Quantifying literature citations, index terms, and Gene Ontology annotations in the Saccharomyces Genome Database to assess results-set clustering utility

MacMullen, W. John Quantifying literature citations, index terms, and Gene Ontology annotations in the Saccharomyces Genome Database to assess results-set clustering utility., 2006 . In 69th Annual Meeting of the American Society for Information Science and Technology (ASIST), Austin (US), 3-8 November 2006. [Conference paper]

[thumbnail of MacMullen_Quantifying.pdf]
Preview
 PDF
MacMullen_Quantifying.pdf
Download (153kB) | Preview

English abstract

A set of 37,325 unique literature citations was identified from 120,078 literature-based annotations in the Saccharomyces Genome Database (SGD). The citations, gene products, and related Gene Ontology (GO) annotations were analyzed to quantify unique articles, journals, genes, and to rank by publication year, language, and GO term frequency. GO terms, MeSH indexing terms, MeSH Journal Descriptors, and SGD Literature Topics were quantified and analyzed to assess their potential utility for results set clustering. Results: Bradford’s Law of Scattering was shown to hold for the citations, journals, gene products, and GO annotations. Only the MeSH terms and article title/abstract pairs had significant numbers of term co-occurrence. Multiple term types may be useful for faceted searching and clustered results set browsing if the strengths of each are leveraged.

Item type: Conference paper
Keywords: citation analysis ; life science
Subjects: B. Information use and sociology of information > BB. Bibliometric methods
Depositing user: Norm Medeiros
Date deposited: 12 Jan 2007
Last modified: 02 Oct 2014 12:06
URI: http://hdl.handle.net/10760/8809

References

Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, et al. (2006) Saccharomyces Genome Database Data files dated January 29, 2006. Available: ftp://genome-ftp.stanford.edu/pub/yeast/data_ download/literature_curation/(Accessed: 2006-02-13.)

Bernhardt, P.J., Humphrey, S.M., & Rindflesch, T.C. (2005) Determining Prominent Subdomains in Medicine Proceedings of the 2005 American Medical Informatics Association (AMIA) Annual Symposium 46-50

Bradford, S.C. (1948) Documentation London: Crosby Lockwood

DuBois, Paul (2000) MySQL Indianapolis, IN: New Riders. p. 188

Dwight, S.S., Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dolinski, K., et al. (2004) Saccharomyces Genome Database: Underlying principles and organisation Briefings in Bioinformatics 5(1):9-22

Gene Ontology Consortium (2006) The Gene Ontology (GO) project in 2006 Nucleic Acids Research 34: D322-D326. PMID: 16381878

Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., et al. (2003) Global analysis of protein localization in budding yeast Nature 425(6959):686-691. PMID: 14562095

Humphrey S.M. (1999) Automatic indexing of documents from journal descriptors: A preliminary investigation Journal of the American Society for Information Science 50(8):661-674

MacMullen, W.J. (2005) Inter-database annotation linkages in model organism databases Proceedings of the 68th Annual Meeting of the American Society for Information Science & Technology (ASIS&T)

NCBI (2006) NCBI eFetch utility Available http://eutils.ncbi.nlm.nih.gov/entrez/eutils/(Accessed: 2006-02-13.)

RefWorks (2006) RefWorks Web-Based Bibliographic Management Software, January 2006 release Licensed to the University of North Carolina, Chapel Hill. Available http://refworks.com/(Accessed: 2006-02-13.)

Schloman B.F. (1997) Mapping the literature of allied health: project overview Bulletin of the Medical Library Assoc 85(3):271-277. PMID: 9285127

SGD (2006) Saccaromyces Genome Database (SGD) Literature Topics http://www.yeastgenome.org/help/Literature_Topics.html(Accessed 2006-02-13.)


Downloads

Downloads per month over past year

Actions (login required)

View Item View Item
Contact us
Send email Sponsors
Sponsor: AIMS Sponsor: D&P Sponsor: UniNa CAB Get connected
Facebook Facebook Twitter Twitter Linkedin LinkedIn RSS RSS