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From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-12-03 20:22:30
|
Hi Gerald, Don't know if you've heard for anyone else but here are my thoughts. The downside is that MAGE-OM and the MAGE-ML.dtd are an OMG standard which cannot, itself, be modified except through an extensive revision process. In fact we are currently working on MAGEv2 but that will probably not be ready for primetime until mid to late 2007. But we should certainly make sure that we cover this use case for protein lysate array (PLA) data. Unfortunately, the format of the modified DTD for caRPLA is very different than the standards so a simple diff doesn't show the differences but it did look like it was from v1.0, not the latest v1.1, the official location is: http://schema.omg.org/lsr/gene_expression/1.0/MAGE-ML.dtd and http://schema.omg.org/lsr/gene_expression/1.0/MAGE-ML.dtd I'm not sure what tool is needed to access the EAP file, it's a new file type to me but is there a UML model that is available? It certainly makes sense to internally use a modified version but are the changes all extensions to existing elements? For MAGEv2 we are leveraging using inheritance in XML schema to make extensions from a base model FuGE (http://fuge.sourceforge.net/). One possible short term solution, especially if the changes are just extensions, is to encode as much as possible in the standard MAGE-ML and then encode the additional information in a separate document based on the extensions and use the identifier attribute to hook up the information between the two. 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 > Gerald Fontenay > Sent: Friday, November 17, 2006 12:34 PM > To: mge...@li... > Cc: GvF...@lb... > Subject: [Mged-mage] Proposed modifications to MAGE-OM for=20 > caRPLA project >=20 >=20 > Hi, >=20 > We would like to get any feedback from members on the list on=20 > proposed=20 > modifications to the MAGE-OM v1.1 model for our caRPLA=20 > project. Thanks=20 > in advance. > --- >=20 > The goal of the caRPLA project is to make the caArray system=20 > compatible=20 > with protein lysate array (PLA) data. We believe modest changes are=20 > required to the MAGE-OM: >=20 > *A new class, PLAFeature, inheriting from Feature, is introduced.=20 > PLAFeature requires composition with Measurement in order to=20 > record the=20 > dilution of the array feature.* > *A new class, PLAReporter, inheriting from Reporter, is introduced.=20 > PLAReporter requires a 1:n assocation with FactorValue in order to=20 > record biologically-significant experimental factor values.* >=20 > An EA project and modified DTD are available at: >=20 > http://sneezy.lbl.gov/caRPLA/EA/caRPLA.EAP > http://sneezy.lbl.gov/caRPLA/XML/ >=20 >=20 > In the EA ( v. 6.0.781 ) project are modified versions of the MAGE-OM=20 > and database schema from caArray 1.4. MAGE-OM was imported into the=20 > project via the MAGE_OM v1.1 MAGE.xmi file available from=20 > http://mged.sourceforge.net/software/docs.php > *All object model modifications required for this project can=20 > be seen in=20 > the "Logical View.Data Model.MAGE-OM.DesignElement Overview" diagram.=20 > They are colored pink/red.* >=20 > The database schema was imported into the project using=20 > Oracle ODBC on=20 > our local caArray 1.4 instance. > *Proposed database schema changes can be seen in the "Logical=20 > View.caRPLA-relevant tables" diagram. They are also colored pink/red.* >=20 > In the XML directory is the modified MAGE-ML DTD. Changes=20 > were made to=20 > the existing DTD model rather than using automatic DTD=20 > generation from=20 > the object model. This was done in order to preserve any=20 > changes made to=20 > the DTD post-generation. >=20 > We would appreciate any feedback, comments, suggestions, etc. >=20 > Thanks again, > Gerald Fontenay > gvf...@lb... >=20 >=20 >=20 >=20 >=20 |
From: Chris S. <sto...@pc...> - 2006-11-21 23:20:41
|
p.s. Some travel support is available Chris On Nov 21, 2006, at 6:04 PM, Chris Stoeckert wrote: > Hi All, > If you have not already done so, please let me know if you will be > attending the MAGE Jamboree to be held at the University of > Pennsylvania Center for Bioinformatics on Dec. 13-15. > > see https://www.cbil.upenn.edu/magewiki/index.php/PhillyMageWorkshop > > A couple updates: > 1. We will have a short open session on "Demystifying MIAME -- > Making your microarray data publishable and accessible" on December > 13th, 10:30 AM - 12 Noon, John Morgan Building - Reunion Hall. > Cathy Ball will explain the MIAME standard and the benefits it > provides to both individual investigators and to the scientific > community. She will also discuss recent debate on MIAME (see for > example Nov. issue of Nature Biotechnology) and address some of the > issues raised. > Helen Parkinson will discuss MAGE-TAB, a new spreadsheet format to > represent microarray experiments. MAGE-TAB has been developed to > make it easier to collect and represent MIAME compliant > experiments. She will also describe plans for its use at the > ArrayExpress public repository. > > 2. MAGE-TAB will be finalized at the Jamboree. Software to create > and load AMGE-TAB will be a major topic > > 3. MAGE Translator developed by the Stanford Microarray Database > will be released at the Jamboree. The MAGE Translator will generate > common formats from MAGE-ML. > > 4. Exploration of OWL parsers for use in MAGE. A parser for OWL 1.1 > is available in Protege 4 using the WonderWeb API. > > Cheers, > Chris > > Chris Stoeckert, Ph.D. > Research Professor, Dept. of Genetics > 1415 Blockley Hall, Center for Bioinformatics > 423 Guardian Dr., University of Pennsylvania > Philadelphia, PA 19104 > Ph: 215-573-4409 FAX: 215-573-3111 > http://www.cbil.upenn.edu > > > ---------------------------------------------------------------------- > --- > 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: Chris S. <sto...@pc...> - 2006-11-21 23:04:52
|
Hi All, If you have not already done so, please let me know if you will be attending the MAGE Jamboree to be held at the University of Pennsylvania Center for Bioinformatics on Dec. 13-15. see https://www.cbil.upenn.edu/magewiki/index.php/PhillyMageWorkshop A couple updates: 1. We will have a short open session on "Demystifying MIAME -- Making your microarray data publishable and accessible" on December 13th, 10:30 AM - 12 Noon, John Morgan Building - Reunion Hall. Cathy Ball will explain the MIAME standard and the benefits it provides to both individual investigators and to the scientific community. She will also discuss recent debate on MIAME (see for example Nov. issue of Nature Biotechnology) and address some of the issues raised. Helen Parkinson will discuss MAGE-TAB, a new spreadsheet format to represent microarray experiments. MAGE-TAB has been developed to make it easier to collect and represent MIAME compliant experiments. She will also describe plans for its use at the ArrayExpress public repository. 2. MAGE-TAB will be finalized at the Jamboree. Software to create and load AMGE-TAB will be a major topic 3. MAGE Translator developed by the Stanford Microarray Database will be released at the Jamboree. The MAGE Translator will generate common formats from MAGE-ML. 4. Exploration of OWL parsers for use in MAGE. A parser for OWL 1.1 is available in Protege 4 using the WonderWeb API. Cheers, Chris Chris Stoeckert, Ph.D. Research Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 http://www.cbil.upenn.edu |
From: Gerald F. <gv...@me...> - 2006-11-17 20:47:08
|
Hi, We would like to get any feedback from members on the list on proposed modifications to the MAGE-OM v1.1 model for our caRPLA project. Thanks in advance. --- The goal of the caRPLA project is to make the caArray system compatible with protein lysate array (PLA) data. We believe modest changes are required to the MAGE-OM: *A new class, PLAFeature, inheriting from Feature, is introduced. PLAFeature requires composition with Measurement in order to record the dilution of the array feature.* *A new class, PLAReporter, inheriting from Reporter, is introduced. PLAReporter requires a 1:n assocation with FactorValue in order to record biologically-significant experimental factor values.* An EA project and modified DTD are available at: http://sneezy.lbl.gov/caRPLA/EA/caRPLA.EAP http://sneezy.lbl.gov/caRPLA/XML/ In the EA ( v. 6.0.781 ) project are modified versions of the MAGE-OM and database schema from caArray 1.4. MAGE-OM was imported into the project via the MAGE_OM v1.1 MAGE.xmi file available from http://mged.sourceforge.net/software/docs.php *All object model modifications required for this project can be seen in the "Logical View.Data Model.MAGE-OM.DesignElement Overview" diagram. They are colored pink/red.* The database schema was imported into the project using Oracle ODBC on our local caArray 1.4 instance. *Proposed database schema changes can be seen in the "Logical View.caRPLA-relevant tables" diagram. They are also colored pink/red.* In the XML directory is the modified MAGE-ML DTD. Changes were made to the existing DTD model rather than using automatic DTD generation from the object model. This was done in order to preserve any changes made to the DTD post-generation. We would appreciate any feedback, comments, suggestions, etc. Thanks again, Gerald Fontenay gvf...@lb... |
From: Chris S. <sto...@pc...> - 2006-10-26 21:16:31
|
Hi Everyone, Please let me know if you are planning to attend the MAGE Jamboree in Philadelphia Dec 13-15. See https://www.cbil.upenn.edu/magewiki/index.php/PhillyMageWorkshop Note that we are planning to have a half day session on Dec. 12 targeting microarray users on "Demystifying MIAME and the MGED Standards." Proposed agenda items so far based on MAGE email threads: MAGE2 modeling Development and use of MAGv2 timeline SampleData Conditions and Characteristics Using ontologies MAGE2 paper plans MAGE-TAB templates MAGE loaders UML2XSD Others? Cheers, Chris Chris Stoeckert, Ph.D. Research Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 http://www.cbil.upenn.edu |
From: Jason S. <jas...@gm...> - 2006-10-14 18:23:09
|
On 10/11/06, Valerie Wagner <val...@sr...> wrote: > > Hi Folks, thanks for all your recent assistance! Our MAGE loader for > the BioWarehouse is nearly complete. > > Another question though: I want to confirm my understanding of the > BioDataCube structure. The type is defined as "any [][][]". My > understanding is that for each QuantitationType (Q), that Q will define > what data type the "any" is via its "dataType" association to > OntologyEntry. Also, the three indexes (B, D, and Q) to the cube can be > in any order and are specified by the "order" attribute of BioDataCube. > Yes. Correct as I understand it. Also, there are three Dimension objects also relevant: * QT Dimension * BA Dimension * DE Dimension Each of these specifies the linear order of the (QuantitationTypes, BioAssays, or DesignElements) as they appear in the cube. > My question is this: given a specific data value, say cube[0][1][2] and > an order "BDQ", how does one back out the specific information for that > B, D, and Q? Is it literally interpreted as (assuming zero-based lists) > "the first B, the second D, and the third Q" listed in the MAGE-ML? Or > is there some other mechanism for pulling out which B, D, and Q a > particular data point is associated with? > Not as listed in the MAGE-ML, but as specified in the three dimensions above. Cheers, jas. |
From: Valerie W. <val...@sr...> - 2006-10-11 16:39:12
|
Hi Michael, Thanks for the slides. I was interested in seeing the plans for the future of MAGE, and I learned a new word, "mathmagically". :) Thanks to the help of those on this list, I've already got the actual parsing code in place for reading in the BioDataCube. I'm just looking for information (or confirmation of my understanding) on how to relate specific data points back to the XML once the data is loaded. cheers, Valerie Miller, Michael D (Rosetta) wrote: > Hi Valerie, > > At a recent MAGE Jamboree at NCI I gave a presentation, the first part > was a bit of the lessons we've learned here using MAGE. > > It's a bit terse but slide 8 was our general approach to the datacube. > Depending on the specific application, the actual data structures will > vary but hopefully the ideas will translate. We essentially create one > result set per bioassy in the datacube where the columns are the QTs and > the rows will be the design element. Then we read the datacube in as a > linear list and depending on the order of the dimensions, pluck out the > values from the list. > > hope this helps, > Michael > >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] On Behalf Of >> Valerie Wagner >> Sent: Wednesday, October 11, 2006 9:03 AM >> To: mge...@li... >> Subject: [Mged-mage] Indexes into the BioDataCube >> >> >> >> Hi Folks, thanks for all your recent assistance! Our MAGE loader for >> the BioWarehouse is nearly complete. >> >> Another question though: I want to confirm my understanding of the >> BioDataCube structure. The type is defined as "any [][][]". My >> understanding is that for each QuantitationType (Q), that Q >> will define >> what data type the "any" is via its "dataType" association to >> OntologyEntry. Also, the three indexes (B, D, and Q) to the >> cube can be >> in any order and are specified by the "order" attribute of >> BioDataCube. >> >> My question is this: given a specific data value, say >> cube[0][1][2] and >> an order "BDQ", how does one back out the specific >> information for that >> B, D, and Q? Is it literally interpreted as (assuming >> zero-based lists) >> "the first B, the second D, and the third Q" listed in the >> MAGE-ML? Or >> is there some other mechanism for pulling out which B, D, and Q a >> particular data point is associated with? >> >> Thanks much, >> 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 |
From: Valerie W. <val...@sr...> - 2006-10-11 16:03:41
|
Hi Folks, thanks for all your recent assistance! Our MAGE loader for the BioWarehouse is nearly complete. Another question though: I want to confirm my understanding of the BioDataCube structure. The type is defined as "any [][][]". My understanding is that for each QuantitationType (Q), that Q will define what data type the "any" is via its "dataType" association to OntologyEntry. Also, the three indexes (B, D, and Q) to the cube can be in any order and are specified by the "order" attribute of BioDataCube. My question is this: given a specific data value, say cube[0][1][2] and an order "BDQ", how does one back out the specific information for that B, D, and Q? Is it literally interpreted as (assuming zero-based lists) "the first B, the second D, and the third Q" listed in the MAGE-ML? Or is there some other mechanism for pulling out which B, D, and Q a particular data point is associated with? Thanks much, Valerie |
From: Valerie W. <val...@sr...> - 2006-09-29 21:06:30
|
Fair enough--thanks for your assistance! cheers, Valerie Miller, Michael D (Rosetta) wrote: > Hi Valerie, > > it is intended for a higher level type (from the documentation): > > "type: The type of biosequence, i.e. gene, exon, UniGene cluster, > fragment, BAC, EST, etc." > >> Are you saying that this BioSequence Type association doesn't >> actually >> tell us the types of the SeqFeatures because people can use >> Descriptions >> or identifiers to determine the type? (And in that case, >> what is meant >> by the BioSequence Type association?) > > I really wasn't saying anything more than I was saying. > >> So >> for arbitrary input, it would be hard to parse an arbitrary >> description >> with any certainty of what might be in it. > > I've seen very few applications use SeqFeature--as an importer/consumer > without knowledge of the source, one can only provide a place to hold > what's in the MAGE elements/objects. How does an importer actually know > much about the BioSequence itself? > > My suggestion was (apparently wrongly) more geared towards an exporter > or in-house application. > > cheers, > Michael > >> -----Original Message----- >> From: Valerie Wagner [mailto:val...@sr...] >> Sent: Friday, September 29, 2006 1:51 PM >> To: Miller, Michael D (Rosetta) >> Cc: Trish Whetzel; mge...@li... >> Subject: Re: [Mged-mage] How to tell SeqFeature type? >> >> >> I'm writing a loader for the BioWarehouse that takes MAGE-ML >> input. So >> for arbitrary input, it would be hard to parse an arbitrary >> description >> with any certainty of what might be in it. If it's the case that the >> BioSequence Type association determines the (single) type of >> SeqFeatures, then that's at least something I can parse. >> >> Are you saying that this BioSequence Type association doesn't >> actually >> tell us the types of the SeqFeatures because people can use >> Descriptions >> or identifiers to determine the type? (And in that case, >> what is meant >> by the BioSequence Type association?) >> >> thanks, >> Valerie >> >> Miller, Michael D (Rosetta) wrote: >>> Hi Trish and Valerie, >>> >>> SeqFeature is Describable so one can add a Description to >> it with text = >>> "FeatureType" and a URI to the appropriate documentation for that >>> particular Feature then add the OntologyEntry using a SO term. >>> >>> But...in truth, when we designed MAGEv1 (and have pretty >> much carried >>> this into FuGE and MAGEv2), to truly model annotating a Sequence was >>> decided to be out of scope. Many users of MAGE form a pseudo-LSID >>> identifier for their genes based on GenBank, RefSeq, >> Entrez, whatever, >>> accession/identifiers then use that sequence database as the >>> Database_ref. Later some other tool/software can come back >> and annotate >>> the genes. >>> >>> But to add limited annotation, I think the above would work >> reasonably >>> well. >>> >>> cheers, >>> Michael >>> >>>> -----Original Message----- >>>> From: mge...@li... >>>> [mailto:mge...@li...] On Behalf Of >>>> Valerie Wagner >>>> Sent: Friday, September 29, 2006 12:41 PM >>>> To: Trish Whetzel >>>> Cc: mge...@li... >>>> Subject: Re: [Mged-mage] How to tell SeqFeature type? >>>> >>>> >>>> Thanks, Trish, that's exactly what I was asking. >>>> >>>> Forgive my ignorance in this area, but can't a BioSequence >> have many >>>> different features associated with it? So are you saying that the >>>> BioSequence in question is only meant to have one type of >> SeqFeature >>>> associated with it? >>>> >>>> Valerie >>>> >>>> Trish Whetzel wrote: >>>>> Hi Valerie, >>>>> >>>>> If I understand the question correctly, the MAGE class >>>> SeqFeature has an >>>>> association to BioSequence which has 4 associations to >>>> OntologyEntry, one >>>>> of which is called Type. The values for this were initially >>>> derived from >>>>> the MGED Ontology (MO) BioSequenceType subclasses, but were >>>>> deprecated in favor of using terms from the Sequence >>>> Ontology (SO). The >>>>> mapping of MO to SO terms can be found at: >>>>> http://song.sourceforge.net/so_mappings.shtml >>>>> >>>>> Trish >>>>> >>>>> >>>>>> How does one discern what type of feature a MAGE >>>> SeqFeature is (gene, >>>>>> binding site, etc.)? >>>> -------------------------------------------------------------- >>>> ----------- >>>>> 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 >>> >>> >> -------------------------------------------------------------- >> ---------- >>> - >>> 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=DEVDE >> V >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage >> >> >> >> > ------------------------------------------------------------------------ > - >> 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=DEVDE > V >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage > > > |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-09-29 21:03:09
|
Hi Valerie, it is intended for a higher level type (from the documentation): "type: The type of biosequence, i.e. gene, exon, UniGene cluster,=20 fragment, BAC, EST, etc." > Are you saying that this BioSequence Type association doesn't=20 > actually=20 > tell us the types of the SeqFeatures because people can use=20 > Descriptions=20 > or identifiers to determine the type? (And in that case,=20 > what is meant=20 > by the BioSequence Type association?) I really wasn't saying anything more than I was saying. > So=20 > for arbitrary input, it would be hard to parse an arbitrary=20 > description=20 > with any certainty of what might be in it. I've seen very few applications use SeqFeature--as an importer/consumer without knowledge of the source, one can only provide a place to hold what's in the MAGE elements/objects. How does an importer actually know much about the BioSequence itself? My suggestion was (apparently wrongly) more geared towards an exporter or in-house application. cheers, Michael > -----Original Message----- > From: Valerie Wagner [mailto:val...@sr...]=20 > Sent: Friday, September 29, 2006 1:51 PM > To: Miller, Michael D (Rosetta) > Cc: Trish Whetzel; mge...@li... > Subject: Re: [Mged-mage] How to tell SeqFeature type? >=20 >=20 > I'm writing a loader for the BioWarehouse that takes MAGE-ML=20 > input. So=20 > for arbitrary input, it would be hard to parse an arbitrary=20 > description=20 > with any certainty of what might be in it. If it's the case that the=20 > BioSequence Type association determines the (single) type of=20 > SeqFeatures, then that's at least something I can parse. >=20 > Are you saying that this BioSequence Type association doesn't=20 > actually=20 > tell us the types of the SeqFeatures because people can use=20 > Descriptions=20 > or identifiers to determine the type? (And in that case,=20 > what is meant=20 > by the BioSequence Type association?) >=20 > thanks, > Valerie >=20 > Miller, Michael D (Rosetta) wrote: > > Hi Trish and Valerie, > >=20 > > SeqFeature is Describable so one can add a Description to=20 > it with text =3D > > "FeatureType" and a URI to the appropriate documentation for that > > particular Feature then add the OntologyEntry using a SO term. > >=20 > > But...in truth, when we designed MAGEv1 (and have pretty=20 > much carried > > this into FuGE and MAGEv2), to truly model annotating a Sequence was > > decided to be out of scope. Many users of MAGE form a pseudo-LSID > > identifier for their genes based on GenBank, RefSeq,=20 > Entrez, whatever, > > accession/identifiers then use that sequence database as the > > Database_ref. Later some other tool/software can come back=20 > and annotate > > the genes. > >=20 > > But to add limited annotation, I think the above would work=20 > reasonably > > well. > >=20 > > cheers, > > Michael > >=20 > >> -----Original Message----- > >> From: mge...@li...=20 > >> [mailto:mge...@li...] On Behalf Of=20 > >> Valerie Wagner > >> Sent: Friday, September 29, 2006 12:41 PM > >> To: Trish Whetzel > >> Cc: mge...@li... > >> Subject: Re: [Mged-mage] How to tell SeqFeature type? > >> > >> > >> Thanks, Trish, that's exactly what I was asking. > >> > >> Forgive my ignorance in this area, but can't a BioSequence=20 > have many=20 > >> different features associated with it? So are you saying that the=20 > >> BioSequence in question is only meant to have one type of=20 > SeqFeature=20 > >> associated with it? > >> > >> Valerie > >> > >> Trish Whetzel wrote: > >>> Hi Valerie, > >>> > >>> If I understand the question correctly, the MAGE class=20 > >> SeqFeature has an=20 > >>> association to BioSequence which has 4 associations to=20 > >> OntologyEntry, one=20 > >>> of which is called Type. The values for this were initially=20 > >> derived from=20 > >>> the MGED Ontology (MO) BioSequenceType subclasses, but were=20 > >>> deprecated in favor of using terms from the Sequence=20 > >> Ontology (SO). The=20 > >>> mapping of MO to SO terms can be found at: > >>> http://song.sourceforge.net/so_mappings.shtml > >>> > >>> Trish > >>> > >>> > >>>> How does one discern what type of feature a MAGE=20 > >> SeqFeature is (gene, > >>>> binding site, etc.)? > >>> > >> -------------------------------------------------------------- > >> ----------- > >>> 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 > >> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge > > &CID=3DDEVDEV > >> _______________________________________________ > >> Mged-mage mailing list > >> Mge...@li... > >> https://lists.sourceforge.net/lists/listinfo/mged-mage > >=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=3DDEVDE > V > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage >=20 >=20 >=20 > ------------------------------------------------------------------------ - > 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-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Valerie W. <val...@sr...> - 2006-09-29 20:51:07
|
I'm writing a loader for the BioWarehouse that takes MAGE-ML input. So for arbitrary input, it would be hard to parse an arbitrary description with any certainty of what might be in it. If it's the case that the BioSequence Type association determines the (single) type of SeqFeatures, then that's at least something I can parse. Are you saying that this BioSequence Type association doesn't actually tell us the types of the SeqFeatures because people can use Descriptions or identifiers to determine the type? (And in that case, what is meant by the BioSequence Type association?) thanks, Valerie Miller, Michael D (Rosetta) wrote: > Hi Trish and Valerie, > > SeqFeature is Describable so one can add a Description to it with text = > "FeatureType" and a URI to the appropriate documentation for that > particular Feature then add the OntologyEntry using a SO term. > > But...in truth, when we designed MAGEv1 (and have pretty much carried > this into FuGE and MAGEv2), to truly model annotating a Sequence was > decided to be out of scope. Many users of MAGE form a pseudo-LSID > identifier for their genes based on GenBank, RefSeq, Entrez, whatever, > accession/identifiers then use that sequence database as the > Database_ref. Later some other tool/software can come back and annotate > the genes. > > But to add limited annotation, I think the above would work reasonably > well. > > cheers, > Michael > >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] On Behalf Of >> Valerie Wagner >> Sent: Friday, September 29, 2006 12:41 PM >> To: Trish Whetzel >> Cc: mge...@li... >> Subject: Re: [Mged-mage] How to tell SeqFeature type? >> >> >> Thanks, Trish, that's exactly what I was asking. >> >> Forgive my ignorance in this area, but can't a BioSequence have many >> different features associated with it? So are you saying that the >> BioSequence in question is only meant to have one type of SeqFeature >> associated with it? >> >> Valerie >> >> Trish Whetzel wrote: >>> Hi Valerie, >>> >>> If I understand the question correctly, the MAGE class >> SeqFeature has an >>> association to BioSequence which has 4 associations to >> OntologyEntry, one >>> of which is called Type. The values for this were initially >> derived from >>> the MGED Ontology (MO) BioSequenceType subclasses, but were >>> deprecated in favor of using terms from the Sequence >> Ontology (SO). The >>> mapping of MO to SO terms can be found at: >>> http://song.sourceforge.net/so_mappings.shtml >>> >>> Trish >>> >>> >>>> How does one discern what type of feature a MAGE >> SeqFeature is (gene, >>>> binding site, etc.)? >>> >> -------------------------------------------------------------- >> ----------- >>> 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 > > > ------------------------------------------------------------------------ > - > 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=DEVDE > V > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > > > > ------------------------------------------------------------------------- > 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: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-09-29 20:45:40
|
Hi Trish and Valerie, SeqFeature is Describable so one can add a Description to it with text = =3D "FeatureType" and a URI to the appropriate documentation for that particular Feature then add the OntologyEntry using a SO term. But...in truth, when we designed MAGEv1 (and have pretty much carried this into FuGE and MAGEv2), to truly model annotating a Sequence was decided to be out of scope. Many users of MAGE form a pseudo-LSID identifier for their genes based on GenBank, RefSeq, Entrez, whatever, accession/identifiers then use that sequence database as the Database_ref. Later some other tool/software can come back and annotate the genes. But to add limited annotation, I think the above would work reasonably well. cheers, Michael > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf Of=20 > Valerie Wagner > Sent: Friday, September 29, 2006 12:41 PM > To: Trish Whetzel > Cc: mge...@li... > Subject: Re: [Mged-mage] How to tell SeqFeature type? >=20 >=20 > Thanks, Trish, that's exactly what I was asking. >=20 > Forgive my ignorance in this area, but can't a BioSequence have many=20 > different features associated with it? So are you saying that the=20 > BioSequence in question is only meant to have one type of SeqFeature=20 > associated with it? >=20 > Valerie >=20 > Trish Whetzel wrote: > > Hi Valerie, > >=20 > > If I understand the question correctly, the MAGE class=20 > SeqFeature has an=20 > > association to BioSequence which has 4 associations to=20 > OntologyEntry, one=20 > > of which is called Type. The values for this were initially=20 > derived from=20 > > the MGED Ontology (MO) BioSequenceType subclasses, but were=20 > > deprecated in favor of using terms from the Sequence=20 > Ontology (SO). The=20 > > mapping of MO to SO terms can be found at: > > http://song.sourceforge.net/so_mappings.shtml > >=20 > > Trish > >=20 > >=20 > >> How does one discern what type of feature a MAGE=20 > SeqFeature is (gene, > >> binding site, etc.)? > >=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-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage ------------------------------------------------------------------------ - 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-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Trish W. <wh...@pc...> - 2006-09-29 19:55:12
|
Hmm... yes I would think that a BioSequence could be annotated with more than one MO BioSequenceType term, however the UML model shows this with a cardinality of 1-1 so I think that limits the annotation to one type per BioSequence. I'll have to defer the reasoning for this (and how it is coded) to others more involved with the model development and generation of MAGE-ML. Trish > Forgive my ignorance in this area, but can't a BioSequence have many > different features associated with it? So are you saying that the > BioSequence in question is only meant to have one type of SeqFeature > associated with it? > > Valerie > > Trish Whetzel wrote: >> Hi Valerie, >> >> If I understand the question correctly, the MAGE class SeqFeature has an >> association to BioSequence which has 4 associations to OntologyEntry, one >> of which is called Type. The values for this were initially derived from >> the MGED Ontology (MO) BioSequenceType subclasses, but were deprecated in >> favor of using terms from the Sequence Ontology (SO). The mapping of MO to >> SO terms can be found at: >> http://song.sourceforge.net/so_mappings.shtml >> >> Trish >> >> >>> How does one discern what type of feature a MAGE SeqFeature is (gene, >>> binding site, etc.)? >> >> ------------------------------------------------------------------------- >> 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: Valerie W. <val...@sr...> - 2006-09-29 19:41:28
|
Thanks, Trish, that's exactly what I was asking. Forgive my ignorance in this area, but can't a BioSequence have many different features associated with it? So are you saying that the BioSequence in question is only meant to have one type of SeqFeature associated with it? Valerie Trish Whetzel wrote: > Hi Valerie, > > If I understand the question correctly, the MAGE class SeqFeature has an > association to BioSequence which has 4 associations to OntologyEntry, one > of which is called Type. The values for this were initially derived from > the MGED Ontology (MO) BioSequenceType subclasses, but were > deprecated in favor of using terms from the Sequence Ontology (SO). The > mapping of MO to SO terms can be found at: > http://song.sourceforge.net/so_mappings.shtml > > Trish > > >> How does one discern what type of feature a MAGE SeqFeature is (gene, >> binding site, etc.)? > > ------------------------------------------------------------------------- > 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: Trish W. <wh...@pc...> - 2006-09-29 19:31:54
|
Hi Valerie, If I understand the question correctly, the MAGE class SeqFeature has an association to BioSequence which has 4 associations to OntologyEntry, one of which is called Type. The values for this were initially derived from the MGED Ontology (MO) BioSequenceType subclasses, but were deprecated in favor of using terms from the Sequence Ontology (SO). The mapping of MO to SO terms can be found at: http://song.sourceforge.net/so_mappings.shtml Trish > How does one discern what type of feature a MAGE SeqFeature is (gene, > binding site, etc.)? |
From: Valerie W. <val...@sr...> - 2006-09-29 15:37:37
|
How does one discern what type of feature a MAGE SeqFeature is (gene, binding site, etc.)? thanks, Valerie |
From: Junmin L. <ju...@pc...> - 2006-09-28 22:49:14
|
Hi, All As I said I would like to discuss about the xml schema in details in the workshop, if time perimitted and people are interested. I have started to collect my thoughts about this on this page: https://www.cbil.upenn.edu/magewiki/index.php/xmlschema Briefly speaking, we need a naming convention for element, type, attribute. And our naming convention should be consistant with FuGE, I hope. But there are some issues with FuGE, I think. 1. propose not using "_" as prefix for children element. e.g. <persson> ... <_affiliations> 2. propose the CCC convention for element, type and LCC for attribute 3. propose element, attribute and type names MUST be in singular form unless the concept itself is plural. 4. The URI used as the target namespace in an XML schema must be a valid URI. 5.Use attributes for data that is semantically tied to the enclosing element. 6.Element names should always be qualified. 7.Attribute names should not be qualified 8.Versioning, major version and minor version 9.Should we define sequence order for the child elements of MAGEroot element? I will start to write MAGE catridge to enforce those rules. ---junmin On Sun, 24 Sep 2006, Miller, Michael D (Rosetta) wrote: > Hi Chris, > > 1) I'm likely more interested in MAGEv2 modeling justification-wise for > making the trip > > 2) Dates look good > > 3) I'm highly likely to attend, especially if it is MAGEv2 modeling. > I'm interested in MAGEstk development but it's not as germane to my work > here at Rosetta Biosoftware. > > thanks for organizing this. > > cheers, > Michael > > -----Original Message----- > From: mge...@li... > [mailto:mge...@li...] On Behalf Of Chris > Stoeckert > Sent: Friday, September 15, 2006 6:54 AM > To: MGED-mage; mged-mage2 > Subject: [Mged-mage2] Next MAGE programming jamboree > > > Hi All, > At the MGED Board meeting in Seattle, there was a vote to hold > the next jamboree in Philadelphia in December/ January so I would like > to set dates before peoples calendars get filled. Also would like to > clarify what people would like to do in Philadelphia (MAGE-wise). The > next jamboree after Philadelphia would be on the west coast in the Bay > area but not sure when that would be held. So questions to the group: > > 1. Do people want to work on MAGE v1 programming or MAGEv2 > modeling in Philadelphia? > 2. How is the week of Dec. 11 for meeting? say the 13th-15th? > 3. Who is likely to attend? (how many people am I likely to be > hosting?) > > Thanks. > Chris > > > Chris Stoeckert, Ph.D. > > Research Associate Professor, Dept. of Genetics > > 1415 Blockley Hall, Center for Bioinformatics > > 423 Guardian Dr., University of Pennsylvania > > Philadelphia, PA 19104 > > Ph: 215-573-4409 FAX: 215-573-3111 > > > |
From: Catherine B. <ba...@ge...> - 2006-09-25 19:59:29
|
Just for us... http://compbiol.plosjournals.org/perlserv/?request=get- document&doi=10.1371/journal.pcbi.0020087 |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-09-25 13:57:55
|
Hi Chris, =20 Sounds good, I'm trying to pull together the results from the last jamboree and reflect that in the task list we had for that. =20 cheers, Michael -----Original Message----- From: mge...@li... [mailto:mge...@li...] On Behalf Of Chris Stoeckert Sent: Sunday, September 24, 2006 1:10 PM To: Miller, Michael D (Rosetta) Cc: mged-mage2; MGED-mage Subject: Re: [Mged-mage2] [Mged-mage] Next MAGE programming jamboree =09 =09 Hi Michael,=20 Great to hear. I've set up a wiki page. All please feel free to add attendees and agenda items (or send them to me). https://www.cbil.upenn.edu/magewiki/index.php/PhillyMageWorkshop I've got meeting rooms booked for Dec. 13-15=20 Chris=20 On Sep 24, 2006, at 3:01 PM, Miller, Michael D (Rosetta) wrote: Hi Chris, =20 1) I'm likely more interested in MAGEv2 modeling justification-wise for making the trip =20 2) Dates look good =20 3) I'm highly likely to attend, especially if it is MAGEv2 modeling. I'm interested in MAGEstk development but it's not as germane to my work here at Rosetta Biosoftware. =20 thanks for organizing this. =20 cheers, Michael -----Original Message----- From: mge...@li... [mailto:mge...@li...] On Behalf Of Chris Stoeckert Sent: Friday, September 15, 2006 6:54 AM To: MGED-mage; mged-mage2 Subject: [Mged-mage2] Next MAGE programming jamboree =09 =09 Hi All,=20 At the MGED Board meeting in Seattle, there was a vote to hold the next jamboree in Philadelphia in December/ January so I would like to set dates before peoples calendars get filled. Also would like to clarify what people would like to do in Philadelphia (MAGE-wise). The next jamboree after Philadelphia would be on the west coast in the Bay area but not sure when that would be held. So questions to the group: 1. Do people want to work on MAGE v1 programming or MAGEv2 modeling in Philadelphia? 2. How is the week of Dec. 11 for meeting? say the 13th-15th? 3. Who is likely to attend? (how many people am I likely to be hosting?) Thanks. Chris Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 =09 ------------------------------------------------------------------------ - 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 =09 http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V_______________________________________________ Mged-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Chris S. <sto...@pc...> - 2006-09-24 20:10:22
|
Hi Michael, Great to hear. I've set up a wiki page. All please feel free to add attendees and agenda items (or send them to me). https://www.cbil.upenn.edu/magewiki/index.php/PhillyMageWorkshop I've got meeting rooms booked for Dec. 13-15 Chris On Sep 24, 2006, at 3:01 PM, Miller, Michael D (Rosetta) wrote: > Hi Chris, > > 1) I'm likely more interested in MAGEv2 modeling justification-wise > for making the trip > > 2) Dates look good > > 3) I'm highly likely to attend, especially if it is MAGEv2 > modeling. I'm interested in MAGEstk development but it's not as > germane to my work here at Rosetta Biosoftware. > > thanks for organizing this. > > cheers, > Michael > -----Original Message----- > From: mge...@li... [mailto:mged-mage2- > bo...@li...] On Behalf Of Chris Stoeckert > Sent: Friday, September 15, 2006 6:54 AM > To: MGED-mage; mged-mage2 > Subject: [Mged-mage2] Next MAGE programming jamboree > > Hi All, > At the MGED Board meeting in Seattle, there was a vote to hold the > next jamboree in Philadelphia in December/ January so I would like > to set dates before peoples calendars get filled. Also would like > to clarify what people would like to do in Philadelphia (MAGE- > wise). The next jamboree after Philadelphia would be on the west > coast in the Bay area but not sure when that would be held. So > questions to the group: > > 1. Do people want to work on MAGE v1 programming or MAGEv2 modeling > in Philadelphia? > 2. How is the week of Dec. 11 for meeting? say the 13th-15th? > 3. Who is likely to attend? (how many people am I likely to be > hosting?) > > Thanks. > Chris > > Chris Stoeckert, Ph.D. > Research Associate Professor, Dept. of Genetics > 1415 Blockley Hall, Center for Bioinformatics > 423 Guardian Dr., University of Pennsylvania > Philadelphia, PA 19104 > Ph: 215-573-4409 FAX: 215-573-3111 > > ---------------------------------------------------------------------- > --- > 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: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-09-24 19:01:20
|
Hi Chris, =20 1) I'm likely more interested in MAGEv2 modeling justification-wise for making the trip =20 2) Dates look good =20 3) I'm highly likely to attend, especially if it is MAGEv2 modeling. I'm interested in MAGEstk development but it's not as germane to my work here at Rosetta Biosoftware. =20 thanks for organizing this. =20 cheers, Michael -----Original Message----- From: mge...@li... [mailto:mge...@li...] On Behalf Of Chris Stoeckert Sent: Friday, September 15, 2006 6:54 AM To: MGED-mage; mged-mage2 Subject: [Mged-mage2] Next MAGE programming jamboree =09 =09 Hi All,=20 At the MGED Board meeting in Seattle, there was a vote to hold the next jamboree in Philadelphia in December/ January so I would like to set dates before peoples calendars get filled. Also would like to clarify what people would like to do in Philadelphia (MAGE-wise). The next jamboree after Philadelphia would be on the west coast in the Bay area but not sure when that would be held. So questions to the group: 1. Do people want to work on MAGE v1 programming or MAGEv2 modeling in Philadelphia? 2. How is the week of Dec. 11 for meeting? say the 13th-15th? 3. Who is likely to attend? (how many people am I likely to be hosting?) Thanks. Chris Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 |
From: Adam W. <aw...@sg...> - 2006-09-20 15:50:26
|
no don't worry Jason, the phpwiki was a test wiki that was setup at a previous jamboree, but i think it is no longer used Jason Stewart wrote: > Hi all, > > On 9/19/06, Miller, Michael D (Rosetta) <Mic...@ro...> > wrote: >> Hi All, >> >> Would these be appropriate to organize and move to the Wiki page? >> > > Hmmm.... > > Where is the wiki hosted? Is it inside htdocs/ on SF? Or was it > *outside* htdocs/ on SF? Or is it someplace else? Because there was an > old Twiki installation that me and Steve set up *years* back that > never got used, that I deleted, and there was also a phpwiki tarball > that I removed, but I also think there may have been a phpwiki > directory that I removed. > > I'm wondering if I just clobbered the wiki :-( > > jas. > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-09-20 15:20:07
|
Hi Jason, And I thought since most of your lists were papers, presentations and such like, that it would be appropriate for those to be on the wiki. Any actual development work or documentation should, of course, stay on the source forge site unless it is totally out of date, then it could go to the wiki site as a historical artifact. cheers, Michael > -----Original Message----- > From: Kjell Petersen [mailto:Kje...@bc...]=20 > Sent: Wednesday, September 20, 2006 2:27 AM > To: Jason Stewart > Cc: Miller, Michael D (Rosetta); Adam Witney; Junmin Liu; MGED-mage > Subject: Re: [Mged-mage] Fwd: SourceForge.net Support:=20 > Over-quota notice for project: mged >=20 >=20 > Hi Jas, >=20 > I think you can relax, the wiki pages in use these days are hosted at=20 > Upenn :) >=20 > K. >=20 > Jason Stewart wrote: > > Hi all, > > > > On 9/19/06, Miller, Michael D (Rosetta)=20 > <Mic...@ro...> wrote: > > =20 > >> Hi All, > >> > >> Would these be appropriate to organize and move to the Wiki page? > >> > >> =20 > > > > Hmmm.... > > > > Where is the wiki hosted? Is it inside htdocs/ on SF? Or was it > > *outside* htdocs/ on SF? Or is it someplace else? Because=20 > there was an > > old Twiki installation that me and Steve set up *years* back that > > never got used, that I deleted, and there was also a phpwiki tarball > > that I removed, but I also think there may have been a phpwiki > > directory that I removed. > > > > I'm wondering if I just clobbered the wiki :-( > > > > jas. > > > >=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-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > =20 |
From: Kjell P. <Kje...@bc...> - 2006-09-20 09:27:23
|
Hi Jas, I think you can relax, the wiki pages in use these days are hosted at Upenn :) K. Jason Stewart wrote: > Hi all, > > On 9/19/06, Miller, Michael D (Rosetta) <Mic...@ro...> wrote: > >> Hi All, >> >> Would these be appropriate to organize and move to the Wiki page? >> >> > > Hmmm.... > > Where is the wiki hosted? Is it inside htdocs/ on SF? Or was it > *outside* htdocs/ on SF? Or is it someplace else? Because there was an > old Twiki installation that me and Steve set up *years* back that > never got used, that I deleted, and there was also a phpwiki tarball > that I removed, but I also think there may have been a phpwiki > directory that I removed. > > I'm wondering if I just clobbered the wiki :-( > > jas. > > ------------------------------------------------------------------------- > 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: Jason S. <jas...@gm...> - 2006-09-20 08:07:38
|
Hi all, On 9/19/06, Miller, Michael D (Rosetta) <Mic...@ro...> wrote: > Hi All, > > Would these be appropriate to organize and move to the Wiki page? > Hmmm.... Where is the wiki hosted? Is it inside htdocs/ on SF? Or was it *outside* htdocs/ on SF? Or is it someplace else? Because there was an old Twiki installation that me and Steve set up *years* back that never got used, that I deleted, and there was also a phpwiki tarball that I removed, but I also think there may have been a phpwiki directory that I removed. I'm wondering if I just clobbered the wiki :-( jas. |