Automated Literature Searching. Literature Databases PubMed (NCBI): 14,000,000 Bio/Med references ISI Web of Science: Bio, Chem and Ag references SciFinder:

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Presentation transcript:

Automated Literature Searching

Literature Databases PubMed (NCBI): 14,000,000 Bio/Med references ISI Web of Science: Bio, Chem and Ag references SciFinder: Bio, Chem and Ag references plus patents

Different Problems 1.Keyword-based searches 2.Sequence-based searches 3.Structure-based searches 4.…

Most Important Approach for ‘Genomics/Proteomics’ 1.Requirements Procedure automated Results complete 2.BLAST/Interpro against GenBank/SwissProt 3.Gene Ontology approach: controlled vocabularies to describe biological processes in an expandable network (not hierarchy) 4.Download user-curated associations from model databases 5.Alternatives 1.PubMatrix (multiplex/filtering) 2.MedMiner (filtering into categories, supports Affy ID#s) 3.XplorMed (filtering into categories) 4.HAPI (key word hierarchies)

Search Modifier Matrix

Conclusion Searches are more convenient but results remain incomplete. GO might be the future for keyword- and sequence-based searches