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Question: org.Hs.eg.db - hg38 build?
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gravatar for Brian Smith
19 months ago by
Brian Smith110
United States
Brian Smith110 wrote:

Hi,

How can I determine which build org.Hs.eg.db based on?

 

thanks!

ADD COMMENTlink modified 19 months ago by Keith Hughitt100 • written 19 months ago by Brian Smith110
0
gravatar for James W. MacDonald
19 months ago by
United States
James W. MacDonald45k wrote:
The orgDb packages don't really contain any positional annotation. They used to, but these days you will be directed to a TxDb package if you try to get positional info. And the TxDb have the build in the package name. The orgDb packages mostly contain mappings between various databases and some functional annotation, none of which is based on any build. In fact, most of that stuff is updated weekly or monthly, so the orgDb packages get outdated to a certain extent rather quickly.
ADD COMMENTlink written 19 months ago by James W. MacDonald45k
0
gravatar for Keith Hughitt
19 months ago by
Keith Hughitt100
United States
Keith Hughitt100 wrote:

The current version of org.Hs.eg.db is based on hg19:

> org.Hs.eg.db
OrgDb object:
| DBSCHEMAVERSION: 2.1
| Db type: OrgDb
| Supporting package: AnnotationDbi
| DBSCHEMA: HUMAN_DB
| ORGANISM: Homo sapiens
| SPECIES: Human
| EGSOURCEDATE: 2016-Mar14
| EGSOURCENAME: Entrez Gene
| EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| CENTRALID: EG
| TAXID: 9606
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 20160305
| GOEGSOURCEDATE: 2016-Mar14
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| KEGGSOURCENAME: KEGG GENOME
| KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
| KEGGSOURCEDATE: 2011-Mar15
| GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
| GPSOURCEURL: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19
| GPSOURCEDATE: 2010-Mar22
| ENSOURCEDATE: 2016-Mar9
| ENSOURCENAME: Ensembl
| ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
| UPSOURCENAME: Uniprot
| UPSOURCEURL: http://www.UniProt.org/
| UPSOURCEDATE: Wed Mar 23 15:50:09 2016

Also, you may want to check out newer Homo.sapiens organism package which combines the org.db and TxDb resources into a single API.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Keith Hughitt100

The only data in the orgDb packages that comes from hg19 is the outdated CHRLOC table, and as I already mentioned, any query to that table will result in a message saying you should use a TxDb package for that info. The remaining data are not based on any build, as things like an Entrez Gene ID are build agnostic. So to say it is based on any build is misleading.

ADD REPLYlink written 19 months ago by James W. MacDonald45k

Thanks for the clarification, James! I don't think I ever fully appreciated the precise scope of the org.db packages. That explanation helps to clear some things up for me.

ADD REPLYlink written 19 months ago by Keith Hughitt100
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