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From: Catherine B. <ba...@ge...> - 2006-03-08 23:20:11
|
Hi all, Just a heads up -- there will be a MAGE jamboree at the NCI (in Bethesda, MD) May 8-12. Cheers, Cathy |
From: Trish W. <wh...@pc...> - 2006-01-27 18:35:49
|
The MO Refactoring call has been confirmed for Monday, Jan. 30 from 10-11 EST, 3-4 GMT. The goal of the call is to prioritize the items listed on the wiki: https://www.cbil.upenn.edu/magewiki/index.php/MgedOntologyRefactoring in terms of a time frame that the items can be delivered for various releases of the MGED Ontology. Talk to you Monday, Trish |
From: Junmin L. <ju...@pc...> - 2006-01-17 17:07:40
|
Using external standard makes sense and at least improve the Unit part of MO. For example, I sent out email to question about the the way TimeUnit in MO presents: days, hours, minutes, months, seconds, weeks. All of the "s" after the unit name are truly language-dependant. In English, we say "5 minutes", in others, they don't. The NIST guide suggests "5 m" to be language-independant. Also many of these tiny little things make MO vulnerable to outside criticizing. ---junmin On Tue, 17 Jan 2006, Miller, Michael D (Rosetta) wrote: > Hi All, > > some of you may have seen this already but it looks like we finally have > a good reference for units so don't have to reinvent the wheel. > > the nice thing is that, java at least, will be supporting it directly in > a not so future release. > > NIST site with links to info: http://physics.nist.gov/cuu/Units/ > > Proposed java support: http://www.javalobby.org/java/forums/t61584.html > > cheers, > Michael > > Michael Miller > Lead Software Developer > Rosetta Biosoftware Business Unit > www.rosettabio.com > > |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-01-17 16:17:30
|
Hi All, =20 some of you may have seen this already but it looks like we finally have a good reference for units so don't have to reinvent the wheel. =20 the nice thing is that, java at least, will be supporting it directly in a not so future release. =20 NIST site with links to info: http://physics.nist.gov/cuu/Units/ =20 Proposed java support: http://www.javalobby.org/java/forums/t61584.html =20 cheers, Michael =20 Michael Miller=20 Lead Software Developer=20 Rosetta Biosoftware Business Unit=20 www.rosettabio.com=20 =20 |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-01-14 18:19:16
|
Hi All, Jason is right that we can't fit it into MAGE v1 in any form but in thinking further about Arto's suggestion, there is merit in stating default naming authorities and their namespaces up front for brevity sake that could be included in MAGE v2. I think it would be a mistake, tho, to confound it with XML namespaces, either there is some way to do this for generic URNs, as part of that specification, or I would suggest specifying a way in FuGE itself. But, I don't think this will necessarily prevent the consistency of format problems Arto's email was concerned with. cheers, Michael > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf Of=20 > Jason Stewart > Sent: Thursday, January 12, 2006 5:24 AM > To: mge...@li... > Subject: Fwd: [Mged-mage] MAGE-ML identifiers >=20 >=20 > sorry meant to send this to the list > ---------- Forwarded message ---------- > From: Jason Stewart <jas...@gm...> > Date: Jan 12, 2006 6:52 PM > Subject: Re: [Mged-mage] MAGE-ML identifiers > To: Arto Viitanen <art...@cs...> >=20 >=20 > Hi, >=20 > On 1/12/06, Arto Viitanen <art...@cs...> wrote: > > Why MAGE-ML identifiers do not use XML namespace features? >=20 > MAGE-ML was written to only support DTD. It would need to be rewritten > using a different schema language to support namespace properly. >=20 > That is one of the plans (I think?) with MAGE2. >=20 > Cheers, jas. >=20 >=20 > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep=20 > through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. =20 > DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id=16865&op=3Dick > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage >=20 >=20 |
From: Arto V. <art...@cs...> - 2006-01-13 06:32:08
|
Miller, Michael D (Rosetta) wrote: > Hi Arto, > > Junmin is pretty much correct here. > > It actually doesn't matter what standard people use, they can still > abuse it. > > Also, these LSID identifiers are not specific to XML, they are specific > to the object itself and are usable outside the context of XML. > Yes, I know. I was only suggesting XML namespaces, since it has this default namespace feature, which would help in several (potential) problems. -- Arto Viitanen, CSC Espoo, Finland |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-01-12 17:37:38
|
Hi Arto, Junmin is pretty much correct here. It actually doesn't matter what standard people use, they can still abuse it. Also, these LSID identifiers are not specific to XML, they are specific to the object itself and are usable outside the context of XML. cheers, Michael > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf Of Junmin Liu > Sent: Thursday, January 12, 2006 9:30 AM > To: Arto Viitanen > Cc: mge...@li... > Subject: Re: [Mged-mage] MAGE-ML identifiers >=20 >=20 > Hi, Arto, > I may not have the complete the answer for this. >=20 > There is a widely recoginzed problem using URI namespace. esp=20 > for this=20 > field, for URI can be used differently and explained in=20 > different ways.=20 > So people propose to use URN, which is the LSID coupling the=20 > naming space=20 > and data-retrieving information. >=20 > ---junmin >=20 >=20 >=20 > On Thu, 12 Jan 2006, Arto Viitanen wrote: >=20 > > Why MAGE-ML identifiers do not use XML namespace features? I know > > they are based on Life Sciences Identifiers, which base on=20 > URN like XML > > identifiers, but there is a small difference. In MAGE-ML,=20 > identifiers are > > of form Institute:Class:id. Problem is, someones drop the=20 > Institute, and > > some write it in different ways. Someones write the Class,=20 > someone don't. > > > > I suggest, that Institute:Class is replaced with=20 > Insitutete_Class, which is > > defined on start of the XML in MAGE-ML element, like > > > > <mage:MAGE-ML identifier=3D"our_experiment_file > > xmlns:ebi_compound=3D"http://ebi.ac.uk/Compound" > > xmlns:ebi_lc=3D"http://ebi.ac.uk/LabelCompound" > > xmlns=3D"http://our.organization" > > xmlns:mage=3D"http://www.omg.org/mage"> > > .. > > </mage:MAGE-ML> > > > > This way, the home institute will be assumed, so there is=20 > no problem with > > several MAGE-ML files containing same identifier (bioassay-1, etc.) > > > > --=20 > > Arto Viitanen, CSC > > Espoo, Finland > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep=20 > through log files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. =20 > DOWNLOAD SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Mged-mage mailing list > > Mge...@li... > > https://lists.sourceforge.net/lists/listinfo/mged-mage > > >=20 >=20 > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep=20 > through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. =20 > DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage >=20 >=20 |
From: Junmin L. <ju...@pc...> - 2006-01-12 17:30:58
|
Hi, Arto, I may not have the complete the answer for this. There is a widely recoginzed problem using URI namespace. esp for this field, for URI can be used differently and explained in different ways. So people propose to use URN, which is the LSID coupling the naming space and data-retrieving information. ---junmin On Thu, 12 Jan 2006, Arto Viitanen wrote: > Why MAGE-ML identifiers do not use XML namespace features? I know > they are based on Life Sciences Identifiers, which base on URN like XML > identifiers, but there is a small difference. In MAGE-ML, identifiers are > of form Institute:Class:id. Problem is, someones drop the Institute, and > some write it in different ways. Someones write the Class, someone don't. > > I suggest, that Institute:Class is replaced with Insitutete_Class, which is > defined on start of the XML in MAGE-ML element, like > > <mage:MAGE-ML identifier="our_experiment_file > xmlns:ebi_compound="http://ebi.ac.uk/Compound" > xmlns:ebi_lc="http://ebi.ac.uk/LabelCompound" > xmlns="http://our.organization" > xmlns:mage="http://www.omg.org/mage"> > .. > </mage:MAGE-ML> > > This way, the home institute will be assumed, so there is no problem with > several MAGE-ML files containing same identifier (bioassay-1, etc.) > > -- > Arto Viitanen, CSC > Espoo, Finland > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Jason S. <jas...@gm...> - 2006-01-12 13:23:54
|
sorry meant to send this to the list ---------- Forwarded message ---------- From: Jason Stewart <jas...@gm...> Date: Jan 12, 2006 6:52 PM Subject: Re: [Mged-mage] MAGE-ML identifiers To: Arto Viitanen <art...@cs...> Hi, On 1/12/06, Arto Viitanen <art...@cs...> wrote: > Why MAGE-ML identifiers do not use XML namespace features? MAGE-ML was written to only support DTD. It would need to be rewritten using a different schema language to support namespace properly. That is one of the plans (I think?) with MAGE2. Cheers, jas. |
From: Arto V. <art...@cs...> - 2006-01-12 09:02:48
|
Why MAGE-ML identifiers do not use XML namespace features? I know they are based on Life Sciences Identifiers, which base on URN like XML identifiers, but there is a small difference. In MAGE-ML, identifiers are of form Institute:Class:id. Problem is, someones drop the Institute, and some write it in different ways. Someones write the Class, someone don't. I suggest, that Institute:Class is replaced with Insitutete_Class, which is defined on start of the XML in MAGE-ML element, like <mage:MAGE-ML identifier="our_experiment_file xmlns:ebi_compound="http://ebi.ac.uk/Compound" xmlns:ebi_lc="http://ebi.ac.uk/LabelCompound" xmlns="http://our.organization" xmlns:mage="http://www.omg.org/mage"> .. </mage:MAGE-ML> This way, the home institute will be assumed, so there is no problem with several MAGE-ML files containing same identifier (bioassay-1, etc.) -- Arto Viitanen, CSC Espoo, Finland |
From: Trish W. <wh...@pc...> - 2006-01-06 22:45:19
|
Hi Helen, Can you list which file formats are in the special cases OR is this information posted somewhere? Trish On Fri, 6 Jan 2006, Helen Parkinson wrote: > Tina > > we have done some work with the tiling path arrays for yeast, we developed a > coding whereby we maintain the cel file as a data external file, converting > these data to mage is not practical, these data are not public yet, but I can > provide an example if you like. In the MAGE discussions we decided to a make > a special case for some file formats, where it's impractical to do a > conversion to a delimited file, > > cheers > > Helen > > Tina Boussard wrote: > >> Hi All, >> >> Does anyone have any experience with Affy's new exon arrays? I have heard >> that the files are much larger than Affy's other gene expression arrays. >> Has anyone tried to export this into mage-ml? If so, I would be >> interested to hear your experience. >> >> Cheers, >> >> Tina B. >> >> >> Tina Hernandez-Boussard, Ph.D. >> Scientific Curator/Computational Biologist, PharmGKB >> Stanford University >> 300 Pasteur Drive >> Stanford, CA 94305-5120 >> >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep through log >> files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage > > > -- > Helen Parkinson, PhD > Curation Coordinator > Microarray Informatics Team, EBI > > and > > Seconded Scientific Programme Manager > NCRI Cancer Informatics Initiative > www.cancerinformatics.org.uk > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Fuge-devel mailing list > Fug...@li... > https://lists.sourceforge.net/lists/listinfo/fuge-devel > |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-01-06 22:18:31
|
Hi Tina, Kind of my take on this at the December meeting was that conceptually, the data is a n-dimension cube with dimensions objects to contain the dimension elements for each axis. For mage v2, we decided the MeasuredBioAssayData will only have two-dimensions, design element and quantitation type. =20 But in the practical world, if software is available for producing the design element dimension and/or quantitation type dimension from the cube itself and the software is available without unreasonable constraints on its use, then that format is acceptable. A CEL file would fulfill that requirement. cheers, Michael > -----Original Message----- > From: fug...@li...=20 > [mailto:fug...@li...] On Behalf Of=20 > Tina Boussard > Sent: Friday, January 06, 2006 12:11 PM > To: Steve Chervitz > Cc: Tina Boussard; 'mge...@li...' MAGE;=20 > fug...@li...; Helen Parkinson > Subject: [Fuge-devel] Re: [Mged-mage] Re: MAGEv2 >=20 >=20 > Hi All, >=20 > It would be great if we could have the cel file and other such =20 > extremely large files as external data files and not converted into =20 > mage, as the exchange of these data would be impractical. >=20 > Steve, I think that we are more interested in getting all of the =20 > annotation data for these exon arrays into MAGE, such as the=20 > data you =20 > will be generating in NetAffx. We will also need to be sure that =20 > these data fit nicely into FUG-O. When you mentioned only=20 > converting =20 > a sub-set of the data, is this what you had in mind? Will you be =20 > going to the next jam in Benicia 3/7-3/10? > It would be great if we could add the exon arrays to the agenda. >=20 >=20 > Cheers, >=20 > Tina B. >=20 >=20 > On Jan 6, 2006, at 1:22 AM, Helen Parkinson wrote: > > Tina > > > > we have done some work with the tiling path arrays for yeast, we =20 > > developed a coding whereby we maintain the cel file as a data =20 > > external file, converting these data to mage is not practical, =20 > > these data are not public yet, but I can provide an example if you =20 > > like. In the MAGE discussions we decided to a make a special case =20 > > for some file formats, where it's impractical to do a=20 > conversion to =20 > > a delimited file, > > > > cheers > > > > Helen >=20 >=20 > On Jan 4, 2006, at 1:14 PM, Steve Chervitz wrote: >=20 > > Tina, > > > > I am responsible for generating the NetAffx annotation files for =20 > > the exon > > array and no, I have not (yet) tried exporting into MAGE-ML=20 > format. =20 > > I'm also > > interested in hearing ideas about the best way to approach it. =20 > > Dealing with > > this type of data will also help inform MAGE v2 development. > > > > The main consideration is the increased amount and complexity of =20 > > data to be > > encoded. There are 1.4 million probe sets, vs. 54 million for HG-=20 > > U133 Plus > > 2.0 (which produces a 90 MB zipped annotation MAGE-ML file). > > > > There are more types of design-time data for each probe set and new > > hierarchical levels: probe sets are grouped into exon clusters and =20 > > further > > into transcript clusters, which have their own types of associated > > annotations. Expression results will also have new encoding =20 > > requirements and > > will be much larger (e.g., there is a 1GB binary CEL file with =20 > > sample data > > on our site). > > > > I'm sure the data can be encoded in MAGE-ML v1.x, it's just a =20 > > question of > > the best way to go about it so that the files aren't prohibitively =20 > > large > > (e.g., 2+ GB zipped). For example, we could include only a subset of > > essential data, or partition it into separate files. > > > > Which data are you most interested in getting in MAGE-ML=20 > format for =20 > > these > > arrays? > > > > Steve > > > > --=20 > > Steve Chervitz | Bioinformatics Engineer | Bioinformatics > > AFFYMETRIX, INC. | 6550 Vallejo St., Ste 100 | Emeryville, CA 94608 > > Tel: 510-428-8530 | Fax: 510-428-8585 |=20 > Ste...@af... > > > > > >> From: Tina Boussard <bou...@st...> > >> Date: Tue, 3 Jan 2006 15:16:03 -0800 > >> To: "'mge...@li...' MAGE" > >> <mge...@li...>, <Ste...@af...> > >> Cc: <fug...@li...> > >> Subject: Re: [Mged-mage] Re: MAGEv2 > >> > >> Hi All, > >> > >> Does anyone have any experience with Affy's new exon=20 > arrays? I have > >> heard that the files are much larger than Affy's other gene > >> expression arrays. Has anyone tried to export this into=20 > mage-ml? If > >> so, I would be interested to hear your experience. > >> > >> Cheers, > >> > >> Tina B. > >> > >> > >> Tina Hernandez-Boussard, Ph.D. > >> Scientific Curator/Computational Biologist, PharmGKB > >> Stanford University > >> 300 Pasteur Drive > >> Stanford, CA 94305-5120 > >> > >> > > >=20 >=20 >=20 > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep=20 > through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. =20 > DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > _______________________________________________ > Fuge-devel mailing list > Fug...@li... > https://lists.sourceforge.net/lists/listinfo/fuge-devel >=20 >=20 |
From: Steve C. <Ste...@af...> - 2006-01-06 20:29:17
|
Tina, Array design information would also be useful to have in MAGE-ML, correct? E.g., probe and target sequences, array location, etc. For the NetAffx data, there is both design-time and annotation-time data. Design-time includes things like the type of evidence a given probe set was based on. Annotation-time includes details on the public mRNAs assigned to a probe set. I imagine the latter are of more interest. As for the Benicia Jam, I've got it penciled in. Steve > From: Tina Boussard <bou...@he...> > Date: Fri, 6 Jan 2006 12:11:01 -0800 > To: Steve Chervitz <Ste...@af...> > Cc: Tina Boussard <bou...@st...>, "'mge...@li...' > MAGE" <mge...@li...>, <fug...@li...>, > Helen Parkinson <par...@eb...> > Subject: Re: [Mged-mage] Re: MAGEv2 > > Hi All, > > It would be great if we could have the cel file and other such > extremely large files as external data files and not converted into > mage, as the exchange of these data would be impractical. > > Steve, I think that we are more interested in getting all of the > annotation data for these exon arrays into MAGE, such as the data you > will be generating in NetAffx. We will also need to be sure that > these data fit nicely into FUG-O. When you mentioned only converting > a sub-set of the data, is this what you had in mind? Will you be > going to the next jam in Benicia 3/7-3/10? > It would be great if we could add the exon arrays to the agenda. > > > Cheers, > > Tina B. > > > On Jan 6, 2006, at 1:22 AM, Helen Parkinson wrote: >> Tina >> >> we have done some work with the tiling path arrays for yeast, we >> developed a coding whereby we maintain the cel file as a data >> external file, converting these data to mage is not practical, >> these data are not public yet, but I can provide an example if you >> like. In the MAGE discussions we decided to a make a special case >> for some file formats, where it's impractical to do a conversion to >> a delimited file, >> >> cheers >> >> Helen > > > On Jan 4, 2006, at 1:14 PM, Steve Chervitz wrote: > >> Tina, >> >> I am responsible for generating the NetAffx annotation files for >> the exon >> array and no, I have not (yet) tried exporting into MAGE-ML format. >> I'm also >> interested in hearing ideas about the best way to approach it. >> Dealing with >> this type of data will also help inform MAGE v2 development. >> >> The main consideration is the increased amount and complexity of >> data to be >> encoded. There are 1.4 million probe sets, vs. 54 million for HG- >> U133 Plus >> 2.0 (which produces a 90 MB zipped annotation MAGE-ML file). >> >> There are more types of design-time data for each probe set and new >> hierarchical levels: probe sets are grouped into exon clusters and >> further >> into transcript clusters, which have their own types of associated >> annotations. Expression results will also have new encoding >> requirements and >> will be much larger (e.g., there is a 1GB binary CEL file with >> sample data >> on our site). >> >> I'm sure the data can be encoded in MAGE-ML v1.x, it's just a >> question of >> the best way to go about it so that the files aren't prohibitively >> large >> (e.g., 2+ GB zipped). For example, we could include only a subset of >> essential data, or partition it into separate files. >> >> Which data are you most interested in getting in MAGE-ML format for >> these >> arrays? >> >> Steve >> >> -- >> Steve Chervitz | Bioinformatics Engineer | Bioinformatics >> AFFYMETRIX, INC. | 6550 Vallejo St., Ste 100 | Emeryville, CA 94608 >> Tel: 510-428-8530 | Fax: 510-428-8585 | Ste...@af... >> >> >>> From: Tina Boussard <bou...@st...> >>> Date: Tue, 3 Jan 2006 15:16:03 -0800 >>> To: "'mge...@li...' MAGE" >>> <mge...@li...>, <Ste...@af...> >>> Cc: <fug...@li...> >>> Subject: Re: [Mged-mage] Re: MAGEv2 >>> >>> Hi All, >>> >>> Does anyone have any experience with Affy's new exon arrays? I have >>> heard that the files are much larger than Affy's other gene >>> expression arrays. Has anyone tried to export this into mage-ml? If >>> so, I would be interested to hear your experience. >>> >>> Cheers, >>> >>> Tina B. >>> >>> >>> Tina Hernandez-Boussard, Ph.D. >>> Scientific Curator/Computational Biologist, PharmGKB >>> Stanford University >>> 300 Pasteur Drive >>> Stanford, CA 94305-5120 >>> >>> >> > |
From: Tina B. <bou...@ge...> - 2006-01-06 20:23:38
|
Hi All, It would be great if we could have the cel file and other such extremely large files as external data files and not converted into mage, as the exchange of these data would be impractical. Steve, I think that we are more interested in getting all of the annotation data for these exon arrays into MAGE, such as the data you will be generating in NetAffx. We will also need to be sure that these data fit nicely into FUG-O. When you mentioned only converting a sub-set of the data, is this what you had in mind? Will you be going to the next jam in Benicia 3/7-3/10? It would be great if we could add the exon arrays to the agenda. Cheers, Tina B. |
From: Tina B. <bou...@he...> - 2006-01-06 20:10:40
|
Hi All, It would be great if we could have the cel file and other such extremely large files as external data files and not converted into mage, as the exchange of these data would be impractical. Steve, I think that we are more interested in getting all of the annotation data for these exon arrays into MAGE, such as the data you will be generating in NetAffx. We will also need to be sure that these data fit nicely into FUG-O. When you mentioned only converting a sub-set of the data, is this what you had in mind? Will you be going to the next jam in Benicia 3/7-3/10? It would be great if we could add the exon arrays to the agenda. Cheers, Tina B. On Jan 6, 2006, at 1:22 AM, Helen Parkinson wrote: > Tina > > we have done some work with the tiling path arrays for yeast, we > developed a coding whereby we maintain the cel file as a data > external file, converting these data to mage is not practical, > these data are not public yet, but I can provide an example if you > like. In the MAGE discussions we decided to a make a special case > for some file formats, where it's impractical to do a conversion to > a delimited file, > > cheers > > Helen On Jan 4, 2006, at 1:14 PM, Steve Chervitz wrote: > Tina, > > I am responsible for generating the NetAffx annotation files for > the exon > array and no, I have not (yet) tried exporting into MAGE-ML format. > I'm also > interested in hearing ideas about the best way to approach it. > Dealing with > this type of data will also help inform MAGE v2 development. > > The main consideration is the increased amount and complexity of > data to be > encoded. There are 1.4 million probe sets, vs. 54 million for HG- > U133 Plus > 2.0 (which produces a 90 MB zipped annotation MAGE-ML file). > > There are more types of design-time data for each probe set and new > hierarchical levels: probe sets are grouped into exon clusters and > further > into transcript clusters, which have their own types of associated > annotations. Expression results will also have new encoding > requirements and > will be much larger (e.g., there is a 1GB binary CEL file with > sample data > on our site). > > I'm sure the data can be encoded in MAGE-ML v1.x, it's just a > question of > the best way to go about it so that the files aren't prohibitively > large > (e.g., 2+ GB zipped). For example, we could include only a subset of > essential data, or partition it into separate files. > > Which data are you most interested in getting in MAGE-ML format for > these > arrays? > > Steve > > -- > Steve Chervitz | Bioinformatics Engineer | Bioinformatics > AFFYMETRIX, INC. | 6550 Vallejo St., Ste 100 | Emeryville, CA 94608 > Tel: 510-428-8530 | Fax: 510-428-8585 | Ste...@af... > > >> From: Tina Boussard <bou...@st...> >> Date: Tue, 3 Jan 2006 15:16:03 -0800 >> To: "'mge...@li...' MAGE" >> <mge...@li...>, <Ste...@af...> >> Cc: <fug...@li...> >> Subject: Re: [Mged-mage] Re: MAGEv2 >> >> Hi All, >> >> Does anyone have any experience with Affy's new exon arrays? I have >> heard that the files are much larger than Affy's other gene >> expression arrays. Has anyone tried to export this into mage-ml? If >> so, I would be interested to hear your experience. >> >> Cheers, >> >> Tina B. >> >> >> Tina Hernandez-Boussard, Ph.D. >> Scientific Curator/Computational Biologist, PharmGKB >> Stanford University >> 300 Pasteur Drive >> Stanford, CA 94305-5120 >> >> > |
From: Helen P. <par...@eb...> - 2006-01-06 09:22:36
|
Tina we have done some work with the tiling path arrays for yeast, we developed a coding whereby we maintain the cel file as a data external file, converting these data to mage is not practical, these data are not public yet, but I can provide an example if you like. In the MAGE discussions we decided to a make a special case for some file formats, where it's impractical to do a conversion to a delimited file, cheers Helen Tina Boussard wrote: > Hi All, > > Does anyone have any experience with Affy's new exon arrays? I have > heard that the files are much larger than Affy's other gene > expression arrays. Has anyone tried to export this into mage-ml? If > so, I would be interested to hear your experience. > > Cheers, > > Tina B. > > > Tina Hernandez-Boussard, Ph.D. > Scientific Curator/Computational Biologist, PharmGKB > Stanford University > 300 Pasteur Drive > Stanford, CA 94305-5120 > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage -- Helen Parkinson, PhD Curation Coordinator Microarray Informatics Team, EBI and Seconded Scientific Programme Manager NCRI Cancer Informatics Initiative www.cancerinformatics.org.uk |
From: Steve C. <Ste...@af...> - 2006-01-04 21:15:00
|
Tina, I am responsible for generating the NetAffx annotation files for the exon array and no, I have not (yet) tried exporting into MAGE-ML format. I'm also interested in hearing ideas about the best way to approach it. Dealing with this type of data will also help inform MAGE v2 development. The main consideration is the increased amount and complexity of data to be encoded. There are 1.4 million probe sets, vs. 54 million for HG-U133 Plus 2.0 (which produces a 90 MB zipped annotation MAGE-ML file). There are more types of design-time data for each probe set and new hierarchical levels: probe sets are grouped into exon clusters and further into transcript clusters, which have their own types of associated annotations. Expression results will also have new encoding requirements and will be much larger (e.g., there is a 1GB binary CEL file with sample data on our site). I'm sure the data can be encoded in MAGE-ML v1.x, it's just a question of the best way to go about it so that the files aren't prohibitively large (e.g., 2+ GB zipped). For example, we could include only a subset of essential data, or partition it into separate files. Which data are you most interested in getting in MAGE-ML format for these arrays? Steve -- Steve Chervitz | Bioinformatics Engineer | Bioinformatics AFFYMETRIX, INC. | 6550 Vallejo St., Ste 100 | Emeryville, CA 94608 Tel: 510-428-8530 | Fax: 510-428-8585 | Ste...@af... > From: Tina Boussard <bou...@st...> > Date: Tue, 3 Jan 2006 15:16:03 -0800 > To: "'mge...@li...' MAGE" > <mge...@li...>, <Ste...@af...> > Cc: <fug...@li...> > Subject: Re: [Mged-mage] Re: MAGEv2 > > Hi All, > > Does anyone have any experience with Affy's new exon arrays? I have > heard that the files are much larger than Affy's other gene > expression arrays. Has anyone tried to export this into mage-ml? If > so, I would be interested to hear your experience. > > Cheers, > > Tina B. > > > Tina Hernandez-Boussard, Ph.D. > Scientific Curator/Computational Biologist, PharmGKB > Stanford University > 300 Pasteur Drive > Stanford, CA 94305-5120 > > |
From: Tina B. <bou...@st...> - 2006-01-03 23:16:14
|
Hi All, Does anyone have any experience with Affy's new exon arrays? I have heard that the files are much larger than Affy's other gene expression arrays. Has anyone tried to export this into mage-ml? If so, I would be interested to hear your experience. Cheers, Tina B. Tina Hernandez-Boussard, Ph.D. Scientific Curator/Computational Biologist, PharmGKB Stanford University 300 Pasteur Drive Stanford, CA 94305-5120 |
From: Paul S. <pts...@sb...> - 2005-12-19 21:29:18
|
From: Joe W. <jw...@ji...> - 2005-12-19 03:16:52
|
Hi Junmin, I think you've made some very good points. During the development of MAGEv1 there were efforts to correct the spellings of the associations to reflect cardinality/plurality. The 2 you point out appear to be ones that got missed, although 'minutes' (plural) is very commonly used. These should be corrected. The Roles association was a bit of a problem for some time in MAGEv1.0 because an individual could only have one role, but I think that the cardinality was corrected in MAGEv1.1--even though the name wasn't changed. The reason for that, if I'm not mistaken, is that we couldn't make any changes to MAGEv1.0 that would break existing code. Changing the name of the association would certainly break existing code. Since MAGEv1.0 was an accepted OMG specification, the changes implemented in MAGEv1.1 were not extensive. MAGEv2 will be an entirely new specification that will have to be accepted by OMG again. In any case, it is well worth taking another look at the associations to catch as many of these plurality problems as possible so that we get the cardinalities right. Cheers, Joe White Junmin Liu wrote: > Hi, Trish, > I just read the wiki page. I can edit it but I think it could be more > appropriate to let you organize things on the page. > > Here is my comments. > 1. Regarding Mike's use case about "death to be the desired instance > of Initial Time Point". I think the approach to solve this is to > associate the properties "is_user_defined" to "death". > > 2. "The cardinality between a MAGE-class and OntolgyEntry in the > MAGE-OM is clearly defined. Is cardinality within MO consistently > encoded with a trailing 's' in the property name?" > > This may be confusing. Because the cardinality between MAGE-class to > OntologyEntry and 's' in property name are totally different things. > > For example, the "Contact" class has association called "Roles" to > OntologyEntry, the end has "o..*" cardinality. Then the MO goes on to > present a class named "Roles" > (http://mged.sourceforge.net/ontologies/MGEDontology.php#Roles). This > should be "Role". For it is model's responsibility to say "Contact can > has many roles", but MO should only define the "Role" not "Roles". > > take the example shown in Array Express: > > <Person identifier="someplace.org:Person:j_bloggs" > email="j.b...@so..." > lastName="Bloggs" > firstName="Joe"> > <Roles_assnlist> > <OntologyEntry category="Roles" value="submitter"> > </OntologyEntry> > </Roles_assnlist> > </Person> > > If you say "category='Roles'", that means user can say > <OntologyEntry category="Roles" value="submitter, curator">, > certainly it is wrong. > > The right way to do this is: > > <Person identifier="someplace.org:Person:j_bloggs" > email="j.b...@so..." > lastName="Bloggs" > firstName="Joe"> > <Roles_assnlist> > <OntologyEntry category="Role" value="submitter"> > </OntologyEntry> > <OntologyEntry category="Role" value="curator"> > </OntologyEntry> > </Roles_assnlist> > </Person> > > Note the "Role" not "Roles" in above example. > > 3. "Add cardinality to unit terms" > I don't think we should have cardinality to the unit term or MO term. > MO doesn't model the real life objects, MAGE-OM does. > > Usin the example shown on Array Express site: > <Measurement value="15" kindCV="time"> > <Unit_assn> > <TimeUnit unitName="minutes" unitNameCV="m"/> > </Unit_assn> > </Measurement> > > I would code it as: > <Measurement value="15" kindCV="time"> > <Unit_assn> > <TimeUnit unitName="minute" unitNameCV="m"/> > </Unit_assn> > </Measurement> > > ---junmin > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Junmin L. <ju...@pc...> - 2005-12-18 02:58:38
|
Hi, Trish, I just read the wiki page. I can edit it but I think it could be more appropriate to let you organize things on the page. Here is my comments. 1. Regarding Mike's use case about "death to be the desired instance of Initial Time Point". I think the approach to solve this is to associate the properties "is_user_defined" to "death". 2. "The cardinality between a MAGE-class and OntolgyEntry in the MAGE-OM is clearly defined. Is cardinality within MO consistently encoded with a trailing 's' in the property name?" This may be confusing. Because the cardinality between MAGE-class to OntologyEntry and 's' in property name are totally different things. For example, the "Contact" class has association called "Roles" to OntologyEntry, the end has "o..*" cardinality. Then the MO goes on to present a class named "Roles" (http://mged.sourceforge.net/ontologies/MGEDontology.php#Roles). This should be "Role". For it is model's responsibility to say "Contact can has many roles", but MO should only define the "Role" not "Roles". take the example shown in Array Express: <Person identifier="someplace.org:Person:j_bloggs" email="j.b...@so..." lastName="Bloggs" firstName="Joe"> <Roles_assnlist> <OntologyEntry category="Roles" value="submitter"> </OntologyEntry> </Roles_assnlist> </Person> If you say "category='Roles'", that means user can say <OntologyEntry category="Roles" value="submitter, curator">, certainly it is wrong. The right way to do this is: <Person identifier="someplace.org:Person:j_bloggs" email="j.b...@so..." lastName="Bloggs" firstName="Joe"> <Roles_assnlist> <OntologyEntry category="Role" value="submitter"> </OntologyEntry> <OntologyEntry category="Role" value="curator"> </OntologyEntry> </Roles_assnlist> </Person> Note the "Role" not "Roles" in above example. 3. "Add cardinality to unit terms" I don't think we should have cardinality to the unit term or MO term. MO doesn't model the real life objects, MAGE-OM does. Usin the example shown on Array Express site: <Measurement value="15" kindCV="time"> <Unit_assn> <TimeUnit unitName="minutes" unitNameCV="m"/> </Unit_assn> </Measurement> I would code it as: <Measurement value="15" kindCV="time"> <Unit_assn> <TimeUnit unitName="minute" unitNameCV="m"/> </Unit_assn> </Measurement> ---junmin |
From: Arto V. <art...@cs...> - 2005-12-13 06:44:08
|
Kjell Petersen wrote: > > (DataExternal and related classes as BioAssayData is devoted a whole > chapter in the OMG Spec, named something like "Transformation of > BioAssayData") > You are right. Actually I was using the Rational Rose version of the MAGE-OM (both 1.0 and 1.1) and it does not contain the DataExternal. When I checked BioAssayData chapter from the OMG Spec, it did not either. I found the chapter you are referring after I sent the email. -- Arto Viitanen, CSC Espoo, Finland |
From: Arto V. <art...@cs...> - 2005-12-12 10:41:07
|
How can one check platform type of an experiment from a MAGE-OM hierarchy or ArrayExpress database ? That is, the arrays used in bioassays are Affymetrix, cDNA, Illumina, ChIP -chips? I guess you can count channel of bioassay and if it is two, the platform is cDNA, but how on other types? I guess if DataExternal (why is it not described in "Gene Expression Specification, October 2003, Version 1.1, formal/03-10-01" of OMG ?) has filenameURI with certain extensions (like cel, chp or cdf) one can guess that experiment uses Affymetrix platform, right? -- Arto Viitanen, CSC Espoo, Finland |
From: Trish W. <wh...@pc...> - 2005-12-09 00:53:48
|
Hi Michael, Thanks for your comments. Reply in-line: > Down near the bottom, one of the bullets is the following: > > "Provide mapping file between MO and MAGE-OM, i.e. which MO class is used to > provide terms for which MAGE-OM class (generate this computationally for > maintenance of the mapping), consider including mapping to other > ontologies???" > > I think this is a great idea but if it can be clearly separate from both the > ontology and MAGE, that would be ideal. In fact, I think it is more > appropriate for a MAGE artifice than MO. > I see the mapping as an aid for application developers in order to efficiently use MO and that this is separate from both the ontology and MAGE. This is a mechanism to de-couple the structure of MO from MAGE, while still providing an efficient mechanism for application delvelopers to find the appropriate class to pick terms from. > Also, when the document mentions Individuals vs Classes--one interesting use > case that I saw was for the Initial Time Point class, we had a case where > 'death' was the desired Instance. So I think it is important that users of > MO, when appropriate, will feel they can have an Individual that isn't part > of MO but semantically fits the Class. Good point. If Individuals are moved to classes, users will continue to need to be able to provide new terms and is this case they would be classes. I believe this type of change to the MO may be one that occurs at a later stage due to possible changes that would occur in processing of the MO, but this is an important point to keep in mind. I have added this to the wiki. Cheers, Trish >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] >> Sent: Thursday, December 08, 2005 3:49 PM >> To: mge...@li...; >> mge...@li... >> Subject: [Mged-mage] MO Refactoring >> >> >> Hi folks, >> >> The MGED Ontology Working Group is beginning to work on a new >> project, called >> the MGED Ontology Refactoring project. This project is aimed >> at refining the >> ontological structure of the MGED Ontology to best utilize >> OWL and enhance the >> usage of MO in applications. This project is being driven by >> requests from >> users, both developers and curators, of the MGED Ontology to >> make the ontology >> more user-friendly and better ontologically structured. An >> initial list of >> requests have been gathered from the last MGED meeting and >> have been posted at: >> https://www.cbil.upenn.edu/magewiki/index.php/MORefactoringToDoList >> >> If there are additional items that you would like to see >> addressed, please add >> those to the wiki. We will be collecting items until Jan. 13. >> After this time, >> we will work to prioritize items into those that can be addressed as >> deliverables within approximately 3 month intervals in order >> to provide >> continued releases of the MGED Ontology that address both the >> re-factoring >> items as well as any requests for new terms. >> >> Trish >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep >> through log files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. >> DOWNLOAD SPLUNK! >> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage >> >> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Mged-ontologies mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-ontologies > |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2005-12-09 00:26:24
|
Hi Trish, I'm not registered so it didn't let me do any edits but I only had two quick points: Down near the bottom, one of the bullets is the following: "Provide mapping file between MO and MAGE-OM, i.e. which MO class is used to provide terms for which MAGE-OM class (generate this computationally for maintenance of the mapping), consider including mapping to other ontologies???" I think this is a great idea but if it can be clearly separate from both the ontology and MAGE, that would be ideal. In fact, I think it is more appropriate for a MAGE artifice than MO. Also, when the document mentions Individuals vs Classes--one interesting use case that I saw was for the Initial Time Point class, we had a case where 'death' was the desired Instance. So I think it is important that users of MO, when appropriate, will feel they can have an Individual that isn't part of MO but semantically fits the Class. cheers, Michael > -----Original Message----- > From: mge...@li... > [mailto:mge...@li...] > Sent: Thursday, December 08, 2005 3:49 PM > To: mge...@li...; > mge...@li... > Subject: [Mged-mage] MO Refactoring > > > Hi folks, > > The MGED Ontology Working Group is beginning to work on a new > project, called > the MGED Ontology Refactoring project. This project is aimed > at refining the > ontological structure of the MGED Ontology to best utilize > OWL and enhance the > usage of MO in applications. This project is being driven by > requests from > users, both developers and curators, of the MGED Ontology to > make the ontology > more user-friendly and better ontologically structured. An > initial list of > requests have been gathered from the last MGED meeting and > have been posted at: > https://www.cbil.upenn.edu/magewiki/index.php/MORefactoringToDoList > > If there are additional items that you would like to see > addressed, please add > those to the wiki. We will be collecting items until Jan. 13. > After this time, > we will work to prioritize items into those that can be addressed as > deliverables within approximately 3 month intervals in order > to provide > continued releases of the MGED Ontology that address both the > re-factoring > items as well as any requests for new terms. > > Trish > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep > through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. > DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > > |