ABSTRACT
Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on 'Text Mining for the BioCuration Workflow' at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.
Subject(s)
Biomedical Research , Data Mining , Natural Language Processing , Workflow , Animals , Databases, Factual , HumansABSTRACT
UNLABELLED: The Biological General Repository for Interaction Datasets (BioGRID) representational state transfer (REST) service allows full URL-based access to curated protein and genetic interaction data at the BioGRID database. Appending URL parameters allows filtering of data by various attributes including gene names and identifiers, PubMed ID and evidence type. We also describe two visualization tools that interface with the REST service, the BiogridPlugin2 for Cytoscape and the BioGRID WebGraph. AVAILABILITY AND IMPLEMENTATION: BioGRID data and applications are completely free for commercial and non-commercial use. http://webservice.thebiogrid.org/resources/interactions (REST Service), http://wiki.thebiogrid.org/doku.php/biogridrest(REST Service parameter list and help), http://webservice.thebiogrid.org/resources/application.wadl(REST Service WADL), http://thebiogrid.org/download.php (BiogridPlugin2, v2.1 download), http://wiki.thebiogrid.org/doku.php/biogridplugin2 (BiogridPlugin2 help) and http://tyerslab.bio.ed.ac.uk/tools/BioGRID_webgraph.php(BioGRID WebGraph).
Subject(s)
Computer Graphics , Gene Regulatory Networks , Software , Computational Biology , Databases, Factual , Internet , User-Computer InterfaceABSTRACT
Cisplatin is the most commonly used chemotherapeutic agent in the treatment of ovarian cancer. One of the mechanisms of resistance of ovarian tumours to cisplatin is increased nucleotide excision repair activity, in particular increased levels of the endonuclease ERCC1. Since 30-40% of ovarian cancers develop resistance to cisplatin after treatment and these tumours are usually incurable, ERCC1 expression is potentially useful as a predictive marker for the effectiveness of cisplatin-based chemotherapy. Using RT-PCR and Northern blotting, we have examined the expression of a 42 bp differentially spliced sequence in exon 1 of the human ERCC1 gene, loss of which has previously been reported to be correlated with higher levels of ERCC1 mRNA in ovarian cancer cell lines. We report here that this alternate transcript is ubiquitous in human tissues and cancer cell lines, is absent in mouse and thus does not appear to be cancer related.
Subject(s)
5' Untranslated Regions/genetics , Alternative Splicing , DNA-Binding Proteins/genetics , Endonucleases/genetics , Genetic Variation , Animals , Base Sequence , Cell Line , Exons/genetics , Female , Humans , Mice , Molecular Sequence Data , Neoplasms/genetics , Ovarian Neoplasms/genetics , RNA/genetics , RNA/isolation & purification , RNA, Ribosomal, 18S/genetics , Sequence DeletionABSTRACT
Class switch recombination (CSR) is a programmed gene rearrangement in which a B cell which is producing IgM and IgD antibody develops into an IgG-, IgA- or IgE-expressing cell. This is achieved by recombination between switch regions located 5' of each of the immunoglobulin heavy chain constant regions, except Cdelta. The mechanism of CSR has not been resolved but it is thought to involve a double-strand break followed by end joining. It has previously been suggested that the nucleotide excision repair protein ERCC1 may be involved in CSR due to its known roles in removal of 3' single-stranded tails in various types of recombination. In this study, we examined class switching in cultured splenocytes from ERCC1-deficient mice and found no evidence of any deficiency.
