>I'm not sure what you mean by saying the program stopped because they
are
>not mapped to "enzyme annotation data"? I don't think you mean that
your
>input has to code for enzymes? :)
No mapping for enzyme was obtained from the source data provided by
KEGG.
>Could you please clarify the path that
>ABPkgBuilder takes
>to get the information from such databases such as LocusLink,
UniGene,
>Golden Path, Gene Ontology, and
>KEGG. My sample input file is representative of the rest of my data.
>I took my clone IDs and went to the I.M.A.G.E. site and got the
>corresponding
>genbank accession numbers. With these numbers I want to ge the
unigene
>information.
Map probe ids to LocusLink ids and then use LocusLink ids as the point
of
linkage to get annotation data from the source data.
Data from UniGene is used for mapping GenBank accesion numbers to
LocusLink ids
only. If you only want data from UniGene for your clones, you may
simple write a
parser to parse the data from UniGene other than building a package
using
AnnBuilder that has a lot of things you do not enve need.
>
>I looked at your example "How to use AnnBuilder" and looked at the
Genbank
>accession numbers and
>compared them to mine. When I type in for example D90278 into Entrez
you
>find that it has a locus and one
>of the link outs is Gene. However, when I type in one of my Genbank
>accession numbers T65425 into Entrez
>a locus is not available and the only useful link is to unigene.
This will
>be the case for my data.
AnnBuilder maps GenBank accession number by unifying the mappings
provided by
LocusLink, UniGene, and "other sources" specified by a user. If a map
is
provided by either LocusLink or UniGene, that map is assinged to a
probe id.
Otherwise, the map provided by the majority of "other sources" will be
assigned
to a probe id.
>Is it possible that ABPkgBuilder requires that there is a locus for
your
>Genbank accession number in order
>to access information from the other databases (LocusLink, UniGene,
Golden
>Path, Gene Ontology, and KEGG)?
AnnBuilder does the mapping using LocusLink id as the point of linkage
between
data souces. If a GenBank accession number can be mapped to a
LocusLink id,
annotation data may be obtained. Otherwise, no annotation data will be
obtained.
>
>If ABPkgBuilder does not allow me to get a unigene cluster from a
Genbank
>Accession number for my clones
>are there other functions within Bioconductor that will enable me to
achieve
>my goal?
When the annotation is done, you do have UniGene ids as one of the
annotation
element. If you want to use UniGene ids as the base mapping type, you
will have
to get the correct UniGene ids yourself.
>
>thanks very much for your help,
>Annie.
>
>-----Original Message-----
>From: John Zhang [mailto:jzhang@jimmy.harvard.edu]
>Sent: Friday, December 12, 2003 1:56 PM
>To: Annie.Law@nrc-cnrc.gc.ca
>Subject: RE: [BioC] Annotation data package is not being created
>
>
>I tried your base file. It stoped because the colones were not mapped
to any
>
>enzyme annotation data. I will add some error traping functions in
but
>meanwhile
>you may try some real data to see how it works for you. The most time
>consumming
>parts are source data processing. The size of your base file does not
reduce
>the
>time of execution much.
>
>>From: "Law, Annie" <annie.law@nrc-cnrc.gc.ca>
>>To: "'John Zhang'" <jzhang@jimmy.harvard.edu>
>>Subject: RE: [BioC] Annotation data package is not being created
>>Date: Thu, 11 Dec 2003 16:00:46 -0500
>>MIME-Version: 1.0
>>X-Keywords:
>>
>>Hi John,
>>
>>Here is my file.
>>
>>thank you,
>>Annie.
>>
>>
>>-----Original Message-----
>>From: John Zhang [mailto:jzhang@jimmy.harvard.edu]
>>Sent: Thursday, December 11, 2003 3:41 PM
>>To: Annie.Law@nrc-cnrc.gc.ca
>>Cc: bioconductor@stat.math.ethz.ch
>>Subject: Re: [BioC] Annotation data package is not being created
>>
>>
>>Could you send me a copy of your base file so that I can try it to
figure
>>out
>>what might be wrong? Thanks.
>>>
>>>I would appreciate help with the following. I was following the
vignette
>>>"How to use AnnBuilder".
>>>I tried to adapt this to my goal of creating an annotation data
package
>>with
>>>the Unigene Identifiers.
>>>I made some very minor changes and used the file samclonegb2 which
is just
>>a
>>>small text file with
>>>the first column being a list of IMAGE cloneIDs and the second
column is a
>>>list of GenBank accesion numbers.
>>>I used the following lines and the sampclonegb2 seem to load
properly and
>>>then finally
>>>I got the error message listed below. I get some output files
formed for
>>>example the XML file is formed
>>>but my input data has not been mapped to any of the information
from the
>>>databases.
>>>"Error in "colnames<-"(`*tmp*`, value = colNames) :
>>> attempt to set colnames on object with less than two
dimensions"
>>>I am not sure what I am missing.
>>>
>>>Also, my current file sampclonegb2 is very simple in that I have
one
>>Genbank
>>>accession number
>>>for each cloneID. My actual source file contains cases where I
have more
>>>than one
>>>Genbank accession number associated with a cloneid. What is the
best way
>>to
>>>approach this?
>>>
>>>thanks very much,
>>>Annie.
>>>
>>>
>>>library(AnnBuilder)
>>>read.table(file.path(.path.package("AnnBuilder"), "data",
"sampclonegb2"),
>>>sep = "\t", header = FALSE, as.is = TRUE)
>>>myBase <- file.path(.path.package("AnnBuilder"), "data",
"sampclonegb2")
>>>myBaseType <- "gb"
>>>mySrcUrls <- getSrcUrl("all", organism = "human")
>>>mySrcUrls
>>>myDir <- tempdir()
>>>if (.Platform$OS.type == "unix") {
>>>fromWeb <- TRUE
>>>} else {
>>>fromWeb <- FALSE
>>>}
>>>if (.Platform$OS.type != "windows") {
>>>ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
>>>myBaseType,
>>>otherSrc = NULL, pkgName = "abmyPkg", pkgPath = myDir,
>>>organism = "human", version = "1.1.0", makeXML = TRUE,
>>>author = list(author = "Annie", maintainer = "myname@myemail.com"),
>>>fromWeb =fromWeb)}
>>>
>>>"It may take me a while to process the data. Be patient!"
>>>Error in "colnames<-"(`*tmp*`, value = colNames) :
>>> attempt to set colnames on object with less than two
dimensions
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
>>>Bioconductor@stat.math.ethz.ch
>>>
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>>
