TRRD: Technology for extraction, storage, and use of knowledge about the structural-functional organization of the transcriptional regulatory regions in the eukaryotic genes

摘要

Abstract. We have developed the Transcription Regulatory Regions Database (TRRD, http://www.bionet.nsc.ru/trrd/) designednfor storage of data on the structural-functional organization of transcriptional regulatory regions of the eukaryotic genes and theirnexpression patterns. TRRDcontains experimentally supported data only. Knowledge extraction from scientific literature, storagenand further application of the results are all stepwise, conforming to the Data Mining technology: i) knowledge extraction fromnscientific publications; ii) preprocessing (data cleaning, syntactic and semantic analysis; iii) data transformation; iv) applicationnfor prediction; v) interpretation of the obtained knowledge to resolve the timely issues in bioinformatics. TRRD contains ancompilation of data on 2 344 genes, their 14 407 expression patterns, 3 490 regulatory units, and 10 135 transcription factornbinding sites. TRRD is filled in by manual annotation of scientific publications. The information incorporated into TRRD is thenresult of annotations of 7 609 scientific papers. Sequence Retrieval System (SRS) is the main tool for search and navigation innTRRD. A large number of indexed fields in its SRS version allow the user to generate queries both within and between libraries.nTRRD has thesauruses and search systems that provide additional options for data access. TRRD is currently linked to 20nworldwide information resources, including EMBL/GeneBank, Ensembl, EPD, SWISS-PROT, TRANSFAC, GDB, GeneCards,nMGD, RGD, GO. The links serve as a framework for integration in a distributed network environment.