org.Dm.egACCNUM2EG
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Tiandao Li ▴ 260
@tiandao-li-2372
Last seen 10.2 years ago
Hello, Recently I installed org.Dm.eg.db for GO analysis. My sequences were blasted against siwssprot, using the following format in the annotation part of genepix files ID Name 16A-A02.g P80096 16A-A03.g Q9U572 ... I tried org.Dm.egACCUM2EG$"P80096" to get Entrez gene id. and it came with NULL. How can I get EG from swissprot acc? Thanks, Tiandao
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.3 years ago
United States
Tiandao Li wrote: > Hello, > > Recently I installed org.Dm.eg.db for GO analysis. My sequences were > blasted against siwssprot, using the following format in the annotation > part of genepix files > > ID Name > 16A-A02.g P80096 > 16A-A03.g Q9U572 > ... > > I tried org.Dm.egACCUM2EG$"P80096" to get Entrez gene id. and it came with > NULL. How can I get EG from swissprot acc? > > Thanks, > > Tiandao > > _______________________________________________ > 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 > > I am afraid that the answer is that the ACCNUM maps are for genbank IDs only. Because of the way that NCBI handles genebank and its affiliated nucleotide sequences, genebank accessions are sometimes connected to TrEMBL (translated sequences), but never to Swissprot IDs. Swissprot IDs have not been included in our annotation packages before. In the past, the focus of the annotation packages has been to make them gene-centric and so to date no protein-centric IDs have been included in these packages. However, the data packages are a work in progress and we are always interested in user feedback to make them better. Do you feel that there is a wide reaching need for the associated protein IDs to be mapped in to these annotation packages? If you feel this is so, please let us know what you think. In the meantime I believe that the biomart package can be used for mapping your swissprot IDs. Marc
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Dear Marc, Thanks for your response. I blasted my sequences against nr, nt, swissprot databases. Since no protein IDs are supported in these annotation packages, however I still can't get EG ids from nt BLAST search. I am thinking do blast search against Unigene Drosophila (Nucleotide) or any other databases, is it OK? I tried to install biomaRt on my Ubuntu box for a week, and it always came the same wrong msg. I just don't know how to handle it. Thanks, Tiandao > source("http://bioconductor.org/getBioC.R") > getBioC("biomaRt",lib="/usr/local/lib/R/site-library/") Running biocinstall version 2.1.8 with R version 2.6.0 Your version of R requires version 2.1 of Bioconductor. also installing the dependencies ‘RCurl’, ‘XML’ trying URL 'http://bioconductor.org/packages/2.1/extra/src/contrib/RCurl_0.8-3.ta r.gz' Content type 'application/x-gzip' length 218153 bytes (213 Kb) opened URL ================================================== downloaded 213 Kb trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.93-2.tar.gz' Content type 'application/x-gzip' length 870234 bytes (849 Kb) opened URL ================================================== downloaded 849 Kb trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/biomaRt_1.12.1. tar.gz' Content type 'application/x-gzip' length 275514 bytes (269 Kb) opened URL ================================================== downloaded 269 Kb * Installing *source* package 'RCurl' ... checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package 'RCurl' ** Removing '/usr/local/lib/R/site-library/RCurl' * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package 'XML' ** Removing '/usr/local/lib/R/site-library/XML' * Installing *source* package 'biomaRt' ... ** R ** inst ** preparing package for lazy loading Loading required package: RCurl Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'RCurl' Error: package 'RCurl' could not be loaded Execution halted ERROR: lazy loading failed for package 'biomaRt' ** Removing '/usr/local/lib/R/site-library/biomaRt' The downloaded packages are in /tmp/Rtmp3SQVK7/downloaded_packages Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'RCurl' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'XML' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'biomaRt' had non-zero exit status > sessionInfo() R version 2.6.0 (2007-10-03) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.0 On Fri, 2 Nov 2007, Marc Carlson wrote: Tiandao Li wrote: > Hello, > > Recently I installed org.Dm.eg.db for GO analysis. My sequences were > blasted against siwssprot, using the following format in the annotation > part of genepix files > > ID Name > 16A-A02.g P80096 > 16A-A03.g Q9U572 > ... > > I tried org.Dm.egACCUM2EG$"P80096" to get Entrez gene id. and it came with > NULL. How can I get EG from swissprot acc? > I am afraid that the answer is that the ACCNUM maps are for genbank IDs only. Because of the way that NCBI handles genebank and its affiliated nucleotide sequences, genebank accessions are sometimes connected to TrEMBL (translated sequences), but never to Swissprot IDs. Swissprot IDs have not been included in our annotation packages before. In the past, the focus of the annotation packages has been to make them gene-centric and so to date no protein-centric IDs have been included in these packages. However, the data packages are a work in progress and we are always interested in user feedback to make them better. Do you feel that there is a wide reaching need for the associated protein IDs to be mapped in to these annotation packages? If you feel this is so, please let us know what you think. In the meantime I believe that the biomart package can be used for mapping your swissprot IDs. Marc
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Hi Tiandao, Tiandao Li wrote: [...] > * Installing *source* package 'RCurl' ... > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package 'RCurl' > ** Removing '/usr/local/lib/R/site-library/RCurl' I think you need to install the libcurl3 Ubuntu package first (use synaptic). > * Installing *source* package 'XML' ... > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > checking for sed... /bin/sed > checking for xml2-config... no > Cannot find xml2-config > ERROR: configuration failed for package 'XML' > ** Removing '/usr/local/lib/R/site-library/XML' And for this one you need libxml2-dev (I think). Cheers, H.
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Dear Herve, I installed libcurl3 and libcurl3-gnutlsbefore, and this time libxml2-dev and libcurl3-dbg. Still get the wrong msg. > source("http://bioconductor.org/getBioC.R") > getBioC("biomaRt",lib="/usr/local/lib/R/site-library/") Running biocinstall version 2.1.8 with R version 2.6.0 Your version of R requires version 2.1 of Bioconductor. also installing the dependencies ‘RCurl’, ‘XML’ trying URL 'http://bioconductor.org/packages/2.1/extra/src/contrib/RCurl_0.8-3.ta r.gz' Content type 'application/x-gzip' length 218153 bytes (213 Kb) opened URL ================================================== downloaded 213 Kb trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.93-2.tar.gz' Content type 'application/x-gzip' length 870234 bytes (849 Kb) opened URL ================================================== downloaded 849 Kb trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/biomaRt_1.12.1. tar.gz' Content type 'application/x-gzip' length 275514 bytes (269 Kb) opened URL ================================================== downloaded 269 Kb * Installing *source* package 'RCurl' ... checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package 'RCurl' ** Removing '/usr/local/lib/R/site-library/RCurl' * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for xml2-config... /usr/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -r Minor 6, Patch 30 for 2.6.30 Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8: -I/usr/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes checking for xmlHashSize in -lxml2... yes Using built-in xmlHashSize Checking DTD parsing (presence of externalSubset)... checking for xmlHashSize in -lxml2... yes Found xmlHashSize checking for xmlOutputBufferCreateBuffer in -lxml2... yes have xmlOutputBufferCreateBuffer() checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes checking libxml/xmlversion.h usability... yes checking libxml/xmlversion.h presence... yes checking for libxml/xmlversion.h... yes Expat: FALSE Checking for return type of xmlHashScan element routine. No return value for xmlHashScan **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -L/usr/lib -lxml2 -lz -lxml2 libxml 2: -DLIBXML2=1 Compilation flags: -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 Link flags: -L/usr/lib -lxml2 -lz -lxml2 **************************************** configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/supports.R config.status: creating inst/scripts/RSXML.csh config.status: creating inst/scripts/RSXML.bsh ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c catalog.c -o catalog.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c DocParse.c -o DocParse.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c EventParse.c -o EventParse.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c ExpatParse.c -o ExpatParse.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c HTMLParse.c -o HTMLParse.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c RSDTD.c -o RSDTD.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c RUtils.c -o RUtils.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c Utils.c -o Utils.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c XMLEventParse.c -o XMLEventParse.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c XMLTree.c -o XMLTree.o gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c xpath.c -o xpath.o gcc -std=gnu99 -shared -o XML.so catalog.o DocParse.o EventParse.o ExpatParse.o HTMLParse.o RSDTD.o RUtils.o Utils.o XMLEventParse.o XMLTree.o xpath.o -L/usr/lib -lxml2 -lz -lxml2 -L/usr/lib/R/lib -lR ** R ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'XML' Formats: text html latex example AssignXMLNode text html latex example Doctype-class text html latex example Doctype text html latex example SAXMethods text html latex example SAXState-class text html latex example XMLInternalDocument text html latex example XMLNode-class text html latex example addChildren text html latex example addNode text html latex example append.XMLNode text html latex example asXMLNode text html latex example asXMLTreeNode text html latex example catalogResolve text html latex example dtdElement text html latex example dtdElementValidEntry text html latex example dtdIsAttribute text html latex example dtdValidElement text html latex example free text html latex example genericSAXHandlers text html latex example getNodeSet text html latex example length.XMLNode text html latex example libxmlVersion text html latex example names.XMLNode text html latex example newXMLDoc text html latex example parseDTD text html latex example parseURI text html latex example print text html latex example saveXML text html latex example supportsExpat text html latex example toHTML text html latex example toString text html latex example xmlApply text html latex example xmlAttributeType text html latex example xmlAttrs text html latex example xmlChildren text html latex example xmlContainsEntity text html latex example xmlDOMApply text html latex example xmlElementsByTagName text html latex example xmlEventHandler text html latex example xmlEventParse text html latex example xmlFlatListTree text html latex example xmlGetAttr text html latex example xmlHandler text html latex example xmlName text html latex example xmlNamespace text html latex example xmlNamespaceDefinitions text html latex example xmlNode text html latex example xmlOutput text html latex example xmlParent text html latex example xmlRoot text html latex example xmlSize text html latex example xmlSource text html latex example xmlSubset text html latex example xmlTree text html latex example xmlTreeParse text html latex example xmlValue text html latex example ** building package indices ... * DONE (XML) * Installing *source* package 'biomaRt' ... ** R ** inst ** preparing package for lazy loading Loading required package: RCurl Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'RCurl' Error: package 'RCurl' could not be loaded Execution halted ERROR: lazy loading failed for package 'biomaRt' ** Removing '/usr/local/lib/R/site-library/biomaRt' The downloaded packages are in /tmp/RtmpUy98cH/downloaded_packages Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'RCurl' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'biomaRt' had non-zero exit status > On Fri, 2 Nov 2007, Herve Pages wrote: Hi Tiandao, Tiandao Li wrote: [...] > * Installing *source* package 'RCurl' ... > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package 'RCurl' > ** Removing '/usr/local/lib/R/site-library/RCurl' I think you need to install the libcurl3 Ubuntu package first (use synaptic). > * Installing *source* package 'XML' ... > ERROR: configuration failed for package 'XML' > ** Removing '/usr/local/lib/R/site-library/XML' And for this one you need libxml2-dev (I think). Cheers, H.
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Tiandao Li wrote: > Dear Herve, > > I installed libcurl3 and libcurl3-gnutlsbefore, and this time libxml2-dev > and libcurl3-dbg. Still get the wrong msg. Well there is some progress, at least now XML is compiling ;-) For RCurl, my mistake, I forgot to say that you also need libcurl3-dev. Let me know if it still doesn't work. Cheers, H.
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However, ther is not libcurl3-dev in synaptic. I use Ubuntu 7.10. Yes, XML is working now. On Fri, 2 Nov 2007, Herve Pages wrote: Tiandao Li wrote: > Dear Herve, > > I installed libcurl3 and libcurl3-gnutlsbefore, and this time libxml2-dev > and libcurl3-dbg. Still get the wrong msg. Well there is some progress, at least now XML is compiling ;-) For RCurl, my mistake, I forgot to say that you also need libcurl3-dev. Let me know if it still doesn't work. Cheers, H.
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Tiandao Li wrote: > However, ther is not libcurl3-dev in synaptic. I use Ubuntu 7.10. Yes, XML > is working now. Argh, the name of the package might have changed. I'm using Ubuntu 6.06. Can you try libcurl3-gnutls-dev? When in Synaptic, if you search for libcurl, you get a bunch of results: any package named libcurl*-dev could contain curl-config (the command that RCurl's configure script is looking for). Unfortunately, Synaptic doesn't allow to search the packages that contain a given file (well, maybe it does, but I don't know how to do that :-/). H.
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