Question: How are GO2PROBE built
0
gravatar for Oura Tomonori
11.0 years ago by
Oura Tomonori30 wrote:
Dear BioC, How are the mappings of Affymetrix probe ids to Gene Ontology terms in metadata package provided by Bioconductor build? I am trying to use some gene set analysis packages and find some pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but another package use the external gene set definition, such as MSigDB. So I want to know the criteria for select specific GO term among possible terms for each probe id in Bioconductor. I already read the documents about AnnBuilder package, however. -- mailto:tomonori.oura at gmail.com Kyoto University School of Public Health Department of Biostatistics
go probe annbuilder • 762 views
ADD COMMENTlink modified 11.0 years ago by Sean Davis21k • written 11.0 years ago by Oura Tomonori30
Answer: How are GO2PROBE built
0
gravatar for Sean Davis
11.0 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: > Dear BioC, > > How are the mappings of Affymetrix probe ids to Gene Ontology terms in > metadata package provided by Bioconductor build? > > I am trying to use some gene set analysis packages and find some > pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but > another package use the external gene set definition, such as MSigDB. > > So I want to know the criteria for select specific GO term among > possible terms for each probe id in Bioconductor. > I already read the documents about AnnBuilder package, however. To make a long story short, the annotations available from affy are mapped to Entrez Gene IDs. Then, the information from Entrez Gene--in this case, gene ontology--is mapped to affy id. The dates associated with the data, the source of the data, and how the data are mapped will all affect the final mapping of affy ID to gene ontology. The nice thing about gene ontology analyses is that they are typically based on "sets" of genes making it much less important to start with EXACTLY the same gene ontology mappings. In fact, in practice, it will be pretty difficult to do so. If you want to see the details of the current Bioconductor annotation package build process, you want to read the AnnotationDbi SQLForge vignette, as AnnBuilder is outdated. Finally, if I have misunderstood your question, perhaps you could clarify. Sean
ADD COMMENTlink written 11.0 years ago by Sean Davis21k
Hi Sean Turning this into a more general question. Whenever I have to deal with a new type of Affymetrix array I seem to have to root around Bioconductor packages to find out how it is annotated etc. By the time I come around to do it again it has all changed and is done in a different way to how it was done before. My difficulty is it all feels a bit adhoc and comes at me in bits and pieces. Also I always feel there is probably a better way to do it that I am missing. Is there anywhere information that gives a better big picture that pulls it together a bit? What are the foundation designs/philosophy that all the packages are following? Is there a routemap type document that describes Bioconductor's approach to all this? Any pointers to useful information gratefully received. Thanks. John Seers --- -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis Sent: 02 October 2008 11:55 To: Oura Tomonori Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] How are GO2PROBE built On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: > Dear BioC, > > How are the mappings of Affymetrix probe ids to Gene Ontology terms in > metadata package provided by Bioconductor build? > > I am trying to use some gene set analysis packages and find some > pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but > another package use the external gene set definition, such as MSigDB. > > So I want to know the criteria for select specific GO term among > possible terms for each probe id in Bioconductor. > I already read the documents about AnnBuilder package, however. To make a long story short, the annotations available from affy are mapped to Entrez Gene IDs. Then, the information from Entrez Gene--in this case, gene ontology--is mapped to affy id. The dates associated with the data, the source of the data, and how the data are mapped will all affect the final mapping of affy ID to gene ontology. The nice thing about gene ontology analyses is that they are typically based on "sets" of genes making it much less important to start with EXACTLY the same gene ontology mappings. In fact, in practice, it will be pretty difficult to do so. If you want to see the details of the current Bioconductor annotation package build process, you want to read the AnnotationDbi SQLForge vignette, as AnnBuilder is outdated. Finally, if I have misunderstood your question, perhaps you could clarify. 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 11.0 years ago by john seers IFR810
Hi John, The annotation system is not meant to be ad hoc although it has been changing a lot recently as we have migrated to a much more powerful database centric system. Please have a look at the vignettes on this page to see more current information: http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html Please let me know if you have any further questions. Marc john seers (IFR) wrote: > > > Hi Sean > > Turning this into a more general question. Whenever I have to deal with > a new type of Affymetrix array I seem to have to root around > Bioconductor packages to find out how it is annotated etc. By the time I > come around to do it again it has all changed and is done in a different > way to how it was done before. My difficulty is it all feels a bit adhoc > and comes at me in bits and pieces. Also I always feel there is probably > a better way to do it that I am missing. > > Is there anywhere information that gives a better big picture that pulls > it together a bit? What are the foundation designs/philosophy that all > the packages are following? Is there a routemap type document that > describes Bioconductor's approach to all this? > > Any pointers to useful information gratefully received. > > Thanks. > > > John Seers > > > > > > > > --- > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis > Sent: 02 October 2008 11:55 > To: Oura Tomonori > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] How are GO2PROBE built > > On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> > wrote: > >> Dear BioC, >> >> How are the mappings of Affymetrix probe ids to Gene Ontology terms in >> > > >> metadata package provided by Bioconductor build? >> >> I am trying to use some gene set analysis packages and find some >> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but >> another package use the external gene set definition, such as MSigDB. >> >> So I want to know the criteria for select specific GO term among >> possible terms for each probe id in Bioconductor. >> I already read the documents about AnnBuilder package, however. >> > > To make a long story short, the annotations available from affy are > mapped to Entrez Gene IDs. Then, the information from Entrez Gene-- in > this case, gene ontology--is mapped to affy id. The dates associated > with the data, the source of the data, and how the data are mapped will > all affect the final mapping of affy ID to gene ontology. The nice > thing about gene ontology analyses is that they are typically based on > "sets" of genes making it much less important to start with EXACTLY the > same gene ontology mappings. In fact, in practice, it will be pretty > difficult to do so. > > If you want to see the details of the current Bioconductor annotation > package build process, you want to read the AnnotationDbi SQLForge > vignette, as AnnBuilder is outdated. > > Finally, if I have misunderstood your question, perhaps you could > clarify. > > 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 11.0 years ago by Marc Carlson7.2k
Hi Marc and Sean Thank you both for your answers. When I said ad-hoc I did not mean to sound critical; it was just coming at me a bit ad-hoc because I could not find an overview of it. I think the change to AnnotationDbi happened at some point so there seemed to be a lot of choices and without the knowledge I could not make sense of it. Plus dealing with some unusual arrays did not help me. However Sean's short description is great and I will have a look at AnnotationDbi.html with interest. Thank you. John Seers --- -----Original Message----- From: Marc Carlson [mailto:mcarlson@fhcrc.org] Sent: 02 October 2008 17:09 To: john seers (IFR) Cc: Sean Davis; Oura Tomonori; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] How are GO2PROBE built Hi John, The annotation system is not meant to be ad hoc although it has been changing a lot recently as we have migrated to a much more powerful database centric system. Please have a look at the vignettes on this page to see more current information: http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html Please let me know if you have any further questions. Marc john seers (IFR) wrote: > > > Hi Sean > > Turning this into a more general question. Whenever I have to deal > with a new type of Affymetrix array I seem to have to root around > Bioconductor packages to find out how it is annotated etc. By the time > I come around to do it again it has all changed and is done in a > different way to how it was done before. My difficulty is it all feels > a bit adhoc and comes at me in bits and pieces. Also I always feel > there is probably a better way to do it that I am missing. > > Is there anywhere information that gives a better big picture that > pulls it together a bit? What are the foundation designs/philosophy > that all the packages are following? Is there a routemap type document > that describes Bioconductor's approach to all this? > > Any pointers to useful information gratefully received. > > Thanks. > > > John Seers > > > > > > > > --- > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean > Davis > Sent: 02 October 2008 11:55 > To: Oura Tomonori > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] How are GO2PROBE built > > On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori > <tomonori.oura at="" gmail.com=""> > wrote: > >> Dear BioC, >> >> How are the mappings of Affymetrix probe ids to Gene Ontology terms >> in >> > > >> metadata package provided by Bioconductor build? >> >> I am trying to use some gene set analysis packages and find some >> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but >> another package use the external gene set definition, such as MSigDB. >> >> So I want to know the criteria for select specific GO term among >> possible terms for each probe id in Bioconductor. >> I already read the documents about AnnBuilder package, however. >> > > To make a long story short, the annotations available from affy are > mapped to Entrez Gene IDs. Then, the information from Entrez Gene-- in > this case, gene ontology--is mapped to affy id. The dates associated > with the data, the source of the data, and how the data are mapped > will all affect the final mapping of affy ID to gene ontology. The > nice thing about gene ontology analyses is that they are typically > based on "sets" of genes making it much less important to start with > EXACTLY the same gene ontology mappings. In fact, in practice, it > will be pretty difficult to do so. > > If you want to see the details of the current Bioconductor annotation > package build process, you want to read the AnnotationDbi SQLForge > vignette, as AnnBuilder is outdated. > > Finally, if I have misunderstood your question, perhaps you could > clarify. > > 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 11.0 years ago by john seers IFR810
On Thu, Oct 2, 2008 at 8:18 AM, john seers (IFR) <john.seers at="" bbsrc.ac.uk=""> wrote: > > > Hi Sean > > Turning this into a more general question. Whenever I have to deal with > a new type of Affymetrix array I seem to have to root around > Bioconductor packages to find out how it is annotated etc. By the time I > come around to do it again it has all changed and is done in a different > way to how it was done before. My difficulty is it all feels a bit adhoc > and comes at me in bits and pieces. Also I always feel there is probably > a better way to do it that I am missing. > > Is there anywhere information that gives a better big picture that pulls > it together a bit? What are the foundation designs/philosophy that all > the packages are following? Is there a routemap type document that > describes Bioconductor's approach to all this? All of the annotation packages from Bioconductor follow the same scheme and contain (generally, depending on organism) the same information. The AnnotationDbi package describes these packages in detail in two vignettes and the help pages. In short, though, all the packages have a "key/value" concept where the key is typically some gene/probe identifier and the values are annotation associated with that gene/probe. Currently (in Bioc-2.2 and forward), the implementation of these packages is a SQLite database accessed via RSQLite and with a significant API build on top of that. Again, see the AnnotationDbi documentation and code for details. Hope that helps. Sean > --- > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis > Sent: 02 October 2008 11:55 > To: Oura Tomonori > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] How are GO2PROBE built > > On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> > wrote: >> Dear BioC, >> >> How are the mappings of Affymetrix probe ids to Gene Ontology terms in > >> metadata package provided by Bioconductor build? >> >> I am trying to use some gene set analysis packages and find some >> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but >> another package use the external gene set definition, such as MSigDB. >> >> So I want to know the criteria for select specific GO term among >> possible terms for each probe id in Bioconductor. >> I already read the documents about AnnBuilder package, however. > > To make a long story short, the annotations available from affy are > mapped to Entrez Gene IDs. Then, the information from Entrez Gene-- in > this case, gene ontology--is mapped to affy id. The dates associated > with the data, the source of the data, and how the data are mapped will > all affect the final mapping of affy ID to gene ontology. The nice > thing about gene ontology analyses is that they are typically based on > "sets" of genes making it much less important to start with EXACTLY the > same gene ontology mappings. In fact, in practice, it will be pretty > difficult to do so. > > If you want to see the details of the current Bioconductor annotation > package build process, you want to read the AnnotationDbi SQLForge > vignette, as AnnBuilder is outdated. > > Finally, if I have misunderstood your question, perhaps you could > clarify. > > 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 11.0 years ago by Sean Davis21k
Hi Sean Thank you for general information about current annotation mapping systems. But, I want to know the specific information about building process of metadata like, how to omit the gene ontology terms with redundant or poor information, like the description of MSigDB C5 collection bellow, >From http://www.broad.mit.edu/gsea/msigdb/collection_details.jsp#C5 GO gene sets for very broad categories, such as Biological Process, have been omitted from MSigDB. GO gene sets with fewer than 10 genes have also been omitted. Gene sets with the same members have been resolved based on the GO tree structure: if a parent term has only one child term and their gene sets have the same members, the child gene set is omitted; if the gene sets of sibling terms have the same members, the sibling gene sets are omitted. Tomonori 2008/10/2 Sean Davis <sdavis2 at="" mail.nih.gov="">: > On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: >> Dear BioC, >> >> How are the mappings of Affymetrix probe ids to Gene Ontology terms in >> metadata package provided by Bioconductor build? >> >> I am trying to use some gene set analysis packages and find some >> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but >> another package use the external gene set definition, such as MSigDB. >> >> So I want to know the criteria for select specific GO term among >> possible terms for each probe id in Bioconductor. >> I already read the documents about AnnBuilder package, however. > > To make a long story short, the annotations available from affy are > mapped to Entrez Gene IDs. Then, the information from Entrez Gene-- in > this case, gene ontology--is mapped to affy id. The dates associated > with the data, the source of the data, and how the data are mapped > will all affect the final mapping of affy ID to gene ontology. The > nice thing about gene ontology analyses is that they are typically > based on "sets" of genes making it much less important to start with > EXACTLY the same gene ontology mappings. In fact, in practice, it > will be pretty difficult to do so. > > If you want to see the details of the current Bioconductor annotation > package build process, you want to read the AnnotationDbi SQLForge > vignette, as AnnBuilder is outdated. > > Finally, if I have misunderstood your question, perhaps you could clarify. > > Sean >
ADD REPLYlink written 11.0 years ago by Oura Tomonori30
On Thu, Oct 2, 2008 at 8:13 PM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: > Hi Sean > > Thank you for general information about current annotation mapping systems. > > But, I want to know the specific information about building process of > metadata like, > how to omit the gene ontology terms with redundant or poor information, > like the description of MSigDB C5 collection bellow, > > >From http://www.broad.mit.edu/gsea/msigdb/collection_details.jsp#C5 > > GO gene sets for very broad categories, such as Biological Process, > have been omitted from MSigDB. GO gene sets with fewer than 10 genes > have also been omitted. Gene sets with the same members have been > resolved based on the GO tree structure: if a parent term has only one > child term and their gene sets have the same members, the child gene > set is omitted; if the gene sets of sibling terms have the same > members, the sibling gene sets are omitted. Marc Carlson can be authoritative on this, but there is no cleanup or omission of the data. The data are taken directly from NCBI Entrez Gene and should agree with that source as of the date that the packages were built. Sean > 2008/10/2 Sean Davis <sdavis2 at="" mail.nih.gov="">: >> On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: >>> Dear BioC, >>> >>> How are the mappings of Affymetrix probe ids to Gene Ontology terms in >>> metadata package provided by Bioconductor build? >>> >>> I am trying to use some gene set analysis packages and find some >>> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but >>> another package use the external gene set definition, such as MSigDB. >>> >>> So I want to know the criteria for select specific GO term among >>> possible terms for each probe id in Bioconductor. >>> I already read the documents about AnnBuilder package, however. >> >> To make a long story short, the annotations available from affy are >> mapped to Entrez Gene IDs. Then, the information from Entrez Gene --in >> this case, gene ontology--is mapped to affy id. The dates associated >> with the data, the source of the data, and how the data are mapped >> will all affect the final mapping of affy ID to gene ontology. The >> nice thing about gene ontology analyses is that they are typically >> based on "sets" of genes making it much less important to start with >> EXACTLY the same gene ontology mappings. In fact, in practice, it >> will be pretty difficult to do so. >> >> If you want to see the details of the current Bioconductor annotation >> package build process, you want to read the AnnotationDbi SQLForge >> vignette, as AnnBuilder is outdated. >> >> Finally, if I have misunderstood your question, perhaps you could clarify. >> >> 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 11.0 years ago by Sean Davis21k
Sean is right, We don't try to guess what parts of GO you may or may want in your analysis. As much as possible, we try to simply present all of the data. Is is sometimes helpful to let people know that our GO annotation data can be found split into two kinds of packages: The GO.db package just provides a snapshot of the GO ontology with no information to affiliate GO IDs to any genes. We don't prune anything off of this ontology. Then the other kinds of annotation packages (chip and entrez gene/organism based) contain the mappings between entrez gene IDs and GO terms which we obtain from NCBI. These too are intended to be complete as possible, and the only things left out are things that specifically don't belong in the scope of that package. So for example, you should not find mappings for mouse genes in the human centric package org.Hs.eg.db. But I am not sure how comparable this really is to MSigDB... Marc Sean Davis wrote: > On Thu, Oct 2, 2008 at 8:13 PM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: > >> Hi Sean >> >> Thank you for general information about current annotation mapping systems. >> >> But, I want to know the specific information about building process of >> metadata like, >> how to omit the gene ontology terms with redundant or poor information, >> like the description of MSigDB C5 collection bellow, >> >> >From http://www.broad.mit.edu/gsea/msigdb/collection_details.jsp#C5 >> >> GO gene sets for very broad categories, such as Biological Process, >> have been omitted from MSigDB. GO gene sets with fewer than 10 genes >> have also been omitted. Gene sets with the same members have been >> resolved based on the GO tree structure: if a parent term has only one >> child term and their gene sets have the same members, the child gene >> set is omitted; if the gene sets of sibling terms have the same >> members, the sibling gene sets are omitted. >> > > Marc Carlson can be authoritative on this, but there is no cleanup or > omission of the data. The data are taken directly from NCBI Entrez > Gene and should agree with that source as of the date that the > packages were built. > > Sean > > >> 2008/10/2 Sean Davis <sdavis2 at="" mail.nih.gov="">: >> >>> On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: >>> >>>> Dear BioC, >>>> >>>> How are the mappings of Affymetrix probe ids to Gene Ontology terms in >>>> metadata package provided by Bioconductor build? >>>> >>>> I am trying to use some gene set analysis packages and find some >>>> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but >>>> another package use the external gene set definition, such as MSigDB. >>>> >>>> So I want to know the criteria for select specific GO term among >>>> possible terms for each probe id in Bioconductor. >>>> I already read the documents about AnnBuilder package, however. >>>> >>> To make a long story short, the annotations available from affy are >>> mapped to Entrez Gene IDs. Then, the information from Entrez Gene --in >>> this case, gene ontology--is mapped to affy id. The dates associated >>> with the data, the source of the data, and how the data are mapped >>> will all affect the final mapping of affy ID to gene ontology. The >>> nice thing about gene ontology analyses is that they are typically >>> based on "sets" of genes making it much less important to start with >>> EXACTLY the same gene ontology mappings. In fact, in practice, it >>> will be pretty difficult to do so. >>> >>> If you want to see the details of the current Bioconductor annotation >>> package build process, you want to read the AnnotationDbi SQLForge >>> vignette, as AnnBuilder is outdated. >>> >>> Finally, if I have misunderstood your question, perhaps you could clarify. >>> >>> 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 11.0 years ago by Marc Carlson7.2k
And you can do any/all of the filtering that is described on the Broad page if you want to (all evidence codes and the entire tree structure is available to you). You could also use GSEAbase and the tools in it to simply retrieve the Broad sets, if you think you want to use them without having to recreate. you may see differences as they downloaded their GO data in January of last year - we downloaded ours more recently (each package gives you explicit dates and sources) Marc Carlson wrote: > Sean is right, > > We don't try to guess what parts of GO you may or may want in your > analysis. As much as possible, we try to simply present all of the > data. Is is sometimes helpful to let people know that our GO annotation > data can be found split into two kinds of packages: > > The GO.db package just provides a snapshot of the GO ontology with no > information to affiliate GO IDs to any genes. We don't prune anything > off of this ontology. > > Then the other kinds of annotation packages (chip and entrez > gene/organism based) contain the mappings between entrez gene IDs and GO > terms which we obtain from NCBI. These too are intended to be complete > as possible, and the only things left out are things that specifically > don't belong in the scope of that package. So for example, you should > not find mappings for mouse genes in the human centric package > org.Hs.eg.db. > > But I am not sure how comparable this really is to MSigDB... > > Marc > > > > Sean Davis wrote: >> On Thu, Oct 2, 2008 at 8:13 PM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: >> >>> Hi Sean >>> >>> Thank you for general information about current annotation mapping systems. >>> >>> But, I want to know the specific information about building process of >>> metadata like, >>> how to omit the gene ontology terms with redundant or poor information, >>> like the description of MSigDB C5 collection bellow, >>> >>> >From http://www.broad.mit.edu/gsea/msigdb/collection_details.jsp#C5 >>> >>> GO gene sets for very broad categories, such as Biological Process, >>> have been omitted from MSigDB. GO gene sets with fewer than 10 genes >>> have also been omitted. Gene sets with the same members have been >>> resolved based on the GO tree structure: if a parent term has only one >>> child term and their gene sets have the same members, the child gene >>> set is omitted; if the gene sets of sibling terms have the same >>> members, the sibling gene sets are omitted. >>> >> Marc Carlson can be authoritative on this, but there is no cleanup or >> omission of the data. The data are taken directly from NCBI Entrez >> Gene and should agree with that source as of the date that the >> packages were built. >> >> Sean >> >> >>> 2008/10/2 Sean Davis <sdavis2 at="" mail.nih.gov="">: >>> >>>> On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at="" gmail.com=""> wrote: >>>> >>>>> Dear BioC, >>>>> >>>>> How are the mappings of Affymetrix probe ids to Gene Ontology terms in >>>>> metadata package provided by Bioconductor build? >>>>> >>>>> I am trying to use some gene set analysis packages and find some >>>>> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but >>>>> another package use the external gene set definition, such as MSigDB. >>>>> >>>>> So I want to know the criteria for select specific GO term among >>>>> possible terms for each probe id in Bioconductor. >>>>> I already read the documents about AnnBuilder package, however. >>>>> >>>> To make a long story short, the annotations available from affy are >>>> mapped to Entrez Gene IDs. Then, the information from Entrez Gene--in >>>> this case, gene ontology--is mapped to affy id. The dates associated >>>> with the data, the source of the data, and how the data are mapped >>>> will all affect the final mapping of affy ID to gene ontology. The >>>> nice thing about gene ontology analyses is that they are typically >>>> based on "sets" of genes making it much less important to start with >>>> EXACTLY the same gene ontology mappings. In fact, in practice, it >>>> will be pretty difficult to do so. >>>> >>>> If you want to see the details of the current Bioconductor annotation >>>> package build process, you want to read the AnnotationDbi SQLForge >>>> vignette, as AnnBuilder is outdated. >>>> >>>> Finally, if I have misunderstood your question, perhaps you could clarify. >>>> >>>> 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD REPLYlink written 11.0 years ago by rgentleman5.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 94 users visited in the last hour