Question: bovine Annotation package(s)
0
gravatar for Nathan.Watson-Haigh@csiro.au
11.2 years ago by
I'd like to be able to conduct metadata analyses on things such as GO with data I have from an Affymetrix bovine chip. I've not done this on other arrays, so I'm not sure what is needed to do this. I saw that there were no bovine or bovine.db packages available, so I used AnnBuilder to create a bovine package from the GenBank IDs provided by Affymetrix. My question/confusion is what's the *.db packages for, do I need one for the bovine chip, and how would I make one? Any pointers greatly appreciated! Cheers, Nathan ------------------------------------------------------------- Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) OCE Post Doctoral Fellow CSIRO Livestock Industries J M Rendel Laboratory Rockhampton QLD 4701 Tel: +61 (0)7 4923 8121 Australia Fax: +61 (0)7 4923 8222 ------------------------------------------------------------- [[alternative HTML version deleted]]
annbuilder • 523 views
ADD COMMENTlink modified 11.2 years ago by Sean Davis21k • written 11.2 years ago by Nathan.Watson-Haigh@csiro.au210
Answer: bovine Annotation package(s)
0
gravatar for Sean Davis
11.2 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Tue, Jul 15, 2008 at 8:08 PM, <nathan.watson-haigh at="" csiro.au=""> wrote: > I'd like to be able to conduct metadata analyses on things such as GO > with data I have from an Affymetrix bovine chip. I've not done this on > other arrays, so I'm not sure what is needed to do this. > > I saw that there were no bovine or bovine.db packages available, so I > used AnnBuilder to create a bovine package from the GenBank IDs provided > by Affymetrix. My question/confusion is what's the *.db packages for, do > I need one for the bovine chip, and how would I make one? The *.db packages are the new standard for annotation packages. Have a look at how to create one by looking at the AnnotationDbi package and, specifically, the SQLForge vignette. Sean
ADD COMMENTlink written 11.2 years ago by Sean Davis21k
Hi Nathan, What Sean says is true. However, I have not yet made a bovine.db0 database, so it is not yet possible to make .db annotation packages for bovines. However, if you would be willing to work with me a little bit, I would be willing to look into it. Lets take this off line and explore it a little bit. In the meantime part of the reason that AnnBuilder is still alive is because of odd corner cases like this one where someone needs support for an unusual organism. So you should be able to use AnnBuilder in the interim. Marc Sean Davis wrote: > On Tue, Jul 15, 2008 at 8:08 PM, <nathan.watson-haigh at="" csiro.au=""> wrote: > >> I'd like to be able to conduct metadata analyses on things such as GO >> with data I have from an Affymetrix bovine chip. I've not done this on >> other arrays, so I'm not sure what is needed to do this. >> >> I saw that there were no bovine or bovine.db packages available, so I >> used AnnBuilder to create a bovine package from the GenBank IDs provided >> by Affymetrix. My question/confusion is what's the *.db packages for, do >> I need one for the bovine chip, and how would I make one? >> > > The *.db packages are the new standard for annotation packages. Have > a look at how to create one by looking at the AnnotationDbi package > and, specifically, the SQLForge vignette. > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 11.2 years ago by Marc Carlson7.2k
Marc- I was wondering how it was going with building a bovine annotation database? I have been reading through the vignette for AnnBuilder and not sure that I have the skills for building the bovine. Is there something else that I need to be reading to assist? Thanks Louisa Rispoli "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein Louisa Rispoli, Ph.D. Reproductive Physiology Department of Animal Science University of Tennessee, Knoxville A105 Johnson Animal Research and Teaching Unit 1750 Alcoa Highway Knoxville, TN 37920 phone:(865) 946-1874 fax:(865) 946-1010 email: lrispoli at utk.edu Marc Carlson <mcarlson at="" fhcrc.o="" rg=""> To Sent by: Sean Davis <sdavis2 at="" mail.nih.gov=""> bioconductor-boun cc ces at stat.math.eth Nathan.Watson-Haigh at csiro.au, z.ch bioconductor at stat.math.ethz.ch Subject Re: [BioC] bovine Annotation 07/16/2008 01:21 package(s) PM Hi Nathan, What Sean says is true. However, I have not yet made a bovine.db0 database, so it is not yet possible to make .db annotation packages for bovines. However, if you would be willing to work with me a little bit, I would be willing to look into it. Lets take this off line and explore it a little bit. In the meantime part of the reason that AnnBuilder is still alive is because of odd corner cases like this one where someone needs support for an unusual organism. So you should be able to use AnnBuilder in the interim. Marc Sean Davis wrote: > On Tue, Jul 15, 2008 at 8:08 PM, <nathan.watson-haigh at="" csiro.au=""> wrote: > >> I'd like to be able to conduct metadata analyses on things such as GO >> with data I have from an Affymetrix bovine chip. I've not done this on >> other arrays, so I'm not sure what is needed to do this. >> >> I saw that there were no bovine or bovine.db packages available, so I >> used AnnBuilder to create a bovine package from the GenBank IDs provided >> by Affymetrix. My question/confusion is what's the *.db packages for, do >> I need one for the bovine chip, and how would I make one? >> > > The *.db packages are the new standard for annotation packages. Have > a look at how to create one by looking at the AnnotationDbi package > and, specifically, the SQLForge vignette. > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 11.1 years ago by Louisa A Rispoli/AS/EXP/UTIA160
Hi Louisa, Just to clarify with a few things I've learnt in the last week or two regarding the Bioconductor annotation packages/framework. There are currently two types of annotation packages: 1) Those built by AnnBuilder 2) Those built by SQLForge The former are the older style annotation packages which I believe are being replaced by the latter. The latter are better as the annotations are actually stored/distributed in a database format using SQLite and are linked to online resources so are far more extensible than the old flat file format. However, the latter requires a certain amount of configuration/setup by the bioconductor devs to create a *.db0 package (not distributed with BioC) for a given organism which are used to generate the "real" annotation package which is distributed with BioC. As a result, if you need an annotation package for an unsupported organism (I think there are currently 7), you need to ask the devs nicely to build the *.db0 package or you can use AnnBuilder to build an old-style annotation package. I have built such a file for the affymatrix bovine chip. However, there are limitations (which I don't yet fully understand) to what packages you can use to analyse the annotations - not sure it it's because those packages expect the new style *.db annotation packages or not. I need to figure out exactly what the issue are, but I can send you the package if you like? Cheers, Nathan Quoting Louisa A Rispoli/AS/EXP/UTIA <larispoli at="" mail.ag.utk.edu="">: > Marc- > > I was wondering how it was going with building a bovine annotation > database? I have been reading through the vignette for AnnBuilder and not > sure that I have the skills for building the bovine. > > > Is there something else that I need to be reading to assist? Thanks > > Louisa Rispoli > > "If we knew what we were doing, it wouldn't be called Research." - Albert > Einstein > > Louisa Rispoli, Ph.D. Reproductive Physiology > Department of Animal Science > University of Tennessee, Knoxville > A105 Johnson Animal Research and Teaching Unit > 1750 Alcoa Highway > Knoxville, TN 37920 > phone:(865) 946-1874 > fax:(865) 946-1010 > email: lrispoli at utk.edu > > > > > > Marc Carlson > <mcarlson at="" fhcrc.o=""> rg> To > Sent by: Sean Davis <sdavis2 at="" mail.nih.gov=""> > bioconductor-boun cc > ces at stat.math.eth Nathan.Watson-Haigh at csiro.au, > z.ch bioconductor at stat.math.ethz.ch > Subject > Re: [BioC] bovine Annotation > 07/16/2008 01:21 package(s) > PM > > > > > > > > > > Hi Nathan, > > What Sean says is true. However, I have not yet made a bovine.db0 > database, so it is not yet possible to make .db annotation packages for > bovines. However, if you would be willing to work with me a little bit, > I would be willing to look into it. Lets take this off line and explore > it a little bit. In the meantime part of the reason that AnnBuilder is > still alive is because of odd corner cases like this one where someone > needs support for an unusual organism. So you should be able to use > AnnBuilder in the interim. > > Marc > > > > > Sean Davis wrote: > > On Tue, Jul 15, 2008 at 8:08 PM, <nathan.watson-haigh at="" csiro.au=""> wrote: > > > >> I'd like to be able to conduct metadata analyses on things such as GO > >> with data I have from an Affymetrix bovine chip. I've not done this on > >> other arrays, so I'm not sure what is needed to do this. > >> > >> I saw that there were no bovine or bovine.db packages available, so I > >> used AnnBuilder to create a bovine package from the GenBank IDs provided > >> by Affymetrix. My question/confusion is what's the *.db packages for, do > >> I need one for the bovine chip, and how would I make one? > >> > > > > The *.db packages are the new standard for annotation packages. Have > > a look at how to create one by looking at the AnnotationDbi package > > and, specifically, the SQLForge vignette. > > > > Sean > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 11.1 years ago by Nathan Haigh120
Hi Nathan- I would greatly appreciate it if you could send the package. A grad student trying to finish her PhD and I are trying to understand annotation so we can apply to the gene lists we finally figured out how to do our linear model, ebayes and fdr on. We are really frustrated since most packages/software only has info for human, mouse, or drosophila and we think cows are kind of important. Any help would be appreciated since we are new to this and want to be as accurate as feasible. Thanks Louisa "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein Louisa Rispoli, Ph.D. Reproductive Physiology Department of Animal Science University of Tennessee, Knoxville A105 Johnson Animal Research and Teaching Unit 1750 Alcoa Highway Knoxville, TN 37920 phone:(865) 946-1874 fax:(865) 946-1010 email: lrispoli at utk.edu "Nathan S. Haigh" <n.haigh at="" sheffiel="" d.ac.uk=""> To Louisa A Rispoli/AS/EXP/UTIA 07/30/2008 07:24 <larispoli at="" mail.ag.utk.edu=""> PM cc Marc Carlson <mcarlson at="" fhcrc.org="">, bioconductor at stat.math.ethz.ch Subject Re: [BioC] bovine Annotation package(s) Hi Louisa, Just to clarify with a few things I've learnt in the last week or two regarding the Bioconductor annotation packages/framework. There are currently two types of annotation packages: 1) Those built by AnnBuilder 2) Those built by SQLForge The former are the older style annotation packages which I believe are being replaced by the latter. The latter are better as the annotations are actually stored/distributed in a database format using SQLite and are linked to online resources so are far more extensible than the old flat file format. However, the latter requires a certain amount of configuration/setup by the bioconductor devs to create a *.db0 package (not distributed with BioC) for a given organism which are used to generate the "real" annotation package which is distributed with BioC. As a result, if you need an annotation package for an unsupported organism (I think there are currently 7), you need to ask the devs nicely to build the *.db0 package or you can use AnnBuilder to build an old-style annotation package. I have built such a file for the affymatrix bovine chip. However, there are limitations (which I don't yet fully understand) to what packages you can use to analyse the annotations - not sure it it's because those packages expect the new style *.db annotation packages or not. I need to figure out exactly what the issue are, but I can send you the package if you like? Cheers, Nathan Quoting Louisa A Rispoli/AS/EXP/UTIA <larispoli at="" mail.ag.utk.edu="">: > Marc- > > I was wondering how it was going with building a bovine annotation > database? I have been reading through the vignette for AnnBuilder and not > sure that I have the skills for building the bovine. > > > Is there something else that I need to be reading to assist? Thanks > > Louisa Rispoli > > "If we knew what we were doing, it wouldn't be called Research." - Albert > Einstein > > Louisa Rispoli, Ph.D. Reproductive Physiology > Department of Animal Science > University of Tennessee, Knoxville > A105 Johnson Animal Research and Teaching Unit > 1750 Alcoa Highway > Knoxville, TN 37920 > phone:(865) 946-1874 > fax:(865) 946-1010 > email: lrispoli at utk.edu > > > > > > Marc Carlson > <mcarlson at="" fhcrc.o=""> rg> To > Sent by: Sean Davis <sdavis2 at="" mail.nih.gov=""> > bioconductor-boun cc > ces at stat.math.eth Nathan.Watson-Haigh at csiro.au, > z.ch bioconductor at stat.math.ethz.ch > Subject > Re: [BioC] bovine Annotation > 07/16/2008 01:21 package(s) > PM > > > > > > > > > > Hi Nathan, > > What Sean says is true. However, I have not yet made a bovine.db0 > database, so it is not yet possible to make .db annotation packages for > bovines. However, if you would be willing to work with me a little bit, > I would be willing to look into it. Lets take this off line and explore > it a little bit. In the meantime part of the reason that AnnBuilder is > still alive is because of odd corner cases like this one where someone > needs support for an unusual organism. So you should be able to use > AnnBuilder in the interim. > > Marc > > > > > Sean Davis wrote: > > On Tue, Jul 15, 2008 at 8:08 PM, <nathan.watson-haigh at="" csiro.au=""> wrote: > > > >> I'd like to be able to conduct metadata analyses on things such as GO > >> with data I have from an Affymetrix bovine chip. I've not done this on > >> other arrays, so I'm not sure what is needed to do this. > >> > >> I saw that there were no bovine or bovine.db packages available, so I > >> used AnnBuilder to create a bovine package from the GenBank IDs provided > >> by Affymetrix. My question/confusion is what's the *.db packages for, do > >> I need one for the bovine chip, and how would I make one? > >> > > > > The *.db packages are the new standard for annotation packages. Have > > a look at how to create one by looking at the AnnotationDbi package > > and, specifically, the SQLForge vignette. > > > > Sean > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 11.1 years ago by Louisa A Rispoli/AS/EXP/UTIA160
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