From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2007-03-23 16:55:49
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hi junmin, that's great work, if i could get a copy of the presentation when it's ready, that would be much appreciated. hi don, > > a) There is thought to be a strong requirement to have=20 > exactly one=20 > > MAGE-TAB parser in one body of code in one language that=20 > can be used from=20 > > either a Java or a Perl programming environment. =20 > Satisfying this requirement=20 > > would ensure that MAGE-TAB never destroys itself on the=20 > shoals of disagreeing=20 > > acceptors. i think this is a great requirement, similar to the OMG compliancy section, but i have one caveat with the wording. yes, we definitely should have as a goal a definitive MAGE-TAB parser that has a mode that verifies that a set of files is MAGE-TAB compliant (including resolving the references between the files). And it should have a mode that developers could certainly use as the basis of their import implementation. > exactly one=20 > > MAGE-TAB parser in one body of code in one language that=20 > can be used from=20 > > either a Java or a Perl programming environment. =20 my caveat is that there is no problem having more than one, often for efficiency reasons for an application there would be a parser tuned to specific database schema and additional application rules for standard, compliant MAGE-TAB files (for instance, the application rules might restrict MAGE-TAB to require certain columns for the application that in general aren't required). i would change the wording to: > exactly one official validating MAGE-TAB parser in one body of code in one language that=20 > can also be used from=20 > > either a Java or a Perl programming environment by any import application. note that if it is in one language there will be by necessity, i think, a bit of an impedance using it in a different language. cheers, michael =20 > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf=20 > Of Junmin Liu > Sent: Friday, March 23, 2007 9:17 AM > To: Don Maier > Cc: mged-mage2; MGED-mage > Subject: Re: [Mged-mage2] MGED Jamboree next week - March 27-30! >=20 > Hi, Don and Jamboree attendees, > Since last Oct., for one of the requirement of our in-house=20 > data loading=20 > pipeline, we developed an extendable framework MR_Ti and a set of=20 > toolkits to help loading MIAMI-compliant documents in=20 > different formats=20 > into our GUS schema. Chris has suggested me to present this on the=20 > Jamboree to get feedback and to see if it can be useful to the=20 > communities. >=20 > Note MAGE-Tab is part of our pipeline, we have started to=20 > generate and=20 > load MAGE-Tabs to GUS, we will also like to show public the files we=20 > have and make sure they are exchangable and compliant with=20 > MAGE-Tab spec.=20 > 1.0 release. >=20 > Thanks, > ---junmin >=20 >=20 >=20 > On Wed, 21 Mar 2007, Don Maier wrote: >=20 > > Hi friends, > > > > We're looking forward to seeing and meeting with you in=20 > next week in sunny=20 > > California. Current forecasts are for a cloudy Tuesday,=20 > but a sunny=20 > > remainder of the week in the upper 60's. > > > > Here's my current list of attendees and agenda. Please=20 > let me know if you=20 > > wish to contribute any more bodies or agenda items! > > > > Regards, > > Don Maier > > > > > > MAGE Jamboree: March 27 - 30 > > Stanford University: Clark Center, Rm. 362 > > > > Attendees: > > > > 1) Cathy Ball (SMD) > > 2) Cate Beauheim (Stanford) > > 3) Alvis Brazma (EBI) > > 4) Steve Chervitz (Affymetrix) > > 5) Junmin Liu (U. Penn) > > 6) Don Maier (SMD) > > 7) Tim Rayner (EBI) > > 8) Ugis Sarkans (EBI) > > 9) Paul Spellman (Lawrence Berkeley National Laboratory) > > 10) Joe White (Dana-Farber/Harvard Cancer Center) > > > > > > Agenda: > > > > 1) Tim - Final version of MAGE-TAB > > > > 2) Alvis/Ugis - MAGE-TAB object model: > > > > a) Possible move to FUGE-TAB > > > > b) Discussion of basic concepts (no formal proposal yet). > > > > 3) Don - The "one-parser" requirement and how to satisfy=20 > it for MAGE-TAB: > > > > a) There is thought to be a strong requirement to have=20 > exactly one=20 > > MAGE-TAB parser in one body of code in one language that=20 > can be used from=20 > > either a Java or a Perl programming environment. =20 > Satisfying this requirement=20 > > would ensure that MAGE-TAB never destroys itself on the=20 > shoals of disagreeing=20 > > acceptors. > > > > b) Proposal for how to satisfy this requirement. >=20 |