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Bioinformatics Web Resource Feature Survey
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Bioinformatics Web Resource Feature Survey



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  • The NCBOBioportal is a product of Stanford’s Musen Lab, the same lab originating the graphical ontology editor, Protégé.
  • Bioportal provides a treeview for various ontologies. Here, the ontology for intracoronary artery thrombolytic infusion is shown, from the ICD-9
  • Entities from the ontology are assigned unique IDs, and can be accessed RESTfully.
  • The ID maps directly to a URI.
  • BioPortal provides a Flash-based interactive viewer for displaying ontological relationships.
  • In this case, we can very clearly see that the operation described is being performed to remove an arterial obstruction, and is an operation on a vessel leading to the heart.
  • There is also a tab for notes, or user-added annotation.
  • Perusing twenty or so entries from the ontology did not yield a single note, but the capacity to annotate entries exists.
  • A powerful feature Bioportal provides is the ability to annotate new information with known ontological relationships and ancillary data.
  • Simply pasting plain text into a box will link recognized terms to associated annotation information. A tag cloud weighted by occurrence in the ontology is also provided.
  • Simply pasting plain text into a box will link recognized terms to associated annotation information.
  • Another resource BioPortal provides is the “All Resources” tab.
  • The “All Resources” feature provided by BioPortalpermits users to search for a term in the available ontologies, select relevant ontologies, and produce a list of information “such as gene expression data sets, descriptions of radiology images, clinical-trial reports, and PubMed abstracts to annotate and index with terms from [the] appropriate ontologies. ”
  • BioGPS is a tool for gene annotation provided by the Genomics Institute of the Novartis Research Foundation
  • for a given a gene symbol or accession number, BioGPS will display a gene report integrating information from a few disparate sources.The creators of BioGPS note that it is based on a model-view-controller paradigm. The model is based on Oracle v11, the controller is implemented using C#, and the web view layer makes use of Django and ExtJS.
  • The BioGPS gene report shows gene expression charts
  • It also provides accession numbers, as well as molecular, biological, and cellular function. Transcript, protein, and reporter references are also included.
  • If the report does not contain the information a user is looking for, user-created plugins can be added to the report to pull in information from other sources.
  • AmiGO is a tool from the Gene Ontology consortium.
  • AmiGO provides a tree for viewing ontological relationships
  • AmiGO
  • AmiGO allows the search result set to be restricted by data source or species
  • The main focus is the ontology tree
  • However, other representations are available. The ontology can be downloaded in OBO (Open Biological and Biomedical Ontologies), RDF, or GraphViz formats. It can also be viewed graphically as a flow chart.
  • This is the graphical view of the ontology for GNMT. Note that it includes Gene Ontology reference numbers.
  • Wikipedia offers a wealth of information
  • Consider this article on an enzyme,glycine N-methyltransferase. Many articles found on Wikipedia include a crowdsourced prose description and references
  • 3D structural information, recognized names, an external IDs or accession numbers may also be included
  • Along with RNA expression information
  • A product of MIT, Wikigenes extracts and organizes gene information from journal articles
  • Searching for the same entry, glycine N-methyltransferase, on wikigenes yields much information.
  • Wikigenes is fairly unique in that it performs fulltext searches of journal articles, selects containing sentences, and lists them by category, with citations.
  • Wikigenes includes information pertinent to disease, anatomical, biological, and other contexts
  • The NCBI maintains a centralizes list of databases they coordinate at Entrez, a federated search engine for –omics and life science information.
  • Many different data sources are available.
  • Much of this information, such as nucleotide data, is available in raw text format
  • The nucleotide tool provides gene data in raw text format.
  • Of note is that users can perform BLAST alignments or pick primers from a given sequence page.
  • Of course, the nucleotide tool provides gene data, including GenBank sequence, protein, SNP, and taxonomic information. Information indicating conservation of a given gene among species, and recent journal articles are also shown.
  • The “Pick Primers” directs users to the NCBI Primer-BLAST tool, and pre-populates fields with known values for the selected gene.
  • NCBI also provides an interactive viewer for sequence information
  • The NCBI map viewer is a starting point to work with genomic data from many different species. From this page, users can view species-specific genomic data, and run BLAST alignments against the genome of one of the available species.
  • The map viewer includes a viewer for viewing the complete genome for a species, at various levels of granularity.
  • For example, human chromosome 3
  • Zoomed in 2x on human chromosome 3
  • The map viewer links to a BLAST webpage
  • The Entrez gene tool provides a wealth of information
  • Among information included are functional references, interactions with other genes, phenotypes of different alleles, homology, pathways, gene ontology,
  • On the same page is information for phenotypes and genotypes of different alleles, homology, pathways, gene ontology, and raw sequence information
  • Of particular note is the gene LinkOutsection; it provides links to external resources relevant to a particular gene.
  • UniProt is the "UNIversalPROTein resource," and combines data from Swiss-Prot, TrEMBL, and PIR.
  • UniProt is the de facto standard reference for protein information
  • UniProt is provides structural, functional, and sequence information for proteins
  • UniProt also includes protein sequence annotation, and includes binding sites and other features
  • UniProt includes publication references
  • UniProt also includes links to related external references
  • In addition to SwissProt, a protein database used by UnitProt, the Swiss Institute of Bioinformatics maintains a service for molecular homology modeling, Swiss-Model
  • Given a protein name, forexample GNMT, Swiss-Model will provide 3D molecular models and alignment information

Bioinformatics Web Resource Feature Survey Bioinformatics Web Resource Feature Survey Presentation Transcript

  • NCBO Bioportal
  • http://bioportal.bioontology.org/
  • http://amigo.geneontology.org
  • A search for GNMT (glycine N-Methyltransferase)…
  • A search for GNMT (glycine N-Methyltransferase)…
  • A search for GNMT (glycine N-Methyltransferase)…
  • A search for GNMT (glycine N-Methyltransferase)…
  • A search for GNMT (glycine N-Methyltransferase)…
  • A search for GNMT (glycine N-Methyltransferase)…
  • Wikipedia
  • A search for GNMT (glycine N-Methyltransferase)…
  • A search for GNMT (glycine N-Methyltransferase)…
  • A search for on GNMT (glycine N-Methyltransferase)…
  • "A wiki for the life sciences where authorship matters."
  • http://www.ncbi.nlm.nih.gov/sites/gquery
  • http://www.uniprot.org/
  • http://swissmodel.expasy.org/