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