Department of Genetics, University of Cambridge

Michael Ashburner - Publications on Databases, Bioinformatics and Ontologies

Urls and doi's have been added to details of publications where these are available. Doi's (document object identifiers) can be accessed by prefixing with: http://dx.doi.org/

M. Ashburner. 1991. The genetic maps of Drosophila. Drosophila Information Service 69: 1-399.
C.M. Tolstoshev, M. Ashburner, T.C. Kaufman, K.A. Matthews, J.R. Merriam, J.M. Ostell and W.M. Gelbart. 1991. Overview of an integrated Drosophila database. NCBI Technical Report Series, Technical Report No. 7. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda.
C.M. Tolstoshev, M. Ashburner, T.C. Kaufman, K.A. Matthews, J.R. Merriam, and W.M. Gelbart. 1991. Drosophila relational database schema. NCBI Technical Report Series, Technical Report No. 8. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda.
M. Ashburner. 1993. Genetic map of Drosophila melanogaster. In: Genetics maps, 6th edition. Edited by S. O'Brien. Cold Spring Harbor Laboratory Press, New York. Volume 3: 137-169.
M. Ashburner and R. Drysdale. 1994. FlyBase: The Drosophila genetic database. Development 120: 2077-2079.
http://dev.biologists.org/cgi/reprint/120/7/2077
The FlyBase Consortium. 1994. FlyBase - The Drosophila database. Nucleic Acids Res. 22: 3456-3458.
http://nar.oxfordjournals.org/cgi/reprint/22/17/3456
doi:10.1093/nar/22.17.3456
FlyBase Consortium. 1995 Invertebrates: Drosophila melanogaster. Trends in Genetics, Genetic Nomenclature Guide. pp. 26-29.
FlyBase consortium. 1996. FlyBase - The Drosophila database. Nucleic Acids Research 24: 53-56.
http://nar.oxfordjournals.org/cgi/reprint/24/1/53
doi:10.1093/nar/24.1.53
FlyBase consortium. 1997. A Drosophila database. Nucleic Acids Research 25: 63-66.
http://nar.oxfordjournals.org/cgi/reprint/25/1/63
doi:10.1093/nar/25.1.63
M. Ashburner and N. Goodman. 1997. Informatics - Genome and Genetic Databases. Current Opinion in Genetics and Development 7: 750-756.
doi:10.1016/S0959-437X(97)80036-6
FlyBase Consortium. 1997. Gene order maps; Transposon and Vector Maps. Drosophila Inf. Serv. 78: 1-544.
FlyBase Consortium. 1997. Genetic nomenclature guidelines; Drosophila anatomical terms; Bibliography of Drosophila 1994-1996; 1982-1993 (Supplement). Drosophila Inf. Serv. 79: 1-399.
FlyBase consortium. 1998. FlyBase - The Drosophila database. Nucleic Acids Research 26: 85-88.
http://nar.oxfordjournals.org/cgi/reprint/26/1/85
doi:10.1093/nar/26.1.85
M. Ashburner. 1998. When names are less than crystal clear. Nature 394: 216. (Correspondence).
http://www.nature.com/nature/journal/v394/n6690/full/394216a0.html
doi:10.1038/28254
H. Lehväslaiho, M. Ashburner and T. Etzold. 1998. Unified access to mutation databases. Trends Genetics 14: 205-206.
doi:10.1016/S0168-9525(98)01442-5
FlyBase Consortium. 1998. Drosophila melanogaster. Trends in Genetics, Genetic Nomenclature Guide, p. 28-31.
FlyBase Consortium. 1999. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 27: 85-88.
http://nar.oxfordjournals.org/cgi/reprint/27/1/85
doi:10.1093/nar/27.1.85
FlyBase Consortium. 1999. FlyBase: Genomic and post-genomic viewpoints. In: Bioinformatics. Edited by S. Letovsky, Kluwer Academic Publishers. pp. 141-150.
Brazma, Robinson, G. Cameron and M. Ashburner, 2000. One-stop shop for microarray data, Nature 403: 699-700. (Note).

http://www.nature.com/nature/journal/v403/n6771/full/403699a0.html

M. Ashburner [et al]. 2000. Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29.
http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html
doi:10.1038/75556
H. Lehväslaiho, E. Stupka, and M. Ashburner. 2000. Sequence Variation Database Project at the European Bioinformatics Institute. Human Mutation 15: 52-56.
doi:10.1002/(SICI)1098-1004(200001)15:1<52::AID-HUMU11>3.0.CO;2-Y
M. Ashburner [et al]. 2001. Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11: 1425-1433.
http://genome.cshlp.org/content/11/8/1425
doi: 10.1101/gr.180801
FlyBase Consortium. 2002. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 30: 106-108.
http://nar.oxfordjournals.org/cgi/reprint/30/1/106
doi:10.1093/nar/30.1.106
M. Ashburner and S.E. Lewis. 2002. Ontologies for biologists: the Gene Ontology - uncoupling the web. In: In Silico Biology. Novartis Symposium 247: 66-83.
C.J. Wroe, R. Stevens, C.A. Goble and M. Ashburner. 2002. An evolutionary methodology to migrate the Gene Ontology to a descriptive logic environment using DAML+OIL. Proc. Pacific Symp. Biocomputing 8: 624-635.
http://psb.stanford.edu/psb-online/proceedings/psb03/wroe.pdf
FlyBase Consortium. 2003. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Research 31: 172-175.
http://nar.oxfordjournals.org/cgi/reprint/31/1/172
doi:10.1093/nar/gkg094
H. Mi, J. Vandergriff, M. Campbell, A. Narechania, W. Majoros, S. Lewis, P.D. Thomas and M. Ashburner. 2003. Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Research 13: 2118-2128.
http://genome.cshlp.org/content/13/9/2118.full?sid=6e8f1e7e-3081-4465-bb1c-1478b9db4c69
doi: 10.1101/gr.771603
M. Ashburner, C.J. Mungall and S. Lewis. 2004. Ontologies for biologists – A community model for the annotation of genomic data. Cold Spring Harbor Symp. Quant. Biol. LXVIII: 227-235.
The Gene Ontology Consortium. 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32: D258-D261.
http://nar.oxfordjournals.org/cgi/reprint/32/suppl_1/D258
doi:10.1093/nar/gkh036
M. Bada, R. Stevens, C. Goble, Y. Gil, M. Ashburner, J.A. Blake, J.M. Cherry, M. Harris, and S. Lewis. 2004. A short study on the success of the Gene Ontology. J. Web Semantics 1: 235-240.
doi:10.1016/j.websem.2003.12.003
R. Drysdale, M.A. Crosby and the FlyBase Consortium. 2005. FlyBase: Genes and gene models. Nucleic Acids Research 33: D390-D395.
http://nar.oxfordjournals.org/cgi/reprint/33/suppl_1/D390
doi:10.1093/nar/gki046
J. Bard, S.Y. Rhee and M. Ashburner. 2005. An ontology for cell types. Genome Biology 6: R21.
http://genomebiology.com/2005/6/2/R21
doi:10.1186/gb-2005-6-2-r21
. Eilbeck, S.E. Lewis, C.J. Mungall, M. Yandell, L. Stein, R. Durbin and M. Ashburner. 2005. The Sequence Ontology: A tool for the unification of genome annotations. Genome Biology 6: R44.
http://genomebiology.com/2005/6/5/R44
doi:10.1186/gb-2005-6-5-r44
D.L. Rubin, S.E. Lewis, C.J. Mungall, S. Misra, M. Westerfield, M. Ashburner, I. Sim, C.G. Chute, H. Solbrig , M.-A. Storey, B. Smith, J. Day-Richter, N.F. Noy, M.A. Musen. 2006. National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge. OMICS: Journal of Integrative Biology 10: 185-198.
R. Guigó, P. Flicek, J.F. Abril, A. Reymond, J. Lagarde, F. Denoeud, S. Antonarakis, M. Ashburner, V.B. Bajic, E. Birney, R. Castelo, E. Eyras, C. Ucla, T.R. Gingeras, J. Harrow, T. Hubbard, S.E. Lewis, M.G. Reese. 2006. EGASP: The human ENCODE Genome Annotation Assessment Project. Genome Biology 7(Suppl.1): S2.
http://genomebiology.com/2006/7/S1/S2
doi:10.1186/gb-2006-7-s1-s2
The Gene Ontology Consortium. 2006. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 34: D322-D326.
http://nar.oxfordjournals.org/cgi/reprint/34/suppl_1/D322
doi:10.1093/nar/gkj021
G. Grumbling, V. Strelets and the FlyBase Consortium. 2006. FlyBase: anatomical data, images and queries. Nucleic Acids Res. 34: D484-D488.
http://nar.oxfordjournals.org/cgi/reprint/34/suppl_1/D484
doi:10.1093/nar/gkj068
B. Smith, M. Ashburner, W. Ceusters, C.J. Mungall, M.A.Musen, N.H. Shah, J. Bard, K. Eilbeck, A. Ireland, N. Leontis, P. Rocca-Serra, C. Rosse, S.E. Lewis. 2007. The OBO Foundry: Remoulding Ontology to Support Data Integration. Nature Biotechnology 25: 1251-1255.
http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html
doi:10.1038/nbt1346
P.M. Mabee, Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C. and Westerfield, M. 2007. Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology and Evolution 22(7): 345—350.
doi:10.1016/j.tree.2007.03.013

http://genomebiology.com/2007/8/7/R129

D. Field [et al]. 2008. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotechnology 26: 541-547.
http://www.nature.com/nbt/journal/v26/n5/full/nbt1360.html
doi:10.1038/nbt1360
The Gene Ontology Consortium. 2008. The Gene Ontology (GO) project in 2008. Nucleic Acids Res. 36: D440-D444.
http://nar.oxfordjournals.org/cgi/screenpdf/36/suppl_1/D440
doi:10.1093/nar/gkm883
R.J. Wilson, J.L. Goodman, V. Strelets and the FlyBase Consortium. 2008. FlyBase: Integration and improvements to query tools. Nucleic Acids Res. 36: D588-D593.
http://nar.oxfordjournals.org/cgi/reprint/36/suppl_1/D588
doi:10.1093/nar/gkm930
P. de Matos, M. Ennis, J. Hastings, M. Zbinden, A. McNaught, R. Alcantara, M. Guedj, M. Ashburner and K. Degtyarenko. 2008. ChEBI; A database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36: D344-D350.
http://nar.oxfordjournals.org/cgi/reprint/36/suppl_1/D344
doi:10.1093/nar/gkm791
C.F. Taylor[et al]. 2008. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotech. 26: 889-896.
http://www.nature.com/nbt/journal/v26/n8/full/nbt.1411.html
doi:10.1038/nbt.1411
B. Mons [et al]. 2008. Calling on a million minds for community annotation in WikiProteins. Genome Biology 9: R89.
http://genomebiology.com/2008/9/5/R89
doi:10.1186/gb-2008-9-5-r89
M. Ashburner, U. Leser and D. Rebholz-Schuhmann (Eds.). 2008. Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives. Dagstuhl Seminar Proceedings 08131.
http://drops.dagstuhl.de/portals/index.php?semnr=08131.
M. Ashburner, U. Leser and D. Rebholz-Schumann. 2008. Executive Summary -- Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives. Dagstuhl Seminar Proceedings 08131.
http://drops.dagstuhl.de/portals/index.php?semnr=08131.
S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi-Sutherland, A. Schroeder, R. Seal, H. Zhang; The FlyBase Consortium. 2009. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 37: D555-D559.
http://nar.oxfordjournals.org/cgi/reprint/37/suppl_1/D555
doi:10.1093/nar/gkn788
The Reference Genome Group of the Gene Ontology Consortium. 2009. The Gene Ontology's Reference Genome Project: A unified framework for functional annotation across species. PLoS Comp. Biol. 5(7): e1000431.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431
doi:10.1371/journal.pcbi.1000431

Page compiled 9 Sept 2009