search for: ontolog

...mber of R packages and related software such as Rcmdr, R4calc, and Rkward where a variable of a certain type is matched to a certain test. For example, a logistic regression model requires a dichotomous variable as its dependent variable. our goal is to formalize this link through a computational ontology, which would standardize and hopefully facilitate package and library development for R. we have started some parallel efforts regarding both our requirements for this ontology as well a search for existing ontologies. So far we couldn't find any existing ontology, which seems odd given the...

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...

Are there any R packages to import and use Web Ontology Language (OWL) ontologies (represented in OWL/RDF or other form)? Thanks, -s [[alternative HTML version deleted]]

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 b...

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...

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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...

...complex lists: list(list(list(.....)). A concrete example where I found this behavior is the following list: > str(as.list(hgu95av2GO)[1:5]) List of 5 $ 1114_at :List of 6 ..$ GO:0005125:List of 3 .. ..$ GOID : chr "GO:0005125" .. ..$ Evidence: chr "IEA" .. ..$ Ontology: chr "MF" ................................... ..$ GO:0040007:List of 3 .. ..$ GOID : chr "GO:0040007" .. ..$ Evidence: chr "IEA" .. ..$ Ontology: chr "BP" $ 36421_at : logi NA $ 329_s_at :List of 5 ..$ GO:0005198:List of 3 .. ..$ GOID...

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 version deleted]]

On 11/14/08, David Flynn <davidf+nntp at woaf.net> wrote: > Correct; there is no metadata handling capability in the current > mapping spec. I'd suggest at some point to look into separate stream solution for metadata, perhaps M3F [1]. -Ivo [1] http://wiki.xiph.org/index.php/M3F

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" > rownames(gomat)[1] [1] "GO:0000002" Which means that ":" is transformed into a "." !! This seems like Excel when it is trying to guess what I am...

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 IPI:IPI00019922.5|SWISS-PROT:Q8N0Y2-1|TREMBL:Q53F81|ENSEMBL:ENSP00000338860;ENSP0...

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 be compatible with the 'annota...

...1/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd" version="1.1"> <cvList count="3"> <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/> <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/> <cv id="IMS"...

...(e.g. BioConductor) - BioConductor: Overview; Installation and Demonstration - Array Quality Inspection - Correction and Normalization; Affymetrix and cDNA arrays - Identification of Differentially Expressed Genes - Visualization of Genomic Information - Clustering Methods in R/Splus - Gene Ontology (GO) and Pathway Analysis - Inference, Strategies for Large Data (2) R/Splus Fundamentals and Programming Techniques Course outline. - An Overview of R and S - Data Manipulation and Graphics - Using Lattice Graphics - A Comparison of R and S-Plus - How can R Complemen...

On Mon, Nov 17, 2008 at 11:41 AM, Ralph Giles <ralph.giles at artifex.com> wrote: > On Sun, Nov 16, 2008 at 3:22 PM, Silvia Pfeiffer > <silviapfeiffer1 at gmail.com> wrote: > >> Plus, the W3C is currently >> investigating a new ontology for video/audio metadata. This may be a >> good extension for vorbiscomment once finished. > > Ooh, can you say anything about it? Are there any documents up yet? > I've been waiting for something better than rdf xml for a looong time. > :) RDF has a very different purpose....

...y will be. Critiques, bug reports and enhancement requests are welcome as GitHub issues. I'm a social scientist and tested this mostly on survey data. I'm sure that shows in some design decisions. I'd be happy to find collaborators who can e.g. fill in my knowledge gaps on metadata and ontologies. https://github.com/rubenarslan/codebook/issues Best, Ruben -- Ruben C. Arslan Center for Adaptive Rationality Max Planck Institute for Human Development Berlin, Germany https://www.mpib-berlin.mpg.de/en/staff/ruben-arslan https://formr.org http://www.the100.ci [[alternative HTML version...

Hello r-help! My name is Dan McGoldrick, I am a statistical geneticist and I work with ontologies, AI and general genetic data analysis. I was wondering aabout the tryCatch function -- don't really understand the implimentation... What I would like to do is within an R API, test a mysql connection object for an error (server has gone away) and if the connection is functional leave it a...

...ives... best wishes Robert Legaie, Roxane wrote: > Dear Robert Gentleman, > I am currently working on Streptomyces coelicolor microarray data. > > I have some clusters of genes and I would like to annotate them, but as you may know, this organism is not yet annotated with Gene Ontologies. There is no database (such as at "ath1121501.db" for Arabidopsis thaliana) available to use with the GOstats package. > > So, I would like to use at least the Kegg.db package with GOstats. > Can you tell me how to include KEGG.db ? I can't find anything about it. > &...

...fication or SVM or neural network approach,checking their success for various queries and then choosing the best. Both the above mentioned projects are being done in Java. In the second project I am ranking among the links which various users using have visited. Principally i am planning to use an ontological approach by classifying the links into various class labels and then ranking within the individual class using AKTiveRank Algorithm . I feel I can contribute to the project however most of the codes that I have written are in Java or Python. Is it essential to use C++ to contribute to this pro...