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From: Jason S. <jas...@gm...> - 2008-05-14 05:25:04
|
Hi Charles, 2008/5/12 Charles Plessy <pl...@de...>: > Dear Jason, > > I have prepared packages of Bio-MAGE and Bio-MAGE-Utils for the Debian > operating system. The one for Bio-MAGE is already available, but the one > for Bio-MAGE-Utils needs a clarification of the license of its files. > The ones in the MAGE/Tools/* directory have their license clearly > indicated in the headers, but I can not find information for the other > modules. I guess that they would be either same as in Bio-MAGE, or same > as Perl itself, but without written evidence, I will not be allowed to > upload the package to Debian. I tried to ask on the mged-mage-perl list > but had no answer. Do you have the information? > This is excellent news! I'm sorry that I have not taken more time to be helpful - I was overwhelmed - but am less so at the moment. The license must be the same as Bio::MAGE - it was funded by the same organization. I am preparing a new release to clean things up. If you have any patches you want me to make - tell me and I will ensure they get put together. There was a lot that didn't get put into the last CPAN version. Cheers, jas. |
From: Charles P. <cha...@pl...> - 2008-04-16 05:51:42
|
Dear MAGE-Perl hackers, I am currently preparing installation packages for Bio-MAGE and Bio-MAGE-Utils on Debian platforms. I am in the final phase of this, where software packages are ready and I proofcheck that Debian can freely redistribute them. While in Bio-MAGE all the files have a header indicating their license, it is not the case in Bio-MAGE-Utils except for the files in the MAGE/Tools/ directory. Can you confirm the license of the other files of Bio-MAGE-Utils? I have another question for Bio-MAGE-Utils: currently Makefile.PL indicates that its modules are in the Bio::MAGE::Utils namespace. However, not only installation does not work with this parameter, but third party programs such as tab2mage seem to expect the utilities in Bio::MAGE. For this reason, the following patch will be applied for Debian: --- a/Makefile.PL +++ b/Makefile.PL @@ -2,7 +2,7 @@ # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( - 'NAME' => 'Bio::MAGE::Utils', + 'NAME' => 'Bio::MAGE', 'VERSION' => '20030502.0', 'PREREQ_PM' => {Tie::IxHash=>1.21}, ($] >= 5.005 ? Can you confirm that this change is correct? Have a nice day, -- Charles Plessy Debian-Med packaging team Wako, Saitama, Japan |
From: Jason E. S. <jas...@gm...> - 2007-05-15 06:49:55
|
Hi All, *** NOTE *** This message only affects those of you that have local checkouts from the MGED SVN repository. *** When I created the svn repository i didn't set up the structure needed for making branches and tags - which we want. i have now made those changes to the repository. That means that if any of you have a local checkout you will need to use the svn switch command to change the URL of your working copy - if you need *help* with the correct usage, WRITE ME. I have already migrated the htdocs/ directory on SF to point to the correct location. Now all the working code lives in trunk/ (e.g. trunk/MAGE-Perl/ or trunk/MAGE-PIM/) and version tags live in tags/ (e.g. tags/MAGE-Perl/2003-05-02.3/). Sorry for the inconvenience. Cheers, jas. |
From: Jason S. <jas...@gm...> - 2007-05-15 03:28:18
|
Hi all, I'm happy to announce an official release of Bio-MAGE available at CPAN and SF. In keeping with past versioning, this release is "2003-05-02-3" which is the third release based on MAGEv1.1 (2003-05-02 release date). This release has a number of bugfixes as well as the newly generated API files using the new Mason templating code to auto-generate the API from the MAGE-OM model. This release also seperates out a number of hand-written helper modules into a separate package Bio-MAGE-Utils, e.g. Bio::MAGE::XMLUtils, etc. That means we can more frequently update these modules without having to release the auto-generated API module. I've also included a new release of the Bio-MAGE examples from lib/Perl. Please try this out and make sure it works for your installation (and send any problems to Tim or Joe or Adam ;-) Cheers! jas. |
From: Jason E. S. <jas...@gm...> - 2007-05-14 08:43:44
|
Hi Mike, Michael Muratet US-Huntsville wrote: > Jason > > Thanks for the reply. I'm still interested in examples or a tutorial. I > got sidetracked onto other projects, but I'm still interested in looking > at the Geo data. > OK. I can help. I'm preparing to make another official release of Bio::MAGE as well as the example applications. If you are familiar with the subversion version control system, you can check out the existing work at: https://svn.sourceforge.net/svnroot/mged/MAGE-Perl and the examples are at: https://svn.sourceforge.net/svnroot/mged/lib/Perl otherwise I can ping you when the tarballs are loaded into SourceForge. Cheers, jas. |
From: Michael M. US-H. <Mic...@op...> - 2007-05-09 13:58:16
|
Jason Thanks for the reply. I'm still interested in examples or a tutorial. I got sidetracked onto other projects, but I'm still interested in looking at the Geo data. Regards Mike > -----Original Message----- > From: Jason E. Stewart [mailto:jas...@gm...] > Sent: Monday, May 07, 2007 5:23 AM > To: Michael Muratet US-Huntsville > Cc: mge...@li... > Subject: Re: [Mged-mage-perl] Bio::MAGE examples? >=20 > Hi Michael, >=20 > Michael Muratet US-Huntsville wrote: > > Greetings > > > > I am in the process of writing a parser for NCBI/Geo data. The MAGE > > suite looks pretty robust, but I'm having a rough time finding an entry > > point to start with. Are there any examples or tutorials to be had? > > >=20 > This is a very late reply. I hope at this point you are past the need > for tutorials. If you still need further help, please let us know. >=20 > Cheers, jas. |
From: Jason E. S. <jas...@gm...> - 2007-05-09 05:19:34
|
Hi Michael, Michael Muratet US-Huntsville wrote: > Greetings > > I am in the process of writing a parser for NCBI/Geo data. The MAGE > suite looks pretty robust, but I'm having a rough time finding an entry > point to start with. Are there any examples or tutorials to be had? > This is a very late reply. I hope at this point you are past the need for tutorials. If you still need further help, please let us know. Cheers, jas. |
From: Michael M. US-H. <Mic...@op...> - 2006-12-07 22:28:53
|
Greetings I am in the process of writing a parser for NCBI/Geo data. The MAGE suite looks pretty robust, but I'm having a rough time finding an entry point to start with. Are there any examples or tutorials to be had?=20 Thanks Mike=20 |
From: Jason S. <jas...@gm...> - 2006-09-13 08:20:24
|
Hey Tim, On 9/12/06, Tim Rayner <ra...@eb...> wrote: > I think I understand, although I don't quite see the point regarding the > MANIFEST file - the suggestion above works with the current MANIFEST, > which is otherwise broken at the moment (try 'make distcheck' on a freshly > checked-out tree). Thanks for catching that - I'll fix it... > Or have I misunderstood completely, such that you're planning to package > these two modules for separate download and installation as well? > Yes, that is my intent - two seperate modules distributed independently. The auto-generated stuff will not often be updated, but the hand-coded bits may be updated much more frequently. >From a maintenance perspective, I think this is much simpler. Cheers, jas. |
From: Jason S. <jas...@gm...> - 2006-09-12 05:15:29
|
Hey Tim, On 9/9/06, Tim Rayner <ra...@eb...> wrote: > Hi Jason, > > I've finally got around to checking this out; looks good Good! Glad to hear it... > , except for one > minor bug in the XML::Writer module that prevented it from handling > objects lacking attributes (e.g. BioMaterialMeasurements). I added a line > to fix it, and it now runs fine in our application: done and commited. > > Another suggestion I'd like to make is that you add the following > svn:externals properties to the MAGE-Perl/MAGE directory in the svn > repository: > > XML https://svn.sourceforge.net/svnroot/mged/MAGE-Perl-Utils/MAGE/XML/ > Tools https://svn.sourceforge.net/svnroot/mged/MAGE-Perl-Utils/MAGE/Tools/ > > This will allow svn users to automatically check out the XML and Tools > directories into the appropriate locations in their working copies, > without having to mix the autogenerated and hand-rolled code in the > repository. I understand, but I'd like to avoid this.... I'd like to keep them as seperate modules completely - one for auto-generated code and the other for hand-written code. Otherwise I will have to edit the MANIFEST file of the MAGE-Perl directory to avoid other problems - not a huge issue, but they are two different modules now, and they should live in seperate directories. I can be convinced otherwise, but my initial response is "I'd prefer not". Cheers, jas. |
From: Jason S. <jas...@gm...> - 2006-08-22 11:54:49
|
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: Jason S. <jas...@gm...> - 2006-07-12 15:36:52
|
Hey Matthew, BTW. always write to the MAGE list or the MAGE-Perl list because I can be a little to occupied. The other MAGE folks are really helpful too, and often respond before I get a chance to. Cheers, jas. |
From: Jason S. <jas...@gm...> - 2006-07-12 15:35:24
|
Hi Matthew, On 7/10/06, Matthew Hibbs <mh...@cs...> wrote: > Hi Jason, > > We've installed the latest version of the Perl API from source forge, > but we're still running into some issues running the example > scripts. When we run the reader test script on the E-SMDB-* xml > files we get errors like this: > -bash-3.00$ perl mageml-reader-test.pl Exptset_1423.xml > ERROR: > FILE: /home/sgrossbe/mage-perl-examples/script/Exptset_1423.xml > LINE: 10455 > COLUMN: 31 > MESSAGE: Unknown element 'ExperimentDesign_assn' > at /usr/lib/perl5/site_perl/5.8.5/Bio/MAGE/XML/Reader.pm line 307 > This is an XML validation error. This message comes directly from the Xerces XML parser. You can run any XML validator and you will get the same basic message. It looks like this is an XML file from v1.1 that allows multiple Experiment Designs - but it is being run against the DTD from v1.0 which doesn't allow this. If you change the DOCTYPE so that it uses the correct DTD things will validate better. BTW. I would get a nice validator like nsgmls or osgmls and always check your XML files before trying to use MAGEstk on them - that will find any validation errors early - MAGEstk is very strict and won't work with invalid files. > However, we are able to run this script on some of the other xml > files, like the E-WMIT-* files. I would guess that those files are based on the v1.0 DTD - which is what Xerces is finding. I'm convinced that Michael is correct, and we should provide a simple XML resolver to make this problem go away. > But some of the other scripts don't > seem to work with these, such as the simple report script, that > generates an error like this one: > -bash-3.00$ perl mageml-report-simple.pl -file=E-WMIT-4_download/E- > WMIT-4.xml > Can't locate object method "reader" via package "SimpleReportHandler" at > /usr/lib/perl5/site_perl/5.8.5/Bio/MAGE/XML/Reader.pm line 486. > Huh. I don't have the code in front of me (at a friends house in ABQ New Mexico), but this is a Perl error because it is trying to register the reader object for later parsing callbacks inside the report generator. But it is not finding the SimpleReportHandler package. Either move SimpleReportHandler.pm into the directory that you are running the program from or include a '-I' switch on the perl command line to tell perl to use an extra library directory (the one with SimpleReportHandler.pm in it). The reason that I didn't make this Bio::MAGE::XML::SimpleReportHandler was that it was just for test purposes to show what could be done with the MAGEstk API - and because those affy chip files were so freakin' HUGE!!!!! It was never intended for prime time. > Both of these errors seem to be with Reader.pm, and we're using the > latest version of this file from source forge (it has a modified date > of Jan 20, 2004). Do you think it's best for us to try and get these > examples running on our system so that we can then modify them to try > and extract the expression levels, or do you think we should work > with you more on figuring out what parts of the API will help us and > code up more ourselves? > Look at these scripts and how they access bits of the MAGE API. The report handler stuff might be useful - for example if you want to grab a matrix of numbers out of the XML and dump it to a spreadsheet. The scripts won't do that for you directly - they are only *rudimentary* examples. Give me an idea of what you would like to do, and then I can let you know how MAGEstk can help you do it. Cheers, jas. |
From: Jason S. <jas...@gm...> - 2006-06-26 12:13:25
|
Hey, Sorry I was so late in responding - I just returned from N. India getting rained on in the Eastern Himalayas... On 6/15/06, Joe White <jw...@ji...> wrote: > Hi Pascal, > > I think you made the right choice by editing the MGEDOntologyHelper > modules. Better to fix these than mess with the main code base; as far > as I know, it is based on the latest MAGEv1 model, so the cardinalities > should be correct. this seems correct to me... > > The ExperimentDesign example looks ok. > > If you run into the line ending problem again, the unix command > 'dos2unix' should correct that problem. (Yes, the linux version does > Mac line endings too :) we should fix that file and check in the corrected version - someone must have done the work on OS X, and checked it in from the command line so CVS didn't auto correct the line endings... Cheers, jas. |
From: Joe W. <jw...@ji...> - 2006-06-15 17:04:34
|
Hi Pascal, I think you made the right choice by editing the MGEDOntologyHelper=20 modules. Better to fix these than mess with the main code base; as far=20 as I know, it is based on the latest MAGEv1 model, so the cardinalities=20 should be correct. The ExperimentDesign example looks ok.=20 If you run into the line ending problem again, the unix command=20 'dos2unix' should correct that problem. (Yes, the linux version does=20 Mac line endings too :)=20 In the Age example, some of the data are not represented in the XML, ie.=20 InitialTimePoint, Unit, 'relative' and birth. I'm not sure why this=20 is. In the <Associations_assnlist> of the Age OE should be an entry for=20 InitialTimePoint, eg.: <OntologyEntry category=3D"initial_time_point" value=3D"initial_time_poi= nt"> <OntologyReference_assn> <DatabaseEntry accession=3D"#initial_time_point" URI=3D"http://mged.s= ourceforge.net/ontologies/MGEDontology.php#initial_time_point"> <Database_assnref> <Database_ref identifier=3D"MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category=3D"InitialTimePoint" value=3D"InitialTimePoin= t"> <OntologyReference_assn> <DatabaseEntry accession=3D"#InitialTimePoint " URI=3D"http://mged.= sourceforge.net/ontologies/MGEDontology.php# InitialTimePoint "> <Database_assnref> <Database_ref identifier=3D"MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category=3D"InitialTimePoint" value=3D"birth"> <OntologyReference_assn> <DatabaseEntry accession=3D"#birth" URI=3D"http://mged.sourceforg= e.net/ontologies/MGEDontology.php#birth"> <Database_assnref> <Database_ref identifier=3D"MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Associations_assnlist> </OntologyEntry>=20 and the OE for Measurement should have an OE for Units, eg: <OntologyEntry category=3D"has_units" value=3D"has_units"> <OntologyReference_assn> <DatabaseEntry accession=3D"#has_units" URI=3D"http://mged.source= forge.net/ontologies/MGEDontology.php#has_units"> <Database_assnref> <Database_ref identifier=3D"MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category=3D"Unit" value=3D"Unit"> <OntologyReference_assn> <DatabaseEntry accession=3D"#Unit" URI=3D"http://mged.sourcefor= ge.net/ontologies/MGEDontology.php#Unit"> <Database_assnref> <Database_ref identifier=3D"MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category=3D"TimeUnit" value=3D"TimeUnit"> <OntologyReference_assn> <DatabaseEntry accession=3D"#TimeUnit" URI=3D"http://mged.sou= rceforge.net/ontologies/MGEDontology.php#TimeUnit"> <Database_assnref> <Database_ref identifier=3D"MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category=3D"TimeUnit" value=3D"years"> <OntologyReference_assn> <DatabaseEntry accession=3D"#years" URI=3D"http://mged.sour= ceforge.net/ontologies/MGEDontology.php#years"> <Database_assnref> <Database_ref identifier=3D"MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> </OntologyEntry>=20 </Associations_assnlist> </OntologyEntry>=20 </Associations_assnlist> </OntologyEntry>=20 </Associations_assnlist> </OntologyEntry> The Age example is detailed in item #4 in the MGEDOntology policy doc=20 located at: http://mged.sourceforge.net/ontologies/MOMAGEpolicy.txt That being said, I can't say that I've ever used this much detail in=20 practice. The age example was one of the test cases for the=20 OntoologyHelper; although the java code probably produces XML that=20 matches the policies, the Perl code needed some work, and I don't think=20 we ever got the code to correctly write this example.=20 I hope you don't have a lot of Age OEs to fix.=20 Cheers, Joe Pascal Hingamp wrote: >Hi folks, > > >I've checked out the MGEDOntology Perl modules from cvs and I have a few= comments=20 >and questions: > >I'm running the modules against the latest v1.3.0 MO owl file and it wor= ks fine in=20 >the cases I've tested so far, but I'm having a catch22 issue with Experi= mentDesignType.=20 >The MGEDOntology Perl code: > >my $experiment =3D Bio::MAGE::Experiment::Experiment->new(identifier=3D>= 'Etest'); >my $design =3D Bio::MAGE::Experiment::ExperimentDesign->new(); >$experiment->setExperimentDesign($design); > my $ontologyEntry3 =3D Bio::MAGE::Tools::MGEDOntologyClassEntry->new( > parentObject =3D> $design, > className =3D> 'ExperimentDesign', > association =3D> 'Types', > values =3D> { > ExperimentDesign=3D>'disease_state_design' > }, > ontology =3D> $ontology); > >throws "ERROR: Unable to determine MO class name from class ExperimentDe= sign with=20 >association Types at MGEDOntologyClassEntry.pm line 327" >because although the MAGE slot is plural "Types" the MO entry is singula= r=20 >"ExperimentDesignType" > >Changing the association parameter to: > association =3D> 'Type', > >passes the MO muster but throws "Can't call method "other" on an undefin= ed value at=20 >MGEDOntologyClassEntry.pm line 496" because the MAGE slot is singular... > >To get past this issue I could only see hacking the MO owl file (to plur= al), hacking=20 >the MAGE::Experiment::ExperimentDesign to singular, or hacking the=20 >MGEDOntologyClassEntry.pm to go plural if singular doesn't do it. I trie= d the latter,=20 >thus around line 495 of MGEDOntologyClassEntry.pm I added the ugly hack = line: > > #### If we know our parent object and association, associate with th= e parent > if (defined($parentObject) && defined($association)) { > my %associations =3D $parentObject->associations(); > $association .=3D 's' if !exists $associations{lcfirst($associatio= n)};# UGLY HACK > my $cardinality =3D $associations{lcfirst($association)}->other()-= >cardinality(); > my $setter =3D "set$association"; > if ($cardinality =3D~ /N$/) { > $setter =3D "add$association"; > } > $parentObject->$setter($self); > } > >which together with "association =3D> 'Type'" in the above MGEDOntologyC= lassEntry=20 >constructor throws no error and produces the following MAGE-ML: > > <Experiment_assnlist> > <Experiment identifier=3D"Etest"> > <ExperimentDesign_assn> > <ExperimentDesign> > <Types_assnlist> > <OntologyEntry value=3D"disease_state_design" > category=3D"ExperimentDesignType"> > <OntologyReference_assn> > <DatabaseEntry=20 >URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#disease_s= tate_design" > accession=3D"#disease_state_design"> > <Database_assnref> > <Database_ref identifier=3D"www.mged.org:Database:= MO"/> > </Database_assnref> > </DatabaseEntry> > </OntologyReference_assn> > </OntologyEntry> > </Types_assnlist> > </ExperimentDesign> > </ExperimentDesign_assn> > >Is this an issue or have I got something wrong?.. > >Also, in case anyone else runs into the same problem I thought I'd menti= on that one=20 >of the modules (MGEDOntologyHelper.pm) has Macintosh style line endings,= which is=20 >fine of course, but it totally threw my LINUX Perl interpreter with "Mod= ule doesn't=20 >evaluate to true" errors, or "Missing right curly bracket" when I tried = to edit the=20 >file... It's a nightmare because the file looks normal in emacs; only wi= th more did I=20 >ffinally see the mangled code. Changing the file to "UNIX line endings" = cured the=20 >problem. > >Finally, is the following code correct for MO age annotation of a biosam= ple: > >my $ontologyEntry2 =3D Bio::MAGE::Tools::MGEDOntologyClassEntry->new( > parentObject =3D> $bioSource, > className =3D> 'BioSource', > association =3D> 'Characteristics', > values =3D> { > Age =3D> 'Age', > IntitialTimePoint =3D> 'birth', > has_measurement =3D> { > has_measurement_type =3D> 'rela= tive', > TimeUnit =3D> 'years', > has_value =3D> 40, > } > }, > ontology =3D> $ontology) >} > >which generates the MAGE-ML: > <Characteristics_assnlist> > <OntologyEntry value=3D"BioMaterialCharacteristics" > category=3D"BioMaterialCharacteristics"> > <OntologyReference_assn> > <DatabaseEntry=20 >URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#BioMateri= alCharacteristics" > accession=3D"#BioMaterialCharacteristics"> > <Database_assnref> > <Database_ref identifier=3D"www.mged.org:Database:MO"/= > > </Database_assnref> > </DatabaseEntry> > </OntologyReference_assn> > <Associations_assnlist> > <OntologyEntry value=3D"Age" > category=3D"Age"> > <OntologyReference_assn> > <DatabaseEntry=20 >URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#Age" > accession=3D"#Age"> > <Database_assnref> > <Database_ref identifier=3D"www.mged.org:Database:= MO"/> > </Database_assnref> > </DatabaseEntry> > </OntologyReference_assn> > <Associations_assnlist> > <OntologyEntry value=3D"has_measurement" > category=3D"has_measurement"> > <OntologyReference_assn> > <DatabaseEntry=20 >URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#has_measu= rement" > accession=3D"#has_measurement"> > <Database_assnref> > <Database_ref identifier=3D"www.mged.org:Datab= ase:MO"/> > </Database_assnref> > </DatabaseEntry> > </OntologyReference_assn> > <Associations_assnlist> > <OntologyEntry value=3D"Measurement" > category=3D"Measurement"> > <OntologyReference_assn> > <DatabaseEntry=20 >URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#Measureme= nt" > accession=3D"#Measurement"> > <Database_assnref> > <Database_ref identifier=3D"www.mged.org:D= atabase:MO"/> > </Database_assnref> > </DatabaseEntry> > </OntologyReference_assn> > <Associations_assnlist> > <OntologyEntry> > </OntologyEntry> > <OntologyEntry value=3D"40" > category=3D"has_value"> > </OntologyEntry> > </Associations_assnlist> > </OntologyEntry> > </Associations_assnlist> > </OntologyEntry> > </Associations_assnlist> > </OntologyEntry> > </Associations_assnlist> > </OntologyEntry> > </Characteristics_assnlist> > >Many thanks! >Pascal >------------------------------------------------------------------------= - >Pascal H I N G A M P >------------------------------------------------------------------------= - >Information G=C3=A9nomique et Structurale Universit=C3=A9 de la M= =C3=A9diterran=C3=A9e >CNRS UPR 2589 Facult=C3=A9 des Sciences de = Luminy >163 Avenue de Luminy Case 934 D=C3=A9partement de Bi= ologie >13288 Marseille cedex 9 France http://biologie.univ-mrs.f= r >http://www.igs.cnrs-mrs.fr pascal.hingamp@univmed.f= r >Tel:+33(0)4 91 82 54 35 Mob:+33(0)6 13 54 65 91 Fax:+33(0)4 91 82 54 2= 1 > > > >_______________________________________________ >Mged-mage-perl mailing list >Mge...@li... >https://lists.sourceforge.net/lists/listinfo/mged-mage-perl > =20 > |
From: Pascal H. <pas...@ig...> - 2006-06-14 19:37:40
|
Hi folks, I've checked out the MGEDOntology Perl modules from cvs and I have a few = comments=20 and questions: I'm running the modules against the latest v1.3.0 MO owl file and it work= s fine in=20 the cases I've tested so far, but I'm having a catch22 issue with Experim= entDesignType.=20 The MGEDOntology Perl code: my $experiment =3D Bio::MAGE::Experiment::Experiment->new(identifier=3D>'= Etest'); my $design =3D Bio::MAGE::Experiment::ExperimentDesign->new(); $experiment->setExperimentDesign($design); my $ontologyEntry3 =3D Bio::MAGE::Tools::MGEDOntologyClassEntry->new( parentObject =3D> $design, className =3D> 'ExperimentDesign', association =3D> 'Types', values =3D> { ExperimentDesign=3D>'disease_state_design' }, ontology =3D> $ontology); throws "ERROR: Unable to determine MO class name from class ExperimentDes= ign with=20 association Types at MGEDOntologyClassEntry.pm line 327" because although the MAGE slot is plural "Types" the MO entry is singular= =20 "ExperimentDesignType" Changing the association parameter to: association =3D> 'Type', passes the MO muster but throws "Can't call method "other" on an undefine= d value at=20 MGEDOntologyClassEntry.pm line 496" because the MAGE slot is singular... To get past this issue I could only see hacking the MO owl file (to plura= l), hacking=20 the MAGE::Experiment::ExperimentDesign to singular, or hacking the=20 MGEDOntologyClassEntry.pm to go plural if singular doesn't do it. I tried= the latter,=20 thus around line 495 of MGEDOntologyClassEntry.pm I added the ugly hack l= ine: #### If we know our parent object and association, associate with the= parent if (defined($parentObject) && defined($association)) { my %associations =3D $parentObject->associations(); $association .=3D 's' if !exists $associations{lcfirst($association= )};# UGLY HACK my $cardinality =3D $associations{lcfirst($association)}->other()->= cardinality(); my $setter =3D "set$association"; if ($cardinality =3D~ /N$/) { $setter =3D "add$association"; } $parentObject->$setter($self); } which together with "association =3D> 'Type'" in the above MGEDOntologyCl= assEntry=20 constructor throws no error and produces the following MAGE-ML: <Experiment_assnlist> <Experiment identifier=3D"Etest"> <ExperimentDesign_assn> <ExperimentDesign> <Types_assnlist> <OntologyEntry value=3D"disease_state_design" category=3D"ExperimentDesignType"> <OntologyReference_assn> <DatabaseEntry=20 URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#disease_st= ate_design" accession=3D"#disease_state_design"> <Database_assnref> <Database_ref identifier=3D"www.mged.org:Database:M= O"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> </OntologyEntry> </Types_assnlist> </ExperimentDesign> </ExperimentDesign_assn> Is this an issue or have I got something wrong?.. Also, in case anyone else runs into the same problem I thought I'd mentio= n that one=20 of the modules (MGEDOntologyHelper.pm) has Macintosh style line endings, = which is=20 fine of course, but it totally threw my LINUX Perl interpreter with "Modu= le doesn't=20 evaluate to true" errors, or "Missing right curly bracket" when I tried t= o edit the=20 file... It's a nightmare because the file looks normal in emacs; only wit= h more did I=20 ffinally see the mangled code. Changing the file to "UNIX line endings" c= ured the=20 problem. Finally, is the following code correct for MO age annotation of a biosamp= le: my $ontologyEntry2 =3D Bio::MAGE::Tools::MGEDOntologyClassEntry->new( parentObject =3D> $bioSource, className =3D> 'BioSource', association =3D> 'Characteristics', values =3D> { Age =3D> 'Age', IntitialTimePoint =3D> 'birth', has_measurement =3D> { has_measurement_type =3D> 'relat= ive', TimeUnit =3D> 'years', has_value =3D> 40, } }, ontology =3D> $ontology) } which generates the MAGE-ML: <Characteristics_assnlist> <OntologyEntry value=3D"BioMaterialCharacteristics" category=3D"BioMaterialCharacteristics"> <OntologyReference_assn> <DatabaseEntry=20 URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#BioMateria= lCharacteristics" accession=3D"#BioMaterialCharacteristics"> <Database_assnref> <Database_ref identifier=3D"www.mged.org:Database:MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry value=3D"Age" category=3D"Age"> <OntologyReference_assn> <DatabaseEntry=20 URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#Age" accession=3D"#Age"> <Database_assnref> <Database_ref identifier=3D"www.mged.org:Database:M= O"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry value=3D"has_measurement" category=3D"has_measurement"> <OntologyReference_assn> <DatabaseEntry=20 URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#has_measur= ement" accession=3D"#has_measurement"> <Database_assnref> <Database_ref identifier=3D"www.mged.org:Databa= se:MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry value=3D"Measurement" category=3D"Measurement"> <OntologyReference_assn> <DatabaseEntry=20 URI=3D"http://mged.sourceforge.net/ontologies/MGEDOntology.php#Measuremen= t" accession=3D"#Measurement"> <Database_assnref> <Database_ref identifier=3D"www.mged.org:Da= tabase:MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry> </OntologyEntry> <OntologyEntry value=3D"40" category=3D"has_value"> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Characteristics_assnlist> Many thanks! Pascal ------------------------------------------------------------------------- Pascal H I N G A M P ------------------------------------------------------------------------- Information G=C3=A9nomique et Structurale Universit=C3=A9 de la M=C3= =A9diterran=C3=A9e CNRS UPR 2589 Facult=C3=A9 des Sciences de L= uminy 163 Avenue de Luminy Case 934 D=C3=A9partement de Bio= logie 13288 Marseille cedex 9 France http://biologie.univ-mrs.fr http://www.igs.cnrs-mrs.fr pas...@un... Tel:+33(0)4 91 82 54 35 Mob:+33(0)6 13 54 65 91 Fax:+33(0)4 91 82 54 21 |
From: Jason S. <jas...@gm...> - 2006-05-24 04:02:55
|
Hi Kevin, There is a mailing list you can send this to: mge...@li... The answer is yes - the examples are included in the tarball in the distribution. You can also ask other questions on the list - they are very friendly and helpful. Cheers, jas. On 5/23/06, Jung, Kevin <kj...@li...> wrote: > > > Hi Jason, > > I had some questions about the MAGE Perl API. Are there any example scri= pts > that I can reference? All I really want to do is to be able to take MAGE= -ML > xml files and convert to flat file format for backend data loading into > database. Do you have any suggestions? > > Thanks, > Kevin Jung > Ligand Pharmaceuticals |
From: Jason S. <jas...@gm...> - 2006-05-17 04:11:40
|
Hey Joe, On 5/17/06, Joseph White <jw...@ji...> wrote: > Hi Adam and Jason, > > Since I'm a new svn user and need to learn it anyway, switching to svn > is fine with me. An overlap period might be in order. I already have > Tortoise running on my windos machines; this is a java app that runs on > linux, right? If not, I"m sure linux has something else that will do. > There are a number of frontends for linux, but there is also the standard command line interface that CVS has used for years - the SVN commands are a superset of CVS commands. Cheers, jas. |
From: Adam W. <aw...@sg...> - 2006-05-15 13:03:08
|
Hi, Sorry for the cross-posting, but sourceforge has moved the location of its CVS system. In the email they sent they recommend re-checking out any modules. In particular we probably need to delete/move the current web site files and check them out again from the new CVS location. So i was wondering, who is actively editing the sourceforge website, and if so do you have any files there that are not currently located in CVS? thanks adam -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. |
From: <njo...@eb...> - 2006-04-06 16:19:31
|
Hi Magi ;) I'm new to MAGE-ML and have been scouring the internet for raw data > MAGE-ML parsers. The ArrayExpress Tab2MAGE utility doesn't seem to cater for my needs at present. Does anyone know of a parser that handles the Nimblegen/scan format? Cheers Nath Nathan Johnson Scientific Programmer in Epigenomics EnsEMBL Functional Genomics Team EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, United Kingdom |
From: <ja...@op...> - 2004-09-30 11:09:30
|
Hi Reazur, What type of object was it (what class)? Remember there is a big difference between an 'attribute', an 'association', and a 'slot'. If the documentation isn't clear about this we need to improve the docs. Attributes and associations come directly from the MAGE model. Slots are internal storage spaces that are not defined by the model, but are used by the Perl implementation of MAGEstk. My guess is that you don't want the slots, you want the attributes and associations. Cheers, jas. Reazur Rahman <re...@ge...> writes: > HI > > I was trying to use the method @names = > $obj->get_slot_names() > on a mage object. It seems that this method calls is not working > properly because it returns nothing. > > It seems that there is also some error in documentation (shown below). > Your feedback will be appreciated. Also a brief description of what > "slot" actually means would be nice. > > Thanks > Reazur Rahman > > > @names = > $obj->get_slot_names() > The get_slot_names() method is used to retrieve the name of all slots > defined for a given object. > > Return value: a single slot value, or undef if the slot > has not been initialized. > > Side effects: none |
From: Reazur R. <re...@ge...> - 2004-09-29 14:48:20
|
HI I was trying to use the method @names = $obj->get_slot_names() on a mage object. It seems that this method calls is not working properly because it returns nothing. It seems that there is also some error in documentation (shown below). Your feedback will be appreciated. Also a brief description of what "slot" actually means would be nice. Thanks Reazur Rahman @names = $obj->get_slot_names() The get_slot_names() method is used to retrieve the name of all slots defined for a given object. Return value: a single slot value, or undef if the slot has not been initialized. Side effects: none |
From: Reazur R. <re...@ge...> - 2004-09-24 15:56:10
|
HI I was trying to use the method @names = $obj->get_slot_names() on a mage object. It seems that this method calls is not working properly because it returns nothing. It seems that there is also some error in documentation (shown below). Your feedback will be appreciated. Also a brief description of what "slot" actually means would be nice. Thanks Reazur Rahman @names = $obj->get_slot_names() The get_slot_names() method is used to retrieve the name of all slots defined for a given object. Return value: a single slot value, or undef if the slot has not been initialized. Side effects: none |
From: White, J. <JW...@ti...> - 2004-08-18 15:45:46
|
Hello Bart, =20 It would be best to avoid using BioAssayTuple. It's use creates HUGE = data files. ArrayExpress doesn't accept submissions that use this part = of the MAGE-OM. The more commonly used approach is to use DataInternal = or DataExternal with BioDataCube. There are example scripts available = to review in the 'lib' module in cvs.sf.net/cvsroot/mged: = lib/Perl/script (BioAssay2.dbi being one of them). =20 =20 Cheers,=20 =20 Joe White =20 =20 =20 -----Original Message----- From: mge...@li... = [mailto:mge...@li...]On Behalf Of Bart = Brown Sent: Wednesday, August 18, 2004 10:56 AM To: mge...@li... Subject: [Mged-mage-perl] another newbie question Dear collegues, I have microarray expression data in the form of gpr files but do = not have accession to Genespring and therefore would like to use the createmageml.pl script to transfer our data into mageml format. I have = been trying to write a mapping_file for doing this but have not yet been = able to get the createmageml.pl script to output the BioAssayTuple tag = and its subtags. Does anyone have an example of a mapping_file that I = could use to give me a 'jump start' or just some advice? Thank you very much, =20 Sincerely, Bartley Brown=20 |
From: Bart B. <bb...@en...> - 2004-08-18 14:56:36
|
Dear collegues, I have microarray expression data in the form of gpr files but do = not have accession to Genespring and therefore would like to use the createmageml.pl script to transfer our data into mageml format. I have = been trying to write a mapping_file for doing this but have not yet been = able to get the createmageml.pl script to output the BioAssayTuple tag = and its subtags. Does anyone have an example of a mapping_file that I = could use to give me a 'jump start' or just some advice? Thank you very much, Sincerely, Bartley Brown |