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Bioinformatics Web Resource Feature Survey
- 21. A search for GNMT (glycine N-Methyltransferase)…
- 22. A search for GNMT (glycine N-Methyltransferase)…
- 23. A search for GNMT (glycine N-Methyltransferase)…
- 24. A search for GNMT (glycine N-Methyltransferase)…
- 25. A search for GNMT (glycine N-Methyltransferase)…
- 26. A search for GNMT (glycine N-Methyltransferase)…
- 28. A search for GNMT (glycine N-Methyltransferase)…
- 29. A search for GNMT (glycine N-Methyltransferase)…
- 30. A search for on GNMT (glycine N-Methyltransferase)…
- 31. "A wiki for the life sciences where authorship matters." http://www.wikigenes.org/
Notes de l'éditeur
- 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