Dear Nianhua,

As a point 1, you wrote
> Not all probeset ids have matching AGI locus ids. Do we need to  
> provide mapping
> to other gene identifiers such as GenBank Accession number or  
> Entrez Gene IDs to
> make annoations more complete? Affymetrix starts to provide  
> probeset id to
> Entrez Gene ID mappings in their annotation files. Should we  
> include that
> information? Also, I can see three possible ways to get probe-to- 
> GenBank
> mapping: 1) from affymetrix annotation file directly, 2)probe to  
> AGI locus and
> then AGI locus to GenBank accession, all from TAIR, 3)probe to  
> Entrez Gene from
> affy, and then Entrez Gene to GenBank from NCBI. Which way is the  
> best? or
> should we use the "voting" algorithm used by ABPkgBuilder?

I have remapped the probes against the transcripts myself, so I don't  
use the ath1121501 annotation package. As far as I know, for  
Arabidopsis, all the annotations of the Arabidopsis genes are based  
on the AGI IDs, and not on the geneIDs or EntrezGene IDs. TAIR does  
provide files with these mappings: you find them on ftp:// 
ftp.arabidopsis.org/home/tair/home/tair/Genes/ ,  
TAIR6_NCBI_mapping_mRNA and TAIR6_NCBI_mapping_prot. They don't store  
the Entrez gene IDs, but one could map the AGI IDs to the Gene IDs  
(from the 2 files I listed above) and use these to obtain the Entrez  
gene IDs (using the gene2accession.gz file on ftp://ftp.ncbi.nih.gov/ 
gene/DATA).

But is this all worth the trouble, since all the metadata are based  
on the AGI IDs? What would be the benefit of using entrez geneIDs?

When you say 'not all probeset if have a matching AGI locus', you are  
still talking about 'affy_ATH1_array_elements-2006-07-14.txt' from  
ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/, right?  
There are indeed 531 probesets without a proper ID, but how would you  
obtain these? From affymetrix? But then you will be mixing the  
affymetrix mappings of the probe sequences to the transcripts and  
those of TAIR...


About KEGG: would it be very difficult to include these in the  
annotation package?

About the PMIDs: I mailed TAIR about this earlier this week (mapping  
locus IDs to PMIDs) and they pointed me to ftp://ftp.arabidopsis.org/ 
home/tair/User_Requests/LocusPublished.08012006.txt .


kind regards,

tine


On 10 Aug 2006, at 11:00, bioconductor-request@stat.math.ethz.ch wrote:

> Message: 10
> Date: Wed, 9 Aug 2006 18:46:09 +0000 (UTC)
> From: Nianhua Li <nli@fhcrc.org>
> Subject: [BioC] athPkgBuilder data source
> To: bioconductor@stat.math.ethz.ch
> Message-ID: <loom.20060809T203415-7@post.gmane.org>
> Content-Type: text/plain; charset=us-ascii
>
> Dear list,
>
> I had some doubts on the data sources used by athPkgBuilder that I  
> post on
> bioc-devel list two months ago, but got no reply. I would like to  
> try one more
> time here. Sorry for the double posting.
>
> ----------------------------------------------------------------
>
> I did a close look at the athPkgBuilder function in AnnBuilder  
> (builder of
> ath1121501 and ag) and have some questions about the data source  
> being used:
>
> 1. probeset id to gene mapping:
> The current mapping strategy was
> 1) map probe id to "Representative.Public.ID" by using Affymetrix  
> GeneChip
> annotation data
> 2) use "Representative.Public.ID" as if it was AGI locus id to get  
> other
> annotations (pathway, go, etc) from TAIR
>
> It seems that the "Representative.Publid.ID is a mix of AGI locus  
> id, UniGene
> Cluster and a small part of other sources. In the affymetrix  
> annotation file,
> there is another column called "Transcript ID (Array Design)",  
> which has almost
> the same value as "Prepresentative.Public.ID". I feel it was  
> originated from
> ftp://ftp.tigr.org/pub/data/a_thaliana/Affymetrix/. Not sure  
> whether affymetrix
> update those two columns on a regular basis or not.
>
> But if all the annotations (chromosome, go, pathway) come from  
> TAIR, maybe we
> should use TAIR's mapping of  probeset id to AGI locus id:
> ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/ :
>     "The oligonucleotide sequences of the probes were mapped to the  
> Arabidopsis
> Transcripts dataset from the Arabidopsis genome TAIR6 version  
> (released November
> 11, 2005).
> The dataset included mitochondria and chloroplast genes, as well as  
> pseudogenes
> and non-
> coding RNAs. The mapping to the TAIR6 Transcripts was performed  
> using the BLASTN
> program
> with e-value cutoff < 9.9e-6. For the 25-mer oligo probes used on  
> the Affy
> chips, the
> required match length to achieve this e-value is 23 or more identical
> nucleotides. To
> assign a probe set to a given locus, at least 9 of the probes  
> included in the
> probe set
> were required to match a transcript at that locus."
>
> Not all probeset ids have matching AGI locus ids. Do we need to  
> provide mapping
> to other gene identifiers such as GenBank Accession number or  
> Entrez Gene IDs to
> make annoations more complete? Affymetrix starts to provide  
> probeset id to
> Entrez Gene ID mappings in their annotation files. Should we  
> include that
> information? Also, I can see three possible ways to get probe-to- 
> GenBank
> mapping: 1) from affymetrix annotation file directly, 2)probe to  
> AGI locus and
> then AGI locus to GenBank accession, all from TAIR, 3)probe to  
> Entrez Gene from
> affy, and then Entrez Gene to GenBank from NCBI. Which way is the  
> best? or
> should we use the "voting" algorithm used by ABPkgBuilder?
>
> 2. chromosome location
> The current package get chromosome locations from
> ftp://ftp.arabidopsis.org/home/tair/Genes/est_mapping/ 
> est.Assignment.Locus
> Even though the file seems being updated very often, the directory  
> it locates in
> and the README file were not. So, it is not clear for me how it was
> generated/updated. Any hint on that? Will
> ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/ be a  
> better source?
> The meaning of chromosome location in those two sources may be  
> different though.
> The former means the location of a GenBank EST, and the later means  
> "chromosome
> coordinates of the best probe set match to the Transcripts
> dataset".
>
> 3. gene description (ath1121501GENENAME)
> The current package (1.12.1) get the description from
> ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes The  
> descriptions
> are the same as ftp://ftp.arabidopsis.org/home/tair/Microarrays/ 
> Affymetrix/ Both
> of them means the description of the AGI locus corresponding to a  
> affy probeset.
> In the Affymetrix annotation file, there is a column called "Target
> Description". It is the description of the gene that a probeset is  
> targeting to.
> All probesets have descriptions, therefore we get a better coverage  
> than getting
> description from TAIR. When the "Representative Public ID" (or  
> "Transcript ID")
> is a AGI locus id, it seems the description was retrieved from  
> TAIR. However, it
> is not clear how this information is updated, and whether it is  
> synchronized
> with TAIR's update or not. Another possible source of description  
> is Entrez
> Gene, since Affymetrix maps probeset to Entrez Gene.
>
> 4. pathway
> Pathway information is currently obtained from AraCyc, a pathway  
> tool in TAIR:
> http://www.arabidopsis.org/tools/aracyc/introduction.jsp . I feel  
> it only
> contains metabolic pathways (it can be wrong as I only read the  
> introduction).
> KEGG contains regulatory pathways as well, and it is also manually  
> curated.
> Those two sources are independant from each other. Shall we include  
> both of them?
>
> 5. pubmed
> Probeset to pubmed mapping is currently obtained from
> ftp://ftp.arabidopsis.org/home/tair/Ontologies/Plant_Ontology/ 
> stru-060309.txt .
> The pubmed ids represents the publications that TAIR used to map a  
> AGI locus id
> to a concept in Plant Ontology. But I think environment like  
> ath1121501PUBMED
> should represent the publications about the matching gene of a  
> probeset. I
> didn't find AGI locus to pubmed mapping in TAIR. So, we have to get  
> it from
> either Entrez Gene id or GenBank accession. This gets back to the  
> frist
> question: what is the best way to map probeset to GenBank/Entrez Gene?
>
> Hope this email is not too long. Any feedback will be highly  
> appreciated. If we
> decide to use a better data source, I will be happy to do the  
> implementation.
>
> many thanks
>
> Nianhua Li
> computational biology, public health, FHCRC
>


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