From suzi at fruitfly.org Tue Sep 13 12:27:14 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Tue, 13 Sep 2005 18:27:14 +0200 Subject: [DAS2] Allen wins big! Message-ID: <9839782e4ca7cb8c16fa6463b399482c@fruitfly.org> Sitting here at the MGED meeting and Allen Day just won (2nd) prize in the poster competition for his work on Assay/DAS2. -S (and for those who are interested E.SIderis got 1st for MEditor, missed the name of the other -Xie?- who tied Allen for 2nd). From allenday at ucla.edu Fri Sep 16 04:56:13 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 16 Sep 2005 01:56:13 -0700 Subject: [DAS2] Allen wins big! In-Reply-To: <9839782e4ca7cb8c16fa6463b399482c@fruitfly.org> References: <9839782e4ca7cb8c16fa6463b399482c@fruitfly.org> Message-ID: <5c24dcc305091601567aa04958@mail.gmail.com> /me takes a bow. I didn't even show the way genome and assay das integrate, beyond the fact that they both type records into ontologies. They really liked the idea of using URIs as XML record identifiers -- I'm going to push to have this incorporated to FuGE and MAGE2. -Allen On 9/13/05, Suzanna Lewis wrote: > > Sitting here at the MGED meeting and Allen Day just won (2nd) prize in > the poster competition for his work on Assay/DAS2. > > -S > > (and for those who are interested E.SIderis got 1st for MEditor, missed > the name of the other -Xie?- who tied Allen for 2nd). > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From allenday at ucla.edu Wed Sep 21 11:04:20 2005 From: allenday at ucla.edu (Allen Day) Date: Wed, 21 Sep 2005 08:04:20 -0700 (PDT) Subject: [DAS2] error 402 Message-ID: I was just perusing the error codes table and found this gem: 402 Payment Required THIS IS HOW LINCOLN AND ED HOPE TO MAKE THEIR FORTUNES.... -Allen From edgrif at sanger.ac.uk Wed Sep 21 12:04:17 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Wed, 21 Sep 2005 17:04:17 +0100 (BST) Subject: [DAS2] error 402 In-Reply-To: References: Message-ID: > I was just perusing the error codes table and found this gem: > > 402 Payment Required THIS IS HOW LINCOLN AND ED HOPE TO MAKE THEIR FORTUNES.... Gee, I just don't know how that got there....sigh...;-) Ed-still-not-rich -- ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus | | Hinxton, Cambridge CB10 1HH | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From jgrg at sanger.ac.uk Wed Sep 28 09:28:01 2005 From: jgrg at sanger.ac.uk (James Gilbert) Date: Wed, 28 Sep 2005 14:28:01 +0100 Subject: [DAS2] Nested features? Message-ID: Hi, I have been looking at the example of features under the "The Das2XML- Formatted Feature Response" heading on: http://biodas.org/documents/das2/das2_get.html How do I represent the translation region within a transcript which contains UTRs? I don't think the example does. I think the definition for das:phase needs to be tied down. Is it the (zero based) index of the dna string where you start the traslation in the exon, or is it the index in the codon broken by the splice site? James ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ James G.R. Gilbert The Morgan Building, Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH From suzi at fruitfly.org Tue Sep 13 16:27:14 2005 From: suzi at fruitfly.org (Suzanna Lewis) Date: Tue, 13 Sep 2005 18:27:14 +0200 Subject: [DAS2] Allen wins big! Message-ID: <9839782e4ca7cb8c16fa6463b399482c@fruitfly.org> Sitting here at the MGED meeting and Allen Day just won (2nd) prize in the poster competition for his work on Assay/DAS2. -S (and for those who are interested E.SIderis got 1st for MEditor, missed the name of the other -Xie?- who tied Allen for 2nd). From allenday at ucla.edu Fri Sep 16 08:56:13 2005 From: allenday at ucla.edu (Allen Day) Date: Fri, 16 Sep 2005 01:56:13 -0700 Subject: [DAS2] Allen wins big! In-Reply-To: <9839782e4ca7cb8c16fa6463b399482c@fruitfly.org> References: <9839782e4ca7cb8c16fa6463b399482c@fruitfly.org> Message-ID: <5c24dcc305091601567aa04958@mail.gmail.com> /me takes a bow. I didn't even show the way genome and assay das integrate, beyond the fact that they both type records into ontologies. They really liked the idea of using URIs as XML record identifiers -- I'm going to push to have this incorporated to FuGE and MAGE2. -Allen On 9/13/05, Suzanna Lewis wrote: > > Sitting here at the MGED meeting and Allen Day just won (2nd) prize in > the poster competition for his work on Assay/DAS2. > > -S > > (and for those who are interested E.SIderis got 1st for MEditor, missed > the name of the other -Xie?- who tied Allen for 2nd). > > _______________________________________________ > DAS2 mailing list > DAS2 at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2 > From allenday at ucla.edu Wed Sep 21 15:04:20 2005 From: allenday at ucla.edu (Allen Day) Date: Wed, 21 Sep 2005 08:04:20 -0700 (PDT) Subject: [DAS2] error 402 Message-ID: I was just perusing the error codes table and found this gem: 402 Payment Required THIS IS HOW LINCOLN AND ED HOPE TO MAKE THEIR FORTUNES.... -Allen From edgrif at sanger.ac.uk Wed Sep 21 16:04:17 2005 From: edgrif at sanger.ac.uk (Ed Griffiths) Date: Wed, 21 Sep 2005 17:04:17 +0100 (BST) Subject: [DAS2] error 402 In-Reply-To: References: Message-ID: > I was just perusing the error codes table and found this gem: > > 402 Payment Required THIS IS HOW LINCOLN AND ED HOPE TO MAKE THEIR FORTUNES.... Gee, I just don't know how that got there....sigh...;-) Ed-still-not-rich -- ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER ** ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus | | Hinxton, Cambridge CB10 1HH | | | | email: edgrif at sanger.ac.uk Tel: +44-1223-496844 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From jgrg at sanger.ac.uk Wed Sep 28 13:28:01 2005 From: jgrg at sanger.ac.uk (James Gilbert) Date: Wed, 28 Sep 2005 14:28:01 +0100 Subject: [DAS2] Nested features? Message-ID: Hi, I have been looking at the example of features under the "The Das2XML- Formatted Feature Response" heading on: http://biodas.org/documents/das2/das2_get.html How do I represent the translation region within a transcript which contains UTRs? I don't think the example does. I think the definition for das:phase needs to be tied down. Is it the (zero based) index of the dna string where you start the traslation in the exon, or is it the index in the codon broken by the splice site? James ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ James G.R. Gilbert The Morgan Building, Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH