References
Ascoli, G. A. (2005) Looking forward to open access. Neuroinformatics 3 (1), 1–4.
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M. and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25 (1), 25–9.
Bada, M., McEntire, R., Wroe, C. and Stevens, R. (2003) GOAT: the gene ontology annotation tool. Proceedings of the 2003 UK e-Science All Hands Meeting, Nottingham, UK 514–519.
Bard, J. B. (2005) Anatomics: the intersection of anatomy and bioinformatics. J Anat 206 (1), 1–16.
Berry, M. W. (2003) Survey of Text Mining: Clustering, Classification, and Retrieval, Springer-Verlag, New York, NY.
Bowden, D. M. and Dubach, M. F. (2003) NeuroNames 2002. Neuroinformatics 1 (1), 43–59.
Burns, G. A. P. C., Khan, A. M., Ghandeharizadeh, S., O’Neill, M. A. and Chen, Y.-S. (2003) Tools and approaches for the construction of knowledge models from the neuroscientific literature. Neuroinformatics 1 (1), 81–110.
Chesler, E. J., Wang, J., Lu, L., Qu, Y., Manly, K. F. and Williams, R. W. (2003) Genetic correlates of gene expression in recombinant inbred strains: a relational model system to explore neurobehavioral phenotypes. Neuroinformatics 1 (4), 343–57.
Cheung, K. H., de Knikker, R., Guo, Y., Zhong, G., Hager, J., Yip, K. Y., Kwan, A. K., Li, P. and Cheung, D. W. (2004) Biosphere: the interoperation of web services in microarray cluster analysis. Appl Bioinformatics 3 (4), 253–6.
Davison, A. P., Morse, T. M., Migliore, M., Shepherd, G. M. and Hines, M. L. (2004) Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation. Neuroinformatics 2 (3), 327–332.
Devlin, K. (1997) Logic and Information, John Wiley & Sons, New York, NY.
Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., Cherry, J. M., Botstein, D., Brown, P. O. and Alizadeh, A. A. (2003) SOURCE: a unified genomic resource of functional annotations, ontologies, and geneexpression data. Nucleic Acids Res 31 (1), 219–23.
Draghici, S., Khatri, P., Bhavsar, P., Shah, A., Krawetz, S. A. and Tainsky, M. A. (2003) Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res 31 (13), 3775–81.
Fagin, R., Halpern, J. Y., Moses, Y. and Vardi, M. Y. (1995) Reasoning About Knowledge, The MIT Press, Cambridge, MA.
Fellbaum, C., ed. (1998) Wordnet: An Electronic Lexical Database, The MIT Press, Cambridge, MA.
Hamosh, A., Scott, A. F., Amberger, J. S., Bocchini, C. A. and McKusick, V. A. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucl. Acids Res. 33 (suppl 1), D514–517.
Humphreys, B. L., Lindberg, D. A. B., Schoolman, H. M. and Barnett, G. O. (1998) The Unified Medical Language System: An Informatics Research Collaboration. J Am Med Inform Assoc 5 (1), 1–11.
Jackson, P. and Moulinier, I., ed. (2002) Natural Language Processing for Online Applications: Text Retrieval, Extraction, and Categorization, John Benjamins Publishing Co, Philadelphia, PA.
Kudla, K. M. and Rallins, M. C. (1998) SNOMED: a controlled vocabulary for computer-based patient records. J AHIMA 69 (5), 40–4.
Lambrix, P., Habbouche, M. and Perez, M. (2003) Evaluation of ontology development tools for bioinformatics. Bioinformatics 19 (12), 1564–71.
Lenat, D. B., Guha, R. V., Pittman, K., Pratt, D. and Shepherd, M. (1990) Cyc: toward programs with common sense. Communications of the ACM 33 (8), 30–49.
Lewis, S. E., Searle, S. M. J., Harris, N., Gibson, M., Iyer, V., Ricter, J., Wiel, C., Bayraktaroglu, L., Birney, E., Crosby, M. A., Kaminker, J. S., Matthews, B., Prochnik, S. E., Smith, C. D., Tupy, J. L., Rubin, G. M., Misra, S., Mungall, C. J. and Clamp, M. E. (2002) Apollo: a sequence annotation editor. Genome Biology 3(12), 0082.1–0082.14.
Mani, I. and Maybury, M. T., ed. (1999) Advances in Automatic Text Summarization, The MIT Press, Cambridge, MA.
Merkel-Sobotta, E. (2005) Elsevier and Open Access. Neuroinformatics 3 (1), 5–10.
Muller, H.-M., Kenny, E. E. and Sternberg, P. W. (2004) Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biology 2 (11), e309.
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) (1992) Enzyme Nomenclature, Academic Press, San Diego, California.
Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K. B., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya, M. A., Zhao, Z., Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, M., Choudhury, D. R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S. K., Madavan, V., Joseph, A., Wong, G. W., Schiemann, W. P., Constantinescu, S. N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G. C., Dang, C. V., Garcia, J. G. N., Pevsner, J., Jensen, O. N., Roepstorff, P., Deshpande, K. S., Chinnaiyan, A. M., Hamosh, A., Chakravarti, A. and Pandey, A. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 13(10), 2363–2371.
Raychaudhuri, S., Chang, J. T., Imam, F. and Altman, R. B. (2003) The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res. 31 (15), 4553–4560.
Romero, P. R. and Karp, P. D. (2004) Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics 20 (5), 709–717.
Schatz, B. (1997) Information retrieval in digital libraries: bringing search to the net. Science 275 (5298), 327–334.
Shatkay, H., Edwards, S., Wilbur, W. J. and Boguski, M. (2000) Genes, themes and microarrays: using information retrieval for large-scale gene analysis. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8 317–28.
Velterop, J. (2005) Necessity is the mother of innovation. Neuroinformatics 3 (1), 11–14.
Xie, H., Wasserman, A., Levine, Z., Novik, A., Grebinskiy, V., Shoshan, A. and Mintz, L. (2002) Large-scale protein annotation through gene ontology. Genome Res 12 (5), 785–794.
Zdobnov, E. M., Lopez, R., Apweiler, R. and Etzold, T. (2002) The EBI SRS server—recent developments. Bioinformatics 18 (2), 368–73.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Bug, W. The impact of the NIH public access policy on literature informatics. Neuroinform 3, 81–91 (2005). https://doi.org/10.1385/NI:3:2:081
Issue Date:
DOI: https://doi.org/10.1385/NI:3:2:081