FACTA is not in this context the Fabricated Access Covers Trade Association or the Fair and Accurate Credit Transactions Act, but a tool from the National Centre for Text Mining at Manchester, which uncovers associations between biomedical concepts mentioned in Medline articles. Enter a search term, and you will be presented with lists of associated concepts covering genes, diseases, drugs, and other things (which things are shown depends on the tick boxes that are selected when you search). You can then click to see "snippets", which highlight your search term. I tried it with HFE (the gene associated with hemochromatosis, the example from the Gene Gateway Workbook, described in a previous posting) and got 1564 hits connecting it with the disease.
Any of the associations are links so that you can see their own associations.
FACTA is described in a open access paper in Bioinformatics:
Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou. 2008. FACTA: a text search engine for finding associated biomedical concepts, Bioinformatics, Vol. 24, No. 21, pp. 2559-2560 (there is a link on the FACTA site to this).
Showing posts with label bioinformatics. Show all posts
Showing posts with label bioinformatics. Show all posts
Monday, December 01, 2008
Tuesday, July 15, 2008
iHOP
Also found in Biotechniques' WebWatch column, iHOP brings together all sorts of information relating to the gene you have searched for - once you have located the gene in the species you are interested in, you get links to information in UniProt, OMIM, and the NCBI databases.
There is a paper in Nature Genetics - doi: 10.1038/ng0704-664, about iHOP, and a PubMed search just for the word "ihop" finds more papers about its uses, but not the Nature Genetics one itself as it has no abstract.
There is a paper in Nature Genetics - doi: 10.1038/ng0704-664, about iHOP, and a PubMed search just for the word "ihop" finds more papers about its uses, but not the Nature Genetics one itself as it has no abstract.
Structural exon database
Found in WebWatch in Biotechniques, the Structural Exon Database, SEDB. Introductory page says:
"Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms."
To be able to use the datasets, you need to install Friend on your PC, but various searches seem to be possible without it: GenBank accession search, sequence searching, and using BLAST.
SEDB is hosted by Northeastern University in Boston, MA and is described in a paper in Bioinformatics, doi: 10.1093/bioinformatics/bth150. (DOI found in the PubMed record - see previous posting on this blog!)
"Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms."
To be able to use the datasets, you need to install Friend on your PC, but various searches seem to be possible without it: GenBank accession search, sequence searching, and using BLAST.
SEDB is hosted by Northeastern University in Boston, MA and is described in a paper in Bioinformatics, doi: 10.1093/bioinformatics/bth150. (DOI found in the PubMed record - see previous posting on this blog!)
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