Data retrieval tools

Data retrieval tools

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  Data retrieval tools Dedicatedto access information for molecular biologists. Most widely used are, 1. Entrez 2. DBGET 3. SRS Each of these allows, - Text based searching of a no. of linked DBs.(Data Bases) - Sequence searching. They differ in, - The DBs they cover - How the retrieved information is accessed and presented. Entrez - WWW-based data retrieval system. - Developed by NCBI (National Centre for Biotechnology Information). - Integrates information held in different DBs. Data bases covered by Entrez are,  Nucleic acid - GenBank, RefSeq, PDB.  Protein seqs - SWISS-PROT, PIR.  3D structures – MMDB  Genomes – Many sources  PopSet – From GenBank  OMIM – OMIM  Taxonomy – NCBI taxonomy database  Books- Bookshelf  ProbeSet – GEO (Gene Expression Omnibus)  Literature - PubMed
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  SRS SRS is aSequence Retrieval System
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  - Data retrievaltool developed by EBI - Integrates 80 molecular biology DBs - An Open source software (Can be installed locally) SRS has an associated scripting language called Icarus Central resource for molecular biology data - more than 250 databanks have been indexed. More than 35 SRS servers over the WWW(world wide) Data analysis applications server - 11 protein applications - 6 nucleic acid applications - Uniform query interface on the web History of SRS 1990 - Main author Dr. Thure Etzold – Development started in EMBL, Heidelberg 1997 – Moved to EBI in Cambridge. Development work was supported by various grants amongst others from the EMBnet. 1998 – Etzold and his group join LionBiosciences Information retrieval – Easy way to retrieve information from sequence and sequence-related databases – Possibility to search for multiple words/other criteria Linkage between different databases – E.g. Find all primary structures with known three-dimensional structure. Different types of database in SRS Sequence & structure – DNA, protein, three-dimensional structures Sequence-related Gene-related – Genome, mapping, mutations, transcription factors – SNP Bibliographic
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  – Medline, enzyme User-defined SRSmain toolbar tabs: Top Page: displays databases in different database groups Query: displays either the standard or extended query form Results or “the query manager”: maintains a history of all the results obtained during a session Projects or “the project manager”: maintains a history of all queries and views used during a session Views: allows a user to define a user specific view for one or more databases Databanks: contains a list and some facts about the databases available in the system Search terms in SRS SRS indexed fields can be searched using any of the following: – Single word search – Multiple word phrases – Numbers and dates – Regular expressions – Wildcards