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GenBank and PubMed: How connected are they?
Holly Miller1, Catherine N Norton, Indra Neil Sarkar
1MBLWHOI Library, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA. hmiller@mbl.edu
BMC Research Notes
|June 11, 2009
Summary
GenBank contains molecular sequence data linked to publications. Most linked sequences connect to PubMed, but many extend beyond biomedical research, suggesting integration opportunities.
Area of Science:
- Bioinformatics
- Genomics
- Scientific Literature Databases
Background:
- GenBank is a public repository for molecular sequence data, including metadata and publication information.
- Linking sequence data to literature aids hypothesis generation.
- PubMed identifiers (PMIDs) link GenBank records to PubMed-indexed literature.
Purpose of the Study:
- To analyze the extent of publication linkage in GenBank records.
- To identify the proportion of GenBank entries associated with publications and PMIDs.
- To determine journals with the most GenBank-linked sequences.
Main Methods:
- Analysis of 87,116,501 GenBank sequence files.
- Identification of associated publications and patents.
- Extraction and analysis of PubMed identifiers (PMIDs).
Main Results:
- 42% of GenBank files are linked to a publication or patent.
- 71% of publication-associated GenBank entries have PMIDs, linking to PubMed.
- 29% of publication-associated GenBank entries lack PMIDs or cite non-PubMed-indexed literature.
Conclusions:
- GenBank includes molecular sequences from diverse scientific disciplines, not limited to biomedicine.
- Findings highlight the potential for integrating biological knowledge beyond the biomedical field.
- Opportunities exist to enhance cross-disciplinary data integration from GenBank.
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