http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/ 2009-11-29T00:24:05-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/ http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/lib/images/favicon.ico text/html 2009-06-03T12:53:49-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=calendar&amp;rev=1244058829 text/html 2007-05-29T17:38:42-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench&amp;rev=1180485522 CLENCH: A program for calculating cluster enrichment using the Gene Ontology Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes none, of them accept Arabi… text/html 2009-10-21T17:30:42-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=download&amp;rev=1256171442 Download the file here .. [Text-extracted_relationships.zip] [Slides for HCLS talk Oct 15th] [ OWL file for BIOMEDIN 210] text/html 2009-07-14T18:01:42-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=home&amp;rev=1247619702 SMI pageLinkedIn PublicationsProjectsResearchcalendar[CV] Academic Interests My research interest is to use bio-ontologies for organizing biomedical information to make it actionable. Specifically, I work on developing ontology based approaches to integrate diverse information types available for biological systems. Currently, we are drowning in information but thirsty for knowledge; ontologies might help fix that. I work on a number of projects around this theme. text/html 2007-10-09T11:10:45-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=hybrow&amp;rev=1191953445 The HyBrow server is moving, meanwhile try: Server 1 Server 2 Motivation: Experimental design, hypothesis-testing, and model-building in the current data-rich environment require the biologist to collect, evaluate and integrate large amounts of information of many disparate kinds. Developing a unified framework for the representation and conceptual integration of biological data and processes is a major challenge in bioinformatics because of the variety of available data and the different … text/html 2008-10-24T10:34:10-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=hyque&amp;rev=1224869650 Award 0849207 HyQue (for Hypothesis-based Querying of pathway models), will take as input working hypotheses about pathway models expressed in a knowledge-based formalism, evaluate their consistency using existing data in a knowledgebase, and provide as output contradictory evidence and suggestions for improving hypotheses. HyQue will incorporate formal knowledge representations based upon Semantic Web standards and an ontology to represent biological objects and relationships. text/html 2009-05-19T15:20:10-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=latest_in_research&amp;rev=1242771610 text/html 2007-04-10T14:17:48-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=ontology_driven_querying&amp;rev=1176239868 Background The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult. text/html 2007-04-10T14:11:03-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=pathway_knowledge_base&amp;rev=1176239463 The role of proteins and their function in pathways is crucial to understanding complex biological processes and their failures that lead to disease. With over 200 pathway databases in existence, it is not possible for biologists to examine a pathway in all of them. The emergence and adoption of Biological Pathways Exchange (BioPAX), a standardized format for exchanging pathway information, provides a unique opportunity to integrate knowledge from multiple pathway databases. We conducted a case … text/html 2007-04-10T14:02:58-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=patterns_of_gene_expression&amp;rev=1176238978 Motivation The cancer state of a cell is characterized by alterations of important cellular processes such as cell proliferation, apoptosis, DNA-damage repair, etc. The expression of genes associated with cancer related pathways, therefore, may exhibit differences between the normal and the cancerous states. We explore various means to find these differences. text/html 2009-05-19T15:11:47-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=projects&amp;rev=1242771107 Ontologies for data integration: Ontology-driven indexing of public datasets for translational bioinformatics The volume of publicly available genomic scale data is increasing. Genomic datasets in public repositories are annotated with free-text fields that are not mapped to concepts in any ontology, making it difficult to integrate these datasets across repositories. In this project we have built a prototype system for ontology based annotation and indexing of biomedical data. The system pro… text/html 2009-11-16T18:35:03-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=publications&amp;rev=1258425303 2009 Nigam H. Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P Chiang and Mark A. Musen Comparison of Concept Recognizers for building the Open Biomedical Annotator BMC Bioinformatics 2009, 10(Suppl 9):S14 See citations Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009 May 29; See citations text/html 2007-06-14T17:21:41-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=research_summary&amp;rev=1181866901 My current research is focused on developing applications of ontologies in the biomedical sciences at the National Center for Biomedical Ontology <http://www.bioontology.org>. My graduate work was focused on developing formal methods for the representation, manipulation and integration of diverse biological data - such as gene expression, protein interactions & annotations - with prior biological knowledge for the purpose of evaluating alternative hypotheses. The prototype system is available a… text/html 2007-04-10T14:05:57-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=scripts&amp;rev=1176239157 We describe two sets of programs for expediting routine tasks in analysis of cDNA microarray data and promoter sequences. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in 3 different ways. It allows combining of result files into comprehensive datasets, evaluation of the quality of both technical and biological replicates and row and/or column standardization of data matrices. The second set supports mapping ESTs in the geno… text/html 2007-11-08T11:22:42-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=sidebar&amp;rev=1194549762 Sidebar text/html 2009-06-09T11:20:50-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=test&amp;rev=1244571650 Test page ... [Test file] text/html 2007-08-02T15:14:10-08:00 http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=umls-query&amp;rev=1186092850 DOWNLOAD [Download UMLS-Query] Download a report describing UMLS-Query SYNOPSIS use UMLSQuery; my $U = new UMLSQuery; $U->init( u => 'username', p => 'password', h => 'hostname', dbname => 'umls'); $U->getCUI(string/aui/sui/lui, sab=>) $U->getAUI(string/cui/sui/lui, sab=>) $U->getSTR(string/cui/aui/sui/lui, sab=>) $U->getSAB(string/cui/aui/sui/lui) $U->mapToId(phrase, idtyp…