Hi Marc, Darn, you're right? there is only 39 entries for S. pombe in the gene_info file? $ wget -qO- ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz |gunzip -c | awk '$1~/^4896$/{print $0}' |wc -l 39 And this is despite the fact that there is 13,211 gene entries associated with this organism (taken from the taxonomy browser web page)!! Is that a bug that should be reported to NCBI? The fact that their publicly available data files don't reflect their internal representations is disconcerting. I feel there something that should be done to rectify the problem. On the other hands, thanks a lot for exploring alternative strategies to populate org database, let me know if you need me to beta test it before the next release. Marco -- Marco Blanchette, Ph.D. Stowers Institute for Medical Research 1000 East 50th Street Kansas City MO 64110 www.stowers.org On 8/26/13 7:25 PM, "Marc Carlson" <mcarlson at="" fhcrc.org=""> wrote: >Hi Marco, > >So the function you are using is downloading this file from NCBI: > >ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz > >And if you grab that file and grep for the lines that start with your >tax ID you will find about 38 lines in it to indicate unique entrez gene >IDs. That means that we currently only have 38 gene IDs to parse from >NCBI (at least from the files that they are giving us). Its frustrating >for me too that fission yeast is not better, but this is what we have. :( > >I am already planning something more general so that when this happens >you will not be stuck using just one annotation resource for org >packages, but unfortunately it is not going to be finished tomorrow. >But hopefully I will have it in time to be in the next release. > > > Marc > > >On 08/23/2013 07:24 PM, Blanchette, Marco wrote: >> I am working on a project involving Schizosaccharomyces pombe as a >>source for genomic analysis and love to use ReportingTools html >>producing wrappers. However, I am struggling as there is no >>AnnotationDbi package available for this organism. I decided to finally >>take the plunge and try to see if I could be one myself using >>AnnotationForge and was quite exciting to find that I could perhaps melt >>one simply by using the makeOrgPackageFromNCBI(). Most likely, something >>went wrong and I suspect a bug somewhere in the pipeline. I have not dug >>deeper then trying to build the package and use it hoping that someone >>closer to the code could shed some lights. Here the steps I took:' >> >>> library(AnnotationForge) >>> makeOrgPackageFromNCBI(version = "0.1", >> author = "Marco Blanchette <mab at="" stowers.org="">", >> maintainer = "Marco Blanchette >><mab at="" stowers.org="">", >> outputDir = ".", >> tax_id = "4896", >> genus = "Schizosaccharomyces", >> species = "pombe") >> >> This step succeeded with only a warning: >> >> Warning message: >> In .makeSimpleTable(ug, table = "unigene", con) : >> no values found for table unigene in this data chunk. >> >> I didn't think this was critical enough to raise any red flag, so I >>then proceeded with the installation that went smoothly >> >>> library(devtools) >>> install('org.Spombe.eg.db') >>> library('org.Spombe.eg.db') >> Then I try to use it with ReportingTools publish() but fail as it >>returns an error related to Entrez ID which I had a conversion table >>from biomaRt. I dug a bit deeper and found that none of the genes I was >>querying were in the database to finally realize that there was only 38 >>entries int the org.Spombe.eg.db database I had just created and >>installed... Check this out: >> >>> keytypes(org.Spombe.eg.db) >> [1] "ENTREZID" "ACCNUM" "ALIAS" "CHR" "PMID" "REFSEQ" >> [7] "SYMBOL" "UNIGENE" "GENENAME" "GO" "EVIDENCE" "ONTOLOGY" >> >> Looking good! However: >> >>> length(keys(org.Spombe.eg.db,'ENTREZID')) >> [1] 38 >> >> Can someone close enough to the code shed some lights has to whether >>there is a bug in AnnotationForge or whether it is the NCBI database >>that is not conforming to what is expected? For instance, biomart has >>5117 entrez ID >> >>> library(biomaRt) >>> mart <- useMart("fungi_mart_18","spombe_eg_gene") >>> ensembl2entrez <- getBM(c('ensembl_gene_id','entrezgene'),mart=mart) >>> sum(!is.na(ensembl2entrez$entrezgene)) >> [1] 5117 >> >> The ids I tested on the NCBI website return the correct genes. However, >>only 10 of the AnnotationForge EntrezID (out of a skirmish 38 ids) are >>found in biomaRt >> >>> sum(keys(org.Spombe.eg.db,'ENTREZID') %in% ensembl2entrez$entrezgene) >> [1] 10 >> >> Again, I would appreciate any comments or suggestions as to whether >>this is a bug or something I did wrong or a miss alignment between the >>NCBI S. pombe annotation and what is expected by AnnotationForge. >> >> Thanks > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor