similar to: OWL ontologies in R?

Hello, Is there a convenient way to import RDF/OWL data into R? I'm interested in importing BioPAX/SBPAX data into R to make them available for a wider audience. One exciting application would be to use pathway data to explain differential microarray measurements by identifying upstream nodes that are likely involved in causing the differences. This could also be used to validate

our group at Duke is currently attempting to connect two data sets fed through a web-based system, one containing research questions (i.e., variables positioned with certain roles) and a database of statistical methods. this connection is done informally in a number of R packages and related software such as Rcmdr, R4calc, and Rkward where a variable of a certain type is matched to a certain

Dear Jean-Marc: Would you please send Thierry an ontology mapping table specification for speex according to the format he links to at the end of his message below? Thank you. On Mon, Oct 11, 2010 at 9:54 AM, Thierry MICHEL <tmichel at w3.org> wrote: > Dear James, > > In your latest email to the MAWG response to your comment, you seem to > disagree with the MAWG proposal. >

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

Dear all, I have an ontology which I would like to load in R to then compute the minimum distance between elements. Since this ontology is not only DAG, the problem is non trivial and therefore decided to use R with the powerful e1071 library (allShortestPaths) to do that. That method requires to provide a distance matrix between the various objects. My ontology contains 32768 objects and

Hi: I have clustered microarray gene expression data and trying to map between microarray probe, gene, pathway, gene ontology, and homology for a set of (affy) microarray probes. Is there any package in R which facilitates this? I am looking at bioconductor, but till now could not find a solution. A link to some worked example would be appreciated. Thanks and regards. John [[alternative HTML

Hello! I don't know if there is some R-package able to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance!

Hi All. Attached is a patch against OpenBSD, based in part on the owl-always-auth patch. The idea is that the only way out of auth_passwd for the failure case is the "return 0" at the bottom. I don't know if this is a good way to do it or not, it's presented for discussion. Also, I don't think 3.6.1p2 is quite right WRT these timing issues (eg, you get a fast failure

FreeBSD 4.10-RELEASE, dovecot-1.0-test29 crashes on sort and thread commands: Jul 25 15:12:08 owl dovecot: imap-login: Login: dima [81.19.64.101] Jul 25 15:12:26 owl dovecot: IMAP(dima): file index-mail-headers.c: line 408 (index_mail_get_header): assertion failed: (ret != 0) Jul 25 15:12:26 owl dovecot: child 20384 (imap) killed with signal 6 (gdb) bt #0 0x281e0fc4 in kill () from

Hello, i''m writing an application that needs geocoding information for locations outside of the US. I''m using the brainoff.com geocoding service mappoint = Net::HTTP.new(''brainoff.com'', 80) response = mappoint.get(''/geocoder/rest/?city=Gent,BE'') logger.debug response.body and the body of the response is in the following form : <rdf:RDF

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Hello All, I have managed to get my cisco and asterisk able to talk to one another I think. But cannot make a call from a phone behind call manager to the asterisk server. I have followed the cisco asterisk integration on the wiki. I have also setup a number 3000 for dialing for current local time and date on asterisk. I can call from a sip phone behind asterisk, no problems. The problem

Hi everbody. I''m at my wit''s end with a tiny bug in my Rails app. The UK pound symbol (?) is being converted to a question mark (?) somewhere when I save my models. Here''s all the information I can think of. * Constructing a model containing a ?-sign and displaying its contents works fine. * Saving a ?-sign into the database on the mysql command line and retrieving

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN

Full_Name: emiel ver loren Version: 2.2.0 OS: Windows XP Submission from: (NULL) (145.117.31.248) Dear R-community and developers, I have been trying to read in a tab delimeted file where the column names and the row names are of the form "GO:0000051" (gene ontology IDs). When using: > gomat<-read.table("test.txt") > colnames(gomat)[1] [1] "GO.0000051"

Dear cateGOry experts, hyperGTest documentation states that YEAST cannot be used as 'annotation' when evaluating gene ontology representation status for a given set of 'geneIds'. Because I am using a custom print I believe I need to create my own data package to use as the annotation file for 'annotation'. Can someone please describe how to make a data package that will

Hi, Following is a proposal to improve location coverage for Function parameters in LLVM. The patches for review will be posted soon. RFC: [DebugInfo] Improving Debug Information in LLVM to Recover Optimized-out Function Parameters Ananthakrishna Sowda(Cisco), asowda at cisco.com Nikola Prica (RT-RK/Cisco), nprica at rtrk.com Djordje Todorovic(RT-RK/Cisco), djtodorovic at rtrk.com Ivan Baev

Hello R-users, I have observed that is.na() behaves strange on some lists. Here is a simple example: > a = list(list('asd')) > a [[1]] [[1]][[1]] [1] "asd" > for(i in 1:5) + print(is.na(a)) [1] TRUE [1] FALSE [1] TRUE [1] TRUE [1] TRUE > > for(i in 1:10) + print(as.integer(is.na(a))) [1] 0 [1] 10 [1] 1 [1] 0 [1] 140897024 [1] 134567568 [1] 1 [1] 1953720684

Thank you for your interest and comments! Please see my responses inline. On 2/7/19, 3:17 PM, "aprantl at apple.com on behalf of Adrian Prantl" <aprantl at apple.com> wrote: > On Feb 7, 2019, at 1:49 PM, Ananthakrishna Sowda (asowda) via llvm-dev <llvm-dev at lists.llvm.org> wrote: > > Hi, > Following is a proposal to improve location

I'm seeing this error in my log file under samba-3.0beta3. "The conflicting domain portions are not supported for NETLOGON calls." I have created a unix/samba user testuser and a unix group pwruser. The testuser's primary group is pwruser. Next I mapped the ntgroup to pwruser with: "net groupmap modify ntgroup="Power Users" unixgroup=pwruser" and net