -----Original Message----- >>> From: mge...@li... >>> [mailto:mge...@li...] On Behalf >>> Of Helen Parkinson >>> Sent: Monday, July 24, 2006 12:59 AM >>> To: Ugis Sarkans >>> Cc: mged-mage2 >>> Subject: Re: [Mged-mage2] Meeting Report for MAGEModelling Meeting >>> >>> >>> Hi all, >>> >>> can we use these and Michael's comments on Array etc as an agenda for >>> the next meeting - I assume this will be at the MGED Jamboree >>> in Seattle? >>> >>> cheers >>> >>> Helen >>> >>> Ugis Sarkans wrote: >>> >>>> Hi all, >>>> >>>> Following up on what I promised to do in the meeting: >>>> >>>> 1) A cleaned-up version of the model has been posted on >>>> http://www.mged.org/Workgroups/MAGE/magev2.html >>>> >>>> a) Associations from ArrayManufacture, Hybridization, >>>> >>> ImageAcquisition >>> >>>> and MeasuredDataExtraction to >>>> GenericProtocol have been added, derived from >>>> ProtocolApplication->Protocol. Data Transformation already >>>> had that, and I didn't touch HLA. >>>> >>>> b) general cleanup of diagrams in Array and Data packages - >>>> >>> again didn't >>> >>>> touch HLA. QPCR is not finished. >>>> >>>> c) Michael enquired about some unnamed assoications in the >>>> >>> Array diagram >>> >>>> - I think this is not quite finished >>>> either, especially in the light of changes to >>>> >>> DesignElements. I still >>> >>>> think that a concept of MaterialReporter would >>>> make sense, and ArrayFeatureMaterial should go. >>>> >>>> d) Some small issues I found: >>>> - ArrayImage - needs format, since it derives directly >>>> >>> from Data, >>> >>>> not ExternalData >>>> - If we want to support post-ImageAcquisition manipulations of >>>> HybridizedArray (e.g. another >>>> ImageAcquisition) like in MAGEv1, then ImageAcquisition should have >>>> outputMaterial HybridizedArray, not >>>> just outputData. >>>> >>>> 2) Mapping v1 to v2. >>>> >>>> I'm trying to describe mapping as a series of diagrams that >>>> >>> show how >>> >>>> various structures of MAGEv1 (objects+links+ >>>> attribute values) should be translated into MAGEv2 structures. 6 >>>> diagrams are in >>>> >>>> http://www.ebi.ac.uk/~ugis/MAGEmapping/ >>>> >>>> This is not finished, I haven't >>>> done any explaining text, but I hope that this way the >>>> >>> explanation might >>> >>>> be easier than when there are only bits >>>> of object models to look at. Feedback welcome on both the >>>> >>> approach and >>> >>>> details of the mapping - there are some >>>> hard bits when dealing with BioAssays. I'll not be able to >>>> >>> do anything >>> >>>> else with this now till September though. >>>> >>>> Cheers, >>>> Ugis >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Helen Parkinson wrote: >>>> >>>> >>>> >>>>> Hi >>>>> >>>>> a draft version of the meeting report with action items >>>>> >>> and comments >>> >>>>> >>>>> >>>> >from Ugis and Andy Jones has now been posted: >>>> >>>> >>>>> www.ebi.ac.uk/~parkinso/MAGE2_modelling_Meeting_Report2_aj.doc >>>>> >>>>> MAGE2_modelling_Meeting_Report2_aj.doc >>>>> >>> <http://www.ebi.ac.uk/%7Eparkinso/MAGE2_modelling_Meeting_Repo >>> rt2_aj.doc> >>> >>>>> >>>>> Final version UML model edited by Ugis is also posted: >>>>> >>>>> www.ebi.ac.uk/~parkinso/MAGEv2_uml20_2006_07_13.zip >>>>> >>>>> MAGEv2_uml20_2006_07_13.zip >>>>> >>> <http://www.ebi.ac.uk/%7Eparkinso/MAGEv2_uml20_2006_07_13.zip> >>> >>>>> >>>>> cheers >>>>> >>>>> Helen >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> -------------------------------------------------------------- >>> ----------- >>> >>>> 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 >> >>> _______________________________________________ >>> Mged-MAGE2 mailing list >>> Mge...@li... >>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >>> >>> >> >> > > -- > Helen Parkinson, PhD > Curation Coordinator > Microarray Informatics Team, > EBI > > and > > Seconded Scientific Programme Manager > NCRI Cancer Informatics Initiative > www.cancerinformatics.org.uk > > Tel: > EBI 01223 494672 > Skype: helen.parkinson.ebi > > > ------------------------------------------------------------------------- > 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 > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Helen P. <par...@eb...> - 2006-07-24 15:24:19
|
Michael, that works for me, Ugis is probably away though, anyone else? cheers Helen Miller, Michael D (Rosetta) wrote: > Hi All, > > This was what I was hoping to put out as part of an agenda early next > month--in fact I would love if there were a teleconference around August > 21st to do a presorting out of issues for MAGEv2. I'm off for vacation > next week and a half but when I return I'll start gathering other > potential agenda items for MAGEstk and MAGE-TAB and any other items > people are interested in. > > cheers, > Michael > > >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] On Behalf >> Of Helen Parkinson >> Sent: Monday, July 24, 2006 12:59 AM >> To: Ugis Sarkans >> Cc: mged-mage2 >> Subject: Re: [Mged-mage2] Meeting Report for MAGEModelling Meeting >> >> >> Hi all, >> >> can we use these and Michael's comments on Array etc as an agenda for >> the next meeting - I assume this will be at the MGED Jamboree >> in Seattle? >> >> cheers >> >> Helen >> >> Ugis Sarkans wrote: >> >>> Hi all, >>> >>> Following up on what I promised to do in the meeting: >>> >>> 1) A cleaned-up version of the model has been posted on >>> http://www.mged.org/Workgroups/MAGE/magev2.html >>> >>> a) Associations from ArrayManufacture, Hybridization, >>> >> ImageAcquisition >> >>> and MeasuredDataExtraction to >>> GenericProtocol have been added, derived from >>> ProtocolApplication->Protocol. Data Transformation already >>> had that, and I didn't touch HLA. >>> >>> b) general cleanup of diagrams in Array and Data packages - >>> >> again didn't >> >>> touch HLA. QPCR is not finished. >>> >>> c) Michael enquired about some unnamed assoications in the >>> >> Array diagram >> >>> - I think this is not quite finished >>> either, especially in the light of changes to >>> >> DesignElements. I still >> >>> think that a concept of MaterialReporter would >>> make sense, and ArrayFeatureMaterial should go. >>> >>> d) Some small issues I found: >>> - ArrayImage - needs format, since it derives directly >>> >> from Data, >> >>> not ExternalData >>> - If we want to support post-ImageAcquisition manipulations of >>> HybridizedArray (e.g. another >>> ImageAcquisition) like in MAGEv1, then ImageAcquisition should have >>> outputMaterial HybridizedArray, not >>> just outputData. >>> >>> 2) Mapping v1 to v2. >>> >>> I'm trying to describe mapping as a series of diagrams that >>> >> show how >> >>> various structures of MAGEv1 (objects+links+ >>> attribute values) should be translated into MAGEv2 structures. 6 >>> diagrams are in >>> >>> http://www.ebi.ac.uk/~ugis/MAGEmapping/ >>> >>> This is not finished, I haven't >>> done any explaining text, but I hope that this way the >>> >> explanation might >> >>> be easier than when there are only bits >>> of object models to look at. Feedback welcome on both the >>> >> approach and >> >>> details of the mapping - there are some >>> hard bits when dealing with BioAssays. I'll not be able to >>> >> do anything >> >>> else with this now till September though. >>> >>> Cheers, >>> Ugis >>> >>> >>> >>> >>> >>> >>> >>> Helen Parkinson wrote: >>> >>> >>> >>>> Hi >>>> >>>> a draft version of the meeting report with action items >>>> >> and comments >> >>>> >>>> >>> >from Ugis and Andy Jones has now been posted: >>> >>> >>>> www.ebi.ac.uk/~parkinso/MAGE2_modelling_Meeting_Report2_aj.doc >>>> >>>> MAGE2_modelling_Meeting_Report2_aj.doc >>>> >> <http://www.ebi.ac.uk/%7Eparkinso/MAGE2_modelling_Meeting_Repo >> rt2_aj.doc> >> >>>> >>>> Final version UML model edited by Ugis is also posted: >>>> >>>> www.ebi.ac.uk/~parkinso/MAGEv2_uml20_2006_07_13.zip >>>> >>>> MAGEv2_uml20_2006_07_13.zip >>>> >> <http://www.ebi.ac.uk/%7Eparkinso/MAGEv2_uml20_2006_07_13.zip> >> >>>> >>>> cheers >>>> >>>> Helen >>>> >>>> >>>> >>>> >>>> >>> >>> >> -------------------------------------------------------------- >> ----------- >> >>> 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 > >> _______________________________________________ >> Mged-MAGE2 mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >> >> > > -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team, EBI and Seconded Scientific Programme Manager NCRI Cancer Informatics Initiative www.cancerinformatics.org.uk Tel: EBI 01223 494672 Skype: helen.parkinson.ebi |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-07-24 15:20:25
|
Hi All, This was what I was hoping to put out as part of an agenda early next month--in fact I would love if there were a teleconference around August 21st to do a presorting out of issues for MAGEv2. I'm off for vacation next week and a half but when I return I'll start gathering other potential agenda items for MAGEstk and MAGE-TAB and any other items people are interested in. cheers, Michael > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf=20 > Of Helen Parkinson > Sent: Monday, July 24, 2006 12:59 AM > To: Ugis Sarkans > Cc: mged-mage2 > Subject: Re: [Mged-mage2] Meeting Report for MAGEModelling Meeting >=20 >=20 > Hi all, >=20 > can we use these and Michael's comments on Array etc as an agenda for=20 > the next meeting - I assume this will be at the MGED Jamboree=20 > in Seattle? >=20 > cheers >=20 > Helen >=20 > Ugis Sarkans wrote: > > Hi all, > > > > Following up on what I promised to do in the meeting: > > > > 1) A cleaned-up version of the model has been posted on=20 > > http://www.mged.org/Workgroups/MAGE/magev2.html > > > > a) Associations from ArrayManufacture, Hybridization,=20 > ImageAcquisition=20 > > and MeasuredDataExtraction to > > GenericProtocol have been added, derived from=20 > > ProtocolApplication->Protocol. Data Transformation already > > had that, and I didn't touch HLA. > > > > b) general cleanup of diagrams in Array and Data packages -=20 > again didn't=20 > > touch HLA. QPCR is not finished. > > > > c) Michael enquired about some unnamed assoications in the=20 > Array diagram=20 > > - I think this is not quite finished > > either, especially in the light of changes to=20 > DesignElements. I still=20 > > think that a concept of MaterialReporter would > > make sense, and ArrayFeatureMaterial should go. > > > > d) Some small issues I found: > > - ArrayImage - needs format, since it derives directly=20 > from Data,=20 > > not ExternalData > > - If we want to support post-ImageAcquisition manipulations of=20 > > HybridizedArray (e.g. another > > ImageAcquisition) like in MAGEv1, then ImageAcquisition should have=20 > > outputMaterial HybridizedArray, not > > just outputData. > > > > 2) Mapping v1 to v2. > > > > I'm trying to describe mapping as a series of diagrams that=20 > show how=20 > > various structures of MAGEv1 (objects+links+ > > attribute values) should be translated into MAGEv2 structures. 6=20 > > diagrams are in > > > > http://www.ebi.ac.uk/~ugis/MAGEmapping/ > > > > This is not finished, I haven't > > done any explaining text, but I hope that this way the=20 > explanation might=20 > > be easier than when there are only bits > > of object models to look at. Feedback welcome on both the=20 > approach and=20 > > details of the mapping - there are some > > hard bits when dealing with BioAssays. I'll not be able to=20 > do anything=20 > > else with this now till September though. > > > > Cheers, > > Ugis > > > > > > > > > > > > > > > > Helen Parkinson wrote: > > > > =20 > >> Hi > >> > >> a draft version of the meeting report with action items=20 > and comments=20 > >> =20 > > >from Ugis and Andy Jones has now been posted: > > =20 > >> www.ebi.ac.uk/~parkinso/MAGE2_modelling_Meeting_Report2_aj.doc > >> > >> MAGE2_modelling_Meeting_Report2_aj.doc=20 > <http://www.ebi.ac.uk/%7Eparkinso/MAGE2_modelling_Meeting_Repo > rt2_aj.doc>=20 > >> > >> > >> > >> Final version UML model edited by Ugis is also posted: > >> > >> www.ebi.ac.uk/~parkinso/MAGEv2_uml20_2006_07_13.zip > >> > >> MAGEv2_uml20_2006_07_13.zip=20 > <http://www.ebi.ac.uk/%7Eparkinso/MAGEv2_uml20_2006_07_13.zip>=20 > >> > >> > >> > >> cheers > >> > >> Helen > >> > >> =20 > >> > >> =20 > > > > > >=20 > -------------------------------------------------------------- > ----------- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the=20 > chance to share your > > opinions on IT & business topics through brief surveys --=20 > and earn cash > >=20 > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge &CID=3DDEVDEV > _______________________________________________ > Mged-MAGE2 mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage2 > =20 --=20 Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team,=20 EBI and Seconded Scientific Programme Manager NCRI Cancer Informatics Initiative www.cancerinformatics.org.uk Tel: EBI 01223 494672 Skype: helen.parkinson.ebi ------------------------------------------------------------------------ - 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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V _______________________________________________ Mged-MAGE2 mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage2 |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-07-14 18:49:06
|
Hi Valerie, > we discourage use of tuples the files are huge and v. slow=20 > when loading=20 > - we have never successfully loaded data of this typ. Most=20 > data is coded=20 > as data external - we prefer this as it's easier to detect a problem=20 > data file e.g. with a simple wc when we have a problem. tuples were part of Rosetta's original format and, although in our experience they weren't tremendously slower than either the external or internal data, they were about 3 times slower so we have moved to either data internal for single MeasuredBioAssays being loaded from feature extraction or data external when there are multiple datacubes. Since many of our customers have data pipelines, we've found when there is only one MeasuredBioAssay to deal with, it is better to have everything in one file. Our java class for implementation of MAGE for handling the data cube is simply given a data stream. This is either fed from the characters in the file or from the external file, so there is virtually no difference to our code between data internal or data external. We also came up with a nifty way of handling the order of dimensions in the datacube so that the method that parses it has an array that specifies the order so that the linear offset in the stream is translated to the correct coordinates. As for other sources of MAGE, take a look at NCI's caBIG and caARRAY. cheers, Michael Michael Miller Lead Software Developer Rosetta Biosoftware Business Unit www.rosettabio.com > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf Of=20 > Helen Parkinson > Sent: Tuesday, July 11, 2006 12:53 AM > To: Valerie Wagner > Cc: mge...@li... > Subject: Re: [Mged-mage] Comprehending the BioDataCube >=20 >=20 > Valerie >=20 > we discourage use of tuples the files are huge and v. slow=20 > when loading=20 > - we have never successfully loaded data of this typ. Most=20 > data is coded=20 > as data external - we prefer this as it's easier to detect a problem=20 > data file e.g. with a simple wc when we have a problem. >=20 >=20 > The tab delimited files 3 dimensions are represented by the=20 > QuantitationType (QTD), DesignElement (DED) and BioAssayDimensions=20 > (BAD), these are expressed in the MAGE-ML and provided the dimensions=20 > needed to understand these tab delimited files. >=20 > The QTD which typically governs the no of columns is made of QTs that=20 > are determined by the sw that generated the matrix. All the=20 > raw data QT=20 > that we are aware of from common sw types are detailed on this=20 > spreadsheet and these are the recommended best practice=20 > coding for these=20 > SW types. >=20 >=20 > http://www.ebi.ac.uk/~ele/ext/submitter.html#qt >=20 > There is also some other information there that may be useful on the=20 > data cube. Note also that early cel files were transformed to tab=20 > delimited or space delimited data. We no longer do this, and use the=20 > native format cel files instead, though the dimensions=20 > described above=20 > are still provided. This allows us to check that the cel file=20 > supplied=20 > is corresponds to what was intended. >=20 > Please ask if we can provide more information. >=20 > best regards >=20 > Helen >=20 > Valerie Wagner wrote: > > Folks, can anyone help me understand the meaning of the data in=20 > > BioDataValues? > > > > What I understand: > > > > * BioDataCube is a 3-dimensional representation of the BDQ=20 > data, where=20 > > BDQ =3D BioAssays, DesignElements, QuantiationTypes. =20 > However, that's not=20 > > a very specific explanation of what the data mean. > > > > * MAGE-ML differs from the MAGE OM in how it represents=20 > this data, using=20 > > instead DataInternal and DataExternal. > > > > What I don't understand: > > > > * Is the format of the external data files subject to a=20 > MAGE standard?=20 > > All the examples I've seen so far are "tab delimited", but=20 > it doesn't=20 > > look to me like the data files all have the same format (differing=20 > > number of columns, some have all numeric data, some mixed=20 > data, etc.).=20 > > How does one tell what one is looking at? > > > > * Similarly, all the examples I've found so far use the=20 > external data=20 > > method. Does anyone have an example of anything using=20 > BioDataTuples=20 > > instead of the cube or using DataInternal instead of external? > > > > Thanks again! > > Valerie > > > > > > > >=20 > -------------------------------------------------------------- > ----------- > > Using Tomcat but need to do more? Need to support web=20 > services, security? > > Get stuff done quickly with pre-integrated technology to=20 > make your job easier > > Download IBM WebSphere Application Server v.1.0.1 based on=20 > Apache Geronimo > >=20 > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057& dat=3D121642 > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > =20 --=20 Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team,=20 EBI and Seconded Scientific Programme Manager NCRI Cancer Informatics Initiative www.cancerinformatics.org.uk Tel: EBI 01223 494672 Skype: helen.parkinson.ebi ------------------------------------------------------------------------ - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 _______________________________________________ Mged-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Ele H. <el...@eb...> - 2006-07-11 08:05:06
|
On Tue, 11 Jul 2006, Arto Viitanen wrote: > mge...@li... wrote: > > > > Can anyone recommend other sources of MAGE-ML data files other than > > ArrayExpress and the examples on the MGEDpage? We'd like to test our > > MAGE loader with a wide variety of input data. > > > > > MAGE Good Practice (http://www.ebi.ac.uk/~ele/ext/submitter.html#mgp) > has some example XML files. I would discourage using these files as MAGE-ML files for loading. These are purely there as examples, they are not real life data. Cheers, Ele ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ele Holloway Scientific Database Curator Microarray Informatics European Bioinformatics Institute ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I guess Affymetrix has also some array designs > in MAGE-ML format. Tab2Mage (http://tab2mage.sourceforge.net/) also has > some example files. They are actually in tab format, but the program > converts > them to XML. Since the tab format is easier, the program might help you make > your own XML files easier. > > -- > Arto Viitanen, CSC Ltd. > Espoo, Finland > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Helen P. <par...@eb...> - 2006-07-11 07:53:26
|
Valerie we discourage use of tuples the files are huge and v. slow when loading - we have never successfully loaded data of this typ. Most data is coded as data external - we prefer this as it's easier to detect a problem data file e.g. with a simple wc when we have a problem. The tab delimited files 3 dimensions are represented by the QuantitationType (QTD), DesignElement (DED) and BioAssayDimensions (BAD), these are expressed in the MAGE-ML and provided the dimensions needed to understand these tab delimited files. The QTD which typically governs the no of columns is made of QTs that are determined by the sw that generated the matrix. All the raw data QT that we are aware of from common sw types are detailed on this spreadsheet and these are the recommended best practice coding for these SW types. http://www.ebi.ac.uk/~ele/ext/submitter.html#qt There is also some other information there that may be useful on the data cube. Note also that early cel files were transformed to tab delimited or space delimited data. We no longer do this, and use the native format cel files instead, though the dimensions described above are still provided. This allows us to check that the cel file supplied is corresponds to what was intended. Please ask if we can provide more information. best regards Helen Valerie Wagner wrote: > Folks, can anyone help me understand the meaning of the data in > BioDataValues? > > What I understand: > > * BioDataCube is a 3-dimensional representation of the BDQ data, where > BDQ = BioAssays, DesignElements, QuantiationTypes. However, that's not > a very specific explanation of what the data mean. > > * MAGE-ML differs from the MAGE OM in how it represents this data, using > instead DataInternal and DataExternal. > > What I don't understand: > > * Is the format of the external data files subject to a MAGE standard? > All the examples I've seen so far are "tab delimited", but it doesn't > look to me like the data files all have the same format (differing > number of columns, some have all numeric data, some mixed data, etc.). > How does one tell what one is looking at? > > * Similarly, all the examples I've found so far use the external data > method. Does anyone have an example of anything using BioDataTuples > instead of the cube or using DataInternal instead of external? > > Thanks again! > Valerie > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team, EBI and Seconded Scientific Programme Manager NCRI Cancer Informatics Initiative www.cancerinformatics.org.uk Tel: EBI 01223 494672 Skype: helen.parkinson.ebi |
From: Helen P. <par...@eb...> - 2006-07-11 07:45:40
|
Arto our files reflect external submissions as well as MAGE-ML generated from our own toola. Try Experiments E-SMDB- prefix from SMD, E-TIGR- prefix from TIGR, and E-BAIR - from an external AE installation. These are a representative set, cheers Helen Arto Viitanen wrote: > mge...@li... wrote: > >> Can anyone recommend other sources of MAGE-ML data files other than >> ArrayExpress and the examples on the MGEDpage? We'd like to test our >> MAGE loader with a wide variety of input data. >> >> >> > MAGE Good Practice (http://www.ebi.ac.uk/~ele/ext/submitter.html#mgp) > has some example XML files. I guess Affymetrix has also some array designs > in MAGE-ML format. Tab2Mage (http://tab2mage.sourceforge.net/) also has > some example files. They are actually in tab format, but the program > converts > them to XML. Since the tab format is easier, the program might help you make > your own XML files easier. > > -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team, EBI and Seconded Scientific Programme Manager NCRI Cancer Informatics Initiative www.cancerinformatics.org.uk Tel: EBI 01223 494672 Skype: helen.parkinson.ebi |
From: Arto V. <art...@cs...> - 2006-07-11 05:27:41
|
mge...@li... wrote: > > Can anyone recommend other sources of MAGE-ML data files other than > ArrayExpress and the examples on the MGEDpage? We'd like to test our > MAGE loader with a wide variety of input data. > > MAGE Good Practice (http://www.ebi.ac.uk/~ele/ext/submitter.html#mgp) has some example XML files. I guess Affymetrix has also some array designs in MAGE-ML format. Tab2Mage (http://tab2mage.sourceforge.net/) also has some example files. They are actually in tab format, but the program converts them to XML. Since the tab format is easier, the program might help you make your own XML files easier. -- Arto Viitanen, CSC Ltd. Espoo, Finland |
From: Ele H. <el...@eb...> - 2006-07-10 20:16:46
|
On Mon, 10 Jul 2006, Valerie Wagner wrote: > > Folks, can anyone help me understand the meaning of the data in > BioDataValues? > > What I understand: > > * BioDataCube is a 3-dimensional representation of the BDQ data, where > BDQ = BioAssays, DesignElements, QuantiationTypes. However, that's not > a very specific explanation of what the data mean. > > * MAGE-ML differs from the MAGE OM in how it represents this data, using > instead DataInternal and DataExternal. > > What I don't understand: > > * Is the format of the external data files subject to a MAGE standard? > All the examples I've seen so far are "tab delimited", but it doesn't > look to me like the data files all have the same format (differing > number of columns, some have all numeric data, some mixed data, etc.). > How does one tell what one is looking at? > > * Similarly, all the examples I've found so far use the external data > method. Does anyone have an example of anything using BioDataTuples > instead of the cube or using DataInternal instead of external? > > Thanks again! > Valerie Valerie, Take a look at our documentation: BioDataCube: http://www.ebi.ac.uk/~ele/ext/submitter.html#bdq QuantitationTypes: http://www.ebi.ac.uk/~ele/ext/submitter.html#qt and http://www.ebi.ac.uk/~ele/tables/QT_details.xls You'll see in the data files section at http://www.ebi.ac.uk/~ele/ext/submitter.html#quirks that we encourage users to submit the data as DataExternal. This makes validation and loading quicker and the MAGE-ML files more manageable. Coding the data as DataInternal greatly increases the size of the MAGE-ML. The data files are usually tab-delimited but they can also be whitespace-delimited. The columns of data supplied depends on the software used to produce the data. This is where the QT table comes in - there are details of the output of several different softwares. We are constantly trying to standardise the QTs so that users have an idea of what they are looking at when they download data from our (or any other) site. Hope this helps. Cheers, Ele ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ele Holloway Scientific Database Curator Microarray Informatics European Bioinformatics Institute ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Valerie W. <val...@sr...> - 2006-07-10 19:41:23
|
Folks, can anyone help me understand the meaning of the data in BioDataValues? What I understand: * BioDataCube is a 3-dimensional representation of the BDQ data, where BDQ = BioAssays, DesignElements, QuantiationTypes. However, that's not a very specific explanation of what the data mean. * MAGE-ML differs from the MAGE OM in how it represents this data, using instead DataInternal and DataExternal. What I don't understand: * Is the format of the external data files subject to a MAGE standard? All the examples I've seen so far are "tab delimited", but it doesn't look to me like the data files all have the same format (differing number of columns, some have all numeric data, some mixed data, etc.). How does one tell what one is looking at? * Similarly, all the examples I've found so far use the external data method. Does anyone have an example of anything using BioDataTuples instead of the cube or using DataInternal instead of external? Thanks again! Valerie |
From: Valerie W. <val...@sr...> - 2006-07-10 19:08:42
|
Can anyone recommend other sources of MAGE-ML data files other than ArrayExpress and the examples on the MGEDpage? We'd like to test our MAGE loader with a wide variety of input data. Thanks for everyone's help on my DTD questions, I may have a few more questions to follow! Valerie |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-07-03 22:14:33
|
Hi All, I have a question about a file I recently downloaded from ArrayExpress that had been submitted from Imperial College, my question is more in the nature of what you think of this issue. This gets back to why I thought the experimental factors should be explicitly listed in MAGE-TAB. It appears in E-MIMR-38 that the BioAssay's <BioAssayFactorValues_assnreflist> that relates them to the <ExperimentDesign>.<ExperimentalFactor> doesn't make the best sense in how the <FactorValues> elements are grouped in the <ExperimentalFactor> elements. I think it would be a good enhancement to the MAGEvalidator to check that the <BioAssayFactorValues_assnreflist> referenced exactly one and only one FactorValue per ExperimentalFactor of the ExperimentDesign. In fact, without the experiment design, one could infer how the FactorValue elements are grouped from the <BioAssayFactorValues_assnreflist>. (at http://www.ebi.ac.uk/~ele/ext/submitter.html it states in the good practice section: 'Null factor values -- All bioassays should have a value for each factor', which, if I recall right, was meant to be the above.) Here is a typical content of a <BioAssayFactorValues_assnreflist> for E-MIMR-38:=20 <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:346"/> <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:353"/> <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:363"/> <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:365"/> both=20 <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:346"/> <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:365"/> are mapped to <ExperimentalFactor>.identifier =3D 'Compound' FactorValue elements, and=20 <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:365"/>=20 is mapped to a <ExperimentalFactor>.identifier =3D 'Timepoint' = FactorValue element and <FactorValue_ref identifier=3D"csc.mrc.ac.uk:mimir/FactorValue:EXP_CCMC_0704_01:363"/> is mapped to a <ExperimentalFactor>.identifier =3D 'Genotype' = FactorValue element with nothing being mapped to the <ExperimentalFactor>.identifier =3D 'GeneticModification' FactorValue element. (in others, the GeneticModification is mapped to and the Genotype is not). So all BioAssays map to two compounds, always one is '365' (name =3D GK1.5_0, the FactorValue '347', name =3D GK1.5_800, is never used) and the other is always either '346' (name =3D YKIX_800) or '366' (name =3D YKIX_0). =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D It would seem by best practice, Occam's razor and the actual intent of the investigator, the ExperimentalFactor Compound should really be split into two or the FactorValue elements should be the combinatorial product of the two compounds, GK1.5 and YKIX. Also that Genotype and GeneticModification should actually be combined into one ExperimentalFactor or a 'null' FactorLevel added to both with the BioAssay references to FactorValues updated accordingly. If the compound is split and Genotype and GeneticModification combined, the factor value refs from the BioAssay now make sense (the ExperimentDesign can actually be easily edited to do this). cheers, Michael |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-06-30 14:59:19
|
Hi Jason, > I thought the issue was that looking at the DTD files, you couldn't > tell which one was 1.1 and which one was 1.0. Valerie suggested adding > a comment to the DTD indicating the version number. The information I sent out in the original e-mail about the differences makes it possible to tell which version of the DTD it is by inspection, so the update to the comment is just a convenience. Even simpler is to download the DTDs from the OMG site one time only to 1.0 and 1.1 subdirectories and use those. So figuring out what version the DTD is not really an issue. > True, it is valid. So I will extend what I said: >=20 > using a MAGE-ML DOCTYPE with only a SYSTEM identifier and not a > PUBLIC identifier should be considered an error... This is a true issue, because it is not an error (although I agree it should be). So Valerie is correct that one potentially has to deal with this if the source of the document is not in best practice. A parser will be set up to know already where to find each version of the DTD. The parser only deals with documents, it most decide which version should be used. If the PUBLIC identifier isn't present and the dtd isn't qualified in the DOCTYPE, what to do? We simply guess the 1.1 version and that has worked so far. If we ever needed to, we might implement my suggestion below, to grep for the four differences but until we need to, we won't bother in our implementation of the parser. But it might not be bad to update the MAGEstk parser for this. cheers, Michael > -----Original Message----- > From: Jason Stewart [mailto:jas...@gm...]=20 > Sent: Friday, June 30, 2006 7:39 AM > To: Miller, Michael D (Rosetta) > Cc: Valerie Wagner; mge...@li... > Subject: Re: [Mged-mage] Versions of MAGE and MAGE-ML >=20 >=20 > Hey, >=20 > On 6/30/06, Miller, Michael D (Rosetta)=20 > <Mic...@ro...> wrote: > > Hi Jason and Valerie, > > > > > Beyond what Michael said, it is an *error* not to reference the > > > DOCTYPE in a MAGE-ML file. > > > > I think the issue is that this is prefectly valid: > > > > <!DOCTYPE MAGE-ML SYSTEM "MAGE-ML.dtd"> > > > > But anyone who does this should still be admonished to change their > > ways. >=20 > True, it is valid. So I will extend what I said: >=20 > using a MAGE-ML DOCTYPE with only a SYSTEM identifier and not a > PUBLIC identifier should be considered an error... >=20 > > > > > Michael, isn't this a 100% backwards compatible idea that=20 > would make > > > life easier for people? Is this change possible? I mean=20 > clearly the > > > version that we distribute from the MGED site could be=20 > modified, but > > > can the *official* version at the OMG be modified like this? > > > > It is definitely 100% backwards compatible, since it is=20 > just a comment. > > Unfortunately, even a minor change like this takes a process at OMG. >=20 > Yes, I see. I think it's worth it. >=20 > > > > In practice, I don't think this is has been a huge issue, it is rare > > that I've seen a DOCTYPE where the dtd isn't qualified by=20 > the version > > directory, and, although it is ugly and inelegant, in the > > resolveEntity() method one can look for the elements that=20 > require one or > > the other DTD and/or special case to look for who produced=20 > the document > > and map to the correct DTD. >=20 > Doesn't this miss the point? >=20 > I thought the issue was that looking at the DTD files, you couldn't > tell which one was 1.1 and which one was 1.0. Valerie suggested adding > a comment to the DTD indicating the version number. >=20 > Or did I misunderstand? >=20 > Cheers, jas. >=20 >=20 |
From: Jason S. <jas...@gm...> - 2006-06-30 14:39:10
|
Hey, On 6/30/06, Miller, Michael D (Rosetta) <Mic...@ro...> wrote: > Hi Jason and Valerie, > > > Beyond what Michael said, it is an *error* not to reference the > > DOCTYPE in a MAGE-ML file. > > I think the issue is that this is prefectly valid: > > <!DOCTYPE MAGE-ML SYSTEM "MAGE-ML.dtd"> > > But anyone who does this should still be admonished to change their > ways. True, it is valid. So I will extend what I said: using a MAGE-ML DOCTYPE with only a SYSTEM identifier and not a PUBLIC identifier should be considered an error... > > > Michael, isn't this a 100% backwards compatible idea that would make > > life easier for people? Is this change possible? I mean clearly the > > version that we distribute from the MGED site could be modified, but > > can the *official* version at the OMG be modified like this? > > It is definitely 100% backwards compatible, since it is just a comment. > Unfortunately, even a minor change like this takes a process at OMG. Yes, I see. I think it's worth it. > > In practice, I don't think this is has been a huge issue, it is rare > that I've seen a DOCTYPE where the dtd isn't qualified by the version > directory, and, although it is ugly and inelegant, in the > resolveEntity() method one can look for the elements that require one or > the other DTD and/or special case to look for who produced the document > and map to the correct DTD. Doesn't this miss the point? I thought the issue was that looking at the DTD files, you couldn't tell which one was 1.1 and which one was 1.0. Valerie suggested adding a comment to the DTD indicating the version number. Or did I misunderstand? Cheers, jas. |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-06-30 14:31:14
|
Hi Jason and Valerie, > Beyond what Michael said, it is an *error* not to reference the > DOCTYPE in a MAGE-ML file.=20 I think the issue is that this is prefectly valid: <!DOCTYPE MAGE-ML SYSTEM "MAGE-ML.dtd"> But anyone who does this should still be admonished to change their ways. > Michael, isn't this a 100% backwards compatible idea that would make > life easier for people? Is this change possible? I mean clearly the > version that we distribute from the MGED site could be modified, but > can the *official* version at the OMG be modified like this? It is definitely 100% backwards compatible, since it is just a comment. Unfortunately, even a minor change like this takes a process at OMG. In practice, I don't think this is has been a huge issue, it is rare that I've seen a DOCTYPE where the dtd isn't qualified by the version directory, and, although it is ugly and inelegant, in the resolveEntity() method one can look for the elements that require one or the other DTD and/or special case to look for who produced the document and map to the correct DTD. In fact, can the MAGEstk parser be updated to do the first option in resolveEntity()? In those documents that don't have the two non-backwards compatible elements, the document is valid for either DTD. A grep could answer 1.0 or 1.1. cheers, Michael > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf Of=20 > Jason Stewart > Sent: Friday, June 30, 2006 4:20 AM > To: Valerie Wagner > Cc: mge...@li... > Subject: Re: [Mged-mage] Versions of MAGE and MAGE-ML >=20 >=20 > Hi Valerie, >=20 > On 6/29/06, Valerie Wagner <val...@sr...> wrote: > > > > Hello folks, > > > > We are currently working on integrating MAGE into the BioWarehouse > > (relational bioinformatics database). > > > > I have a few questions about the versions of MAGE and MAGE-ML: > > > > 1. I don't see any element or attribute in MAGE-ML that=20 > would indicate > > which version the XML instance is (1.0 or 1.1), other than=20 > if the XML > > file happens to reference a MAGE-ML DTD with a version=20 > number in it. Is > > there any simple way to determine which version of MAGE-ML=20 > a given XML > > file is? > > >=20 > Beyond what Michael said, it is an *error* not to reference the > DOCTYPE in a MAGE-ML file. The entire purpose of creating the DTD was > so that people like yourselves can validate what they get - without > the DOCTYPE there can be no validation. >=20 > > 2. Similarly, I don't see any indicate in the MAGE-ML.DTD=20 > document that > > indicates what version it is. I've see both version 1.0=20 > and 1.1 of the > > DTD given the same name "MAGE-ML.dtd" and I don't see any=20 > comment inside > > these files that indicates which version they are. =20 > Shouldn't at least a > > comment be added to the DTDs to indicate what version they are? > > Preferably, the XML files would also indicate which version=20 > of MAGE-ML > > they are. > > >=20 > Michael, isn't this a 100% backwards compatible idea that would make > life easier for people? Is this change possible? I mean clearly the > version that we distribute from the MGED site could be modified, but > can the *official* version at the OMG be modified like this? >=20 > Cheers, jas. >=20 > Using Tomcat but need to do more? Need to support web=20 > services, security? > Get stuff done quickly with pre-integrated technology to make=20 > your job easier > Download IBM WebSphere Application Server v.1.0.1 based on=20 > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057& dat=3D121642 _______________________________________________ Mged-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Jason S. <jas...@gm...> - 2006-06-30 11:19:58
|
Hi Valerie, On 6/29/06, Valerie Wagner <val...@sr...> wrote: > > Hello folks, > > We are currently working on integrating MAGE into the BioWarehouse > (relational bioinformatics database). > > I have a few questions about the versions of MAGE and MAGE-ML: > > 1. I don't see any element or attribute in MAGE-ML that would indicate > which version the XML instance is (1.0 or 1.1), other than if the XML > file happens to reference a MAGE-ML DTD with a version number in it. Is > there any simple way to determine which version of MAGE-ML a given XML > file is? > Beyond what Michael said, it is an *error* not to reference the DOCTYPE in a MAGE-ML file. The entire purpose of creating the DTD was so that people like yourselves can validate what they get - without the DOCTYPE there can be no validation. > 2. Similarly, I don't see any indicate in the MAGE-ML.DTD document that > indicates what version it is. I've see both version 1.0 and 1.1 of the > DTD given the same name "MAGE-ML.dtd" and I don't see any comment inside > these files that indicates which version they are. Shouldn't at least a > comment be added to the DTDs to indicate what version they are? > Preferably, the XML files would also indicate which version of MAGE-ML > they are. > Michael, isn't this a 100% backwards compatible idea that would make life easier for people? Is this change possible? I mean clearly the version that we distribute from the MGED site could be modified, but can the *official* version at the OMG be modified like this? Cheers, jas. |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-06-29 22:36:40
|
Hi Valerie, > 1. I don't see any element or attribute in MAGE-ML that=20 > would indicate=20 > which version the XML instance is (1.0 or 1.1), other than if the XML=20 > file happens to reference a MAGE-ML DTD with a version number=20 > in it. Is=20 > there any simple way to determine which version of MAGE-ML a=20 > given XML=20 > file is? This is specified in the DOCTYPE element at the top. The convention that was adopted was that the DTD name would be qualified by a directory, 1.0/MAGE-ML.dtd or 1.1/MAGE-ML.dtd, there is also an accepted PUBLIC identifier for the two formats so one will typically see for version 1.1 (if the MAGE file is in best practice): <!DOCTYPE MAGE-ML PUBLIC "-//OMG//DTD MAGE-ML 1.1//EN" "http://schema.omg.org/lsr/gene_expression/1.1/MAGE-ML.dtd"> The OMG site is the official site of the two versions of the DTD. In fact, the FTF report at the OMG web site for the Gene Expression specification official documents all the changes. We also stash the two DTDs in well known locations in their subdirectories of 1.0 and 1.1 and implement the SAX EntityResolver interface, so we will shorten this to: <!DOCTYPE MAGE-ML PUBLIC "-//OMG//DTD MAGE-ML 1.1//EN" "1.1/MAGE-ML.dtd"> and in the resolveEntity() method, look locally first then look to the OMG website. > 2. Similarly, I don't see any indicate in the MAGE-ML.DTD=20 > document that=20 > indicates what version it is. I've see both version 1.0 and=20 > 1.1 of the=20 > DTD given the same name "MAGE-ML.dtd" and I don't see any=20 > comment inside=20 > these files that indicates which version they are. Shouldn't=20 > at least a=20 > comment be added to the DTDs to indicate what version they are?=20 > Preferably, the XML files would also indicate which version=20 > of MAGE-ML=20 > they are. We actually, in hindsight, realized this would have been good to have in the description at the top of the DTD. But the XML file, itself, should always qualify the DTD with either 1.0/MAGE-ML.dtd or 1.1/MAGE-ML.dtd. Our convention, if it isn't, is to assume 1.1. By the by, on Unix, case matters and it must be MAGE-ML.dtd. > 2. Similarly, I don't see any indicate in the MAGE-ML.DTD=20 > document that=20 > indicates what version it is. I've see both version 1.0 and=20 > 1.1 of the=20 > DTD given the same name "MAGE-ML.dtd" and I don't see any=20 > comment inside=20 > these files that indicates which version they are. Shouldn't=20 > at least a=20 > comment be added to the DTDs to indicate what version they are?=20 > Preferably, the XML files would also indicate which version=20 > of MAGE-ML=20 > they are. There are only two incompatibilities between the two, it would be possible in the EntityResolver.resolveEntity() to look to see if either of these occur, and what version, to decide what version to use. =20 The major difference is that there can be multiple ExperimentDesign tags in an experiment, so the association changed. <!ELEMENT ExperimentDesign_assn (ExperimentDesign) > becomes <!ELEMENT ExperimentDesigns_assnlist (ExperimentDesign+) > =20 The other is that the MerckIndex association for Compound to OntologyEntry changed to CompoundIndicies. <!ELEMENT MerckIndex_assn (OntologyEntry) > becomes <!ELEMENT CompoundIndices_assnlist (OntologyEntry+) >=20 There was also an association added from BibliographicReference to databases: Accessions_assnlist? The Type association was made option for BioSample: Type_assn becomes Type_assn? cheers, Michael Michael Miller Lead Software Developer Rosetta Biosoftware Business Unit www.rosettabio.com > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf Of=20 > Valerie Wagner > Sent: Thursday, June 29, 2006 9:59 AM > Cc: mge...@li... > Subject: [Mged-mage] Versions of MAGE and MAGE-ML >=20 >=20 >=20 > Hello folks, >=20 > We are currently working on integrating MAGE into the BioWarehouse=20 > (relational bioinformatics database). >=20 > I have a few questions about the versions of MAGE and MAGE-ML: >=20 > 1. I don't see any element or attribute in MAGE-ML that=20 > would indicate=20 > which version the XML instance is (1.0 or 1.1), other than if the XML=20 > file happens to reference a MAGE-ML DTD with a version number=20 > in it. Is=20 > there any simple way to determine which version of MAGE-ML a=20 > given XML=20 > file is? >=20 > 2. Similarly, I don't see any indicate in the MAGE-ML.DTD=20 > document that=20 > indicates what version it is. I've see both version 1.0 and=20 > 1.1 of the=20 > DTD given the same name "MAGE-ML.dtd" and I don't see any=20 > comment inside=20 > these files that indicates which version they are. Shouldn't=20 > at least a=20 > comment be added to the DTDs to indicate what version they are?=20 > Preferably, the XML files would also indicate which version=20 > of MAGE-ML=20 > they are. >=20 > 3. I also don't see anything in the MAGE.xmi file to indicate which=20 > version of the MAGE-OM it is. I assuming that since there are two=20 > versions of MAGE-ML, there must have been two versions of the OM?=20 > Granted, I haven't dug completely through the XMI file, but=20 > does anyone=20 > know if it indicates the version number of the OM? >=20 > Since we're writing a parser/loader to allow people to load arbitrary=20 > MAGE-ML into our BioWarehouse, it's important that we be able to=20 > determine which version the input file is and which version=20 > of MAGE we=20 > want to support, or if it would be feasible to support both. =20 > With that=20 > in mind, >=20 > 4. Can anyone offer their opinion on which version of MAGE-ML (1.0 or=20 > 1.1) is more widely used? >=20 > Thanks, > Valerie Wagner > Software Engineer > SRI International >=20 >=20 >=20 >=20 >=20 > Using Tomcat but need to do more? Need to support web=20 > services, security? > Get stuff done quickly with pre-integrated technology to make=20 > your job easier > Download IBM WebSphere Application Server v.1.0.1 based on=20 > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057& dat=3D121642 _______________________________________________ Mged-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Helen P. <par...@eb...> - 2006-06-29 22:09:19
|
Dear Valerie, most of our inout pipelines have upgraded to 1.1 but we still accept 1.0. We do not upgrade legacy XML to 1.1 so you will still see some 1.0 in downloads from ArrayExpress. best regards Helen > > Hello folks, > > We are currently working on integrating MAGE into the BioWarehouse > (relational bioinformatics database). > > I have a few questions about the versions of MAGE and MAGE-ML: > > 1. I don't see any element or attribute in MAGE-ML that would indicate > which version the XML instance is (1.0 or 1.1), other than if the XML > file happens to reference a MAGE-ML DTD with a version number in it. Is > there any simple way to determine which version of MAGE-ML a given XML > file is? > > 2. Similarly, I don't see any indicate in the MAGE-ML.DTD document that > indicates what version it is. I've see both version 1.0 and 1.1 of the > DTD given the same name "MAGE-ML.dtd" and I don't see any comment inside > these files that indicates which version they are. Shouldn't at least a > comment be added to the DTDs to indicate what version they are? > Preferably, the XML files would also indicate which version of MAGE-ML > they are. > > 3. I also don't see anything in the MAGE.xmi file to indicate which > version of the MAGE-OM it is. I assuming that since there are two > versions of MAGE-ML, there must have been two versions of the OM? > Granted, I haven't dug completely through the XMI file, but does anyone > know if it indicates the version number of the OM? > > Since we're writing a parser/loader to allow people to load arbitrary > MAGE-ML into our BioWarehouse, it's important that we be able to > determine which version the input file is and which version of MAGE we > want to support, or if it would be feasible to support both. With that > in mind, > > 4. Can anyone offer their opinion on which version of MAGE-ML (1.0 or > 1.1) is more widely used? > > Thanks, > Valerie Wagner > Software Engineer > SRI International > > > > > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > -- Helen Parkinson, PhD Microarray Informatics Team EBI and Seconded Scientific Programme Manager NCRI Informatics Initiative www.cancerinformatics.org.uk EBI: 01223 494672 Skype: helen.parkinson.ebi |
From: Valerie W. <val...@sr...> - 2006-06-29 16:59:12
|
Hello folks, We are currently working on integrating MAGE into the BioWarehouse (relational bioinformatics database). I have a few questions about the versions of MAGE and MAGE-ML: 1. I don't see any element or attribute in MAGE-ML that would indicate which version the XML instance is (1.0 or 1.1), other than if the XML file happens to reference a MAGE-ML DTD with a version number in it. Is there any simple way to determine which version of MAGE-ML a given XML file is? 2. Similarly, I don't see any indicate in the MAGE-ML.DTD document that indicates what version it is. I've see both version 1.0 and 1.1 of the DTD given the same name "MAGE-ML.dtd" and I don't see any comment inside these files that indicates which version they are. Shouldn't at least a comment be added to the DTDs to indicate what version they are? Preferably, the XML files would also indicate which version of MAGE-ML they are. 3. I also don't see anything in the MAGE.xmi file to indicate which version of the MAGE-OM it is. I assuming that since there are two versions of MAGE-ML, there must have been two versions of the OM? Granted, I haven't dug completely through the XMI file, but does anyone know if it indicates the version number of the OM? Since we're writing a parser/loader to allow people to load arbitrary MAGE-ML into our BioWarehouse, it's important that we be able to determine which version the input file is and which version of MAGE we want to support, or if it would be feasible to support both. With that in mind, 4. Can anyone offer their opinion on which version of MAGE-ML (1.0 or 1.1) is more widely used? Thanks, Valerie Wagner Software Engineer SRI International |