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Bioinformatics Web Resource Feature Survey

by tomkinsc on Jun 22, 2010

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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 Presentation Transcript

NCBO Bioportal
http://bioportal.bioontology.org/
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
http://en.wikipedia.org/wiki/Category:Human_proteins
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.wikigenes.org/
http://www.ncbi.nlm.nih.gov/sites/gquery
http://www.uniprot.org/
http://swissmodel.expasy.org/

Bioinformatics Web Resource Feature Survey

by tomkinsc on Jun 22, 2010

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Bioinformatics Web Resource Feature Survey Presentation Transcript