Recall and bias of retrieving gene expression microarray datasets through PubMed identifiers

Journal of Biomedical Discovery and Collaboration

Volumn 5, Issue 1, 2010, Pages 7-20

  Piwowar, Heather A ^a   Chapman, Wendy W ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79951505036     PISSN: None     EISSN: 17475333     Source Type: Journal    
DOI: 10.5210%2Fdisco.v5i0.2785     Document Type: Article

References (27)

1. Taylor C, Field, D, Sansone, SA, Aerts, J, Apweiler, R, Ashburner, M, Ball, CA, Binz, PA, Bogue, M, Booth, T: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology 2008, 26(8):889-896.
2. Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA: Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics 2007, 8:296.
3. Butte AJ, Chen R: Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annual Symposium Proceedings 2006:106-110.
4. Williams-Devane CR, Wolf MK, Richard AM: Towards a public toxicogenomics capability for supporting predictive toxicology: Survey of current resources and chemical indexing of experiments in GEO and ArrayExpress. Toxicological Sciences 2009, 109(2):358-371.
5. Dudley J, Butte AJ: Enabling integrative genomic analysis of high-impact human diseases through text mining. Pacific Symposium on Biocomputing 2008:580-591.
6. Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ: Methodologies for extracting functional pharmacogenomic experiments from international repository. AMIA Annual Symposium Proceedings 2007:463-467.
7. Jensen L, Saric J, Bork P: Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews Genetics 2006, 7(2):119-129.
8. Djebbari A, Karamycheva S, Howe E, Quackenbush J: MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinformatics 2005, 21(15):3324-3326.
9. Butte AJ, Kohane IS: Creation and implications of a phenome-genome network. Nature Biotechnology 2006, 24(1):55-62.
10. Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P: Systematic Association of Genes to Phenotypes by Genome and Literature Mining. PLoS Biol 2005, 3(5):e134.
11. Scherf M, Epple A, Werner T: The next generation of literature analysis: integration of genomic analysis into text mining. Briefings in Bioinformatics 2005, 6(3):287-297.
12. Fink JL, Kushch, Sergey, Williams, Parker R, Bourne, Philip E: BioLit: integrating biological literature with databases. Nucleic Acids Research 2008, 36(Web Servier issue):W385-W389.
13. Tanabe L, Scherf U, Smith LH, Lee JK, Hunter L, Weinstein JN: MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques 1999, 27(6):1210-1214, 1216-1217.
14. Hearst M, Divoli A, Guturu H, Ksikes A, Nakov P, Wooldridge M, Ye J: BioText Search Engine: beyond abstract search. Bioinformatics 2007, 23(16):2196-2197.
15. Free PubMed Facelifts: Alternative Interfaces to an Essential Database. In: University of Manitoba Info-Rx Newsletter. vol. March 27, 2007: URL:http://myuminfo.umanitoba.ca/index.asp?sec=857&too=100&dat=3/26/2007&sta=3&wee=5&eve=8&npa=12437. (Archived by WebCite® at http://www.webcitation.org/5ibUYdS3X)
16. Ochsner SA, Steffen DL, Stoeckert CJ, McKenna NJ: Much room for improvement in deposition rates of expression microarray datasets. Nature Methods 2008, 5(12):991.
17. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R: NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Reasearch 2007, 35(Database issue):D760-D765.
18. Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, and Brazma A: ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Research 2007, 35(Database issue): D747-D750.
19. Piwowar HA, Chapman WW: A review of journal policies for sharing research data. In: ELPUB. 2008.
20. EUtils Python library [http://sourceforge.net/projects/eutils/]
21. Morales M, R Development Core Team, R-help listserv community and especially Duncan Murdoch: sciplot: Scientific Graphing Functions for Factorial Designs.
22. Harrell, FE with contributions from many other users: Hmisc: Harrell Miscellaneous. 2007.
23. R Development Core Team: R: A Language and Environment for Statistical Computing. In. Vienna, Austria: ISBN 3-900051-07-0; 2008.
24. Bhat TN, Bourne P, Feng Z, Gilliland G, Jain S, Ravichandran V, Schneider B, Schneider K, Thanki N, Weissig H, Westbrook J, Berman HM: The PDB data uniformity project. Nucleic Acids Research 2001, 29(1):214-218.
25. PDBj News Letter. In: Volume 7, March 2006 http://www.pdbj.org/NewsLetter/newsletter_vol7_e.pdf. Accessed: 2009-11-18. (Archived by WebCite® at http://www.webcitation.org/5lNczfJZJ)
26. Compete, collaborate, compel. Nature Genetics 2007, 39(8):931.
27. Piwowar HA, Day RS, Fridsma DB: Sharing detailed research data is associated with increased citation rate. PLoS ONE 2007, 2(3):e308.