Proposal References

From HAO Wiki

Alpert, G.D. 2007. A review of the ant genus Metapone Forel from Madagascar. Memoirs of the American Entomological Institute, 80: 8-18.

Antoniou, G., and Van Harmelen, F. A (2004) Semantic Web Primer. Boston, MIT Press.

Bao, J., Hu, Z., Caragea, D., Reecy, J., & Honavar, V. (2006) A Tool for Collaborative Construction of Large Biological Ontologies. Fourth International Workshop on Biological Data Management – DEXA 2006, Krakow, Poland

Barbas, A.J., Galceran, J., Torroja, L., Prado, A. & Feerus, A. 1993. Abnormal muscle development in the heldup3 mutant of Drosophila melanogaster is caused by a splicing defect affecting selected troponin I isoforms. Molecular and Cellular Biology 13(3): 433-1439.

Bard, L. 2008. Anatomical ontologies for model organisms: the fungi and animals. pp. 3-25 in: Anatomical Ontologies for Bioinformatics, Burger, A., Davidson, D. & Baldock, R. (eds.) Springer. 354 pp.

Berkov, A., Rodríguez, N. & Centeno, P. 2008. Convergent evolution in the antennae of a cerambycid beetle, Onychocerus albitarsis, and the sting of a scorpion. Naturwissenschaften, 95:257–261

Crampton, G.C. 1920. A comparison of the genitalia of male Hymenoptera, Mecoptera, Neuroptera, Diptera, Trichoptera, Lepidoptera, Homoptera, and Strepsiptera, with those of lower insects. Psyche, 27(2-3): 34–45

Crickmore, M.A. & Mann, R.S. Hox Control of Organ Size by Regulation of Morphogen Production and Mobility. Science, 313: 63-68.

Donner, A. L. & Maas, R. L. 2004. Conservation and non-conservation of genetic pathways in eye specification. Int. J. Dev. Biol. 48, 743–753.

Crozier, R.H., Crozier, Y.C. 1993. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 133: 97-117.

Deans, A. R. & F. Ronquist. 2006. Ontologizing morphological terms for Hymenoptera - implementing and benefiting from a controlled vocabulary. 6th International Conference of Hymenopterists, Sun City South Africa. January 2006.

Davies, J., Fensel, D., & Van Harmelen, F. (eds.). Towards the Semantic Web: Ontology-driven Knowledge Management. John Wiley & Sons., West Sussex, England (2004)

Donner, A. L. & Maas, R. L. 2004. Conservation and non-conservation of genetic pathways in eye specification. Int. J. Dev. Biol. 48, 743–753.

Duncan, C. D. 1939. A contribution to the biology of North American vespine wasps. Stanford University Publications, Biological Sciences 8:1-233.

Fellbaum, C. (1998) WordNet: An Electronic Lexical Database (Language, Speech, and Communication). MIT Press: Boston. 423 pp.

Fontal-Cazalla, F.M., Buffington, M.L., Nordlander, G., Liljeblad, J., Ros-Farré, P., Nieves-Aldrey, J.L., Pujade-Villar, J. & Ronquist F. 2002. Phylogeny of the Eucoilinae (Hymenoptera: Cynipoidea: Figitidae). Cladistics, 18: 154–199.

Gaston, K. J., I. D. Gauld & P. Hanson (1996) The size and composition of the hymenopteran fauna of Costa Rica. Journal of Biogeography 23: 105-113.

Gauch, S., & Chandramouli, A. (2006) Semi-Automatic Update of Existing Taxonomy using Text Mining. 5th International Conference on Ecological Informatics (ISEI5)

Gauld, I.D. 1976. A Revision of the Anomaloninae (Hymenoptera : Ichneumonidae) of Australia. Australian Journal of Zoology, 24: 597–634.

Gibson, G. A. P. 1985. Some pro- and mesothoracic structures important for phylogenetic analysis of Hymenoptera, with a review of the terms used for the structures. Canadian Entomologist 117:1395-1443.

Grissell, E. (1999) Hymenopteran biodiversity: some alien notions. American Entomologist, 45, 236–244.

Grumbling, G, Strelets, V. & The FlyBase Consortium. 2006. FlyBase: anatomical data, images and queries. Nucleic Acids Research. 34:484-488.

Gene Ontology Consortium. (2000) Gene Ontology: tool for the unification of biology. Nature Genet. 25: 25-29.

Gene Ontology Consortium. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research 32: D258-D261.

Haendel, M. A., F. Neuhaus, D. Osumi-Sutherland, P. M. Mabee, J. L. V. Mejino, C. J. Mungall, & B. Smith. CARO - The Common Anatomy Reference Ontology. pp. 327-349 in: Anatomical Ontologies for Bioinformatics, Burger, A., Davidson, D. & Baldock, R. (eds.) Springer. 354 pp.

Herranz, R., Mateos, J., Mas, J.A., García-Zaragoza, E., Cervera, M. & Marco, R. 2005. The Coevolution of Insect Muscle TpnT and TpnI Gene Isoforms. Molecular Biology and Evolution, 22 (11): 2231-2242.

Hooper, S.L. & Thuma, J.B. 2005. Invertebrate Muscles: Muscle specific genes and proteins. Physiological Reviews, 85: 1001-1060.

Ilic, K., E. A. Kellogg, P. Jaiswal, F. Zapata, P. F. Stevens, L. P. Vincent, S. Avraham, L. Reiser, A. Pujar, M. M. Sachs, N. T. Whitman, S. R. McCouch, M. L. Schaeffer, D. H. Ware, L. D. Stein and S. Y. Rhee. 2007. The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology 143:587-599

Johnson, N. F. 1988. Midcoxal articulations and the phylogeny of the order Hymenoptera. Annals of the Entomological Society of America 81:870-881.

Knublauch, H. Fergerson, R. W., Noy, N. F., & Musen, M. A. (2004) The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. Third International Semantic Web conference – ISWC 2004, Hiroshima, Japan

Leopold, J., Maglia, A., & Hoeft, T. (2005) Interactive Anatomy Online: The MorphologyNet Digital Library of Anatomy. IEEE Potentials 24(2):39–41

Liu J., Mercer J.M., Stam L.F., Gibson G.C., Zeng Z.B., Laurie C.C. 1996. Genetic analysis of a morphological shape difference in the male genitalia of Drosophila simulans and D. mauritiana. Genetics, 142:1129-1145.

Mabee, P. M., M. Ashburner, Q. Cronk, G. V. Gkoutos, M. Haendel, E. Segerdell, Chris Mungall, & M. Westerfield. 2007a. Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution 22 (7): 345-350

Mabee, P. M., G. Arratia, M. Coburn, M. Haendel, E. J. Hilton, J. G. Lundberg, R. L. Mayden, N. Rios, M. Westerfield. 2007b. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 308B (5): 655-668.

Maglia, A. M., Pugener, L. A., and Trueb, L. Comparative Development of Anurans: Using Phylogeny to Understand Ontogeny. Amer. Zool., 41:538–551 (2001)

Matsuda, R. 1965. Morphology and Evolution of the insect head. Mem. Am. ent. Inst. 4: 1–334.

Matsuda, R. 1970. Morphology and Evolution of the insect thorax. Mem. Ent. Soc. Can. 76: 1–431.

Mikó, I., L. Vilhelmsen, N. F. Johnson, L. Masner, & Z. Pénzes. 2007. Morphology of Scelionidae (Hymenoptera: Platygastroidea): head and mesosoma. Zootaxa 1571:1-78.

Morse R. A. & Calderone, N. W. 2000. The value of honey bees as pollinators of U. S. crops in 2000. Bee Culture 128(3): 15 pp. (special section).

Page, R. D. M. 2006. Taxonomic names, metadata, and the semanticweb. Biodiversity Informatics 3:1–15.

Perrichot, V., Nel, A., Néraudeau, D., Lacau, S. & Guyot, T. 2008. New fossil ants in French Cretaceous amber (Hymenoptera: Formicidae) Naturwissenschaften, 95: 91–97.

Ronquist, F. & Nieves-Aldrey, J.-L. 2001. A new subfamily of Figitidae (Hymenoptera, Cynipoidea). Zoological Journal of the Linnean Society, 133: 483–494.

Ronquist, F. & Nordlander, G. 1989. Skeletal morphology of an archaic cynipoid, Ibalia rufipes (Hymenoptera: Ibaliidae). Entomologica scandinavica, 33: 1–60.

Rosse, C., Shapiro, L. G., Brinkley, J. F. (1998) The Digital Anatomist Foundational Model: principles for defining and structuring its concept domain. Proc AMIA Symp 820–4

Pease, A., Niles, I., and Li, J (2002). The Suggested Upper Merged Ontology: A Large Ontology for the Semantic Web and its Applications. In Working Notes of the AAAI-2002 Workshop on Ontologies and the Semantic Web, Edmonton, Canada

Ramírez, M. J., J. A. Coddington, W. P. Maddison, P. Midford, L. Prendini, J. Miller, C. E. Griswold, G. Hormiga, P. Sierwald, N. Scharff, S. P. Benjamin, & W. C. Wheeler. 2007. Linking of digital images to phylogenetic data matrices using a morphological ontology. Syst. Biology 56 (2): 283-294.

Schulmeister, S. 2003. Morphology and evolution of the tarsal plantulae in Hymenoptera (Insecta), focusing on the basal lineages. Zoologica Scripta 32:153-172.

Sharkey, M.J. (2007) Phylogeny, taxonomy and classification of the Hymenoptera. Zootaxa, 1668, 521– 548.

Smith, M. A., Rodriguez, J. J., Whitfield, J. B., Deans, A. R., Janzen, D. H., Hallwachs, W., & Hebert, P. D. N. 2008. Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology and collections. Proceedings of the National Academy of Sciences, USA

Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall CJ, Neuhaus F, Rector A, Rosse C. 2005 Relations in Biomedical Ontologies. Genome Biology, 2005, 6:R46

Smith, B., & Ross, C. (2004) The Role of Foundational Relations in the Alignment of Biomedical Ontologies. 11th World Congress on Medical Informatics (MEDINFO)

Scudder, G.G.E. 1971. Comparative morphology of Insect genitalia. Annual Review of Entomology. 16: 379–406.

Snodgrass, R. E. 1935. Principles of insect morphology. McGraw-Hill Book Co., Inc., New York & London 667 pp..

Soldatova, L., & King, R. Are the current ontologies in biology good ontologies? Nature Biotech. 23:1095–1098 (2005)

Torre-Bueno, J.R. de la. 1989. The Torre-Bueno Glossary of Entomology. Revised edition, compiled by S.W. Nichols. New York: New York Entomological Society. 840pp.

Traut, W., Niimi, T., Ikeo, Sahara, K. 2006. Phylogeny of the sex-determining gene Sex-lethal in insects. Genome 49(3): 254-262.

van Noort, S. & Compton, S.G. 1996. Convergent evolution of Agaoninae and Sycoecinae (Agaonidae, Chalcidoidea) head shape in response to the constraints of host fig morphology. Journal of Biogeography, 23: 415-424.

Vilhelmsen, L. 1996. The preoral cavity of lower Hymenoptera (Insecta): comparative morphology and phylogenetic significance. Zoologica Scripta 25:143-170.

Vilhelmsen, L., Turrisi, G.F. & Beutel, R.G. 2008. Distal leg morphology, subgenual organs and host detection in Stephanidae (Insecta, Hymenoptera). Journal of Natural History, 42(23): 1649–1663.

Wagner, G.P. 2007. The developmental genetics of homology. Nature Review Genetics 8: 473-479.

Weatherbee, S.D., Halder, G., Kim, J., Hudson, A. & Carroll, S. 1998. Ultrabithorax regulates genes at several levels of the wing-patterning hierarchy to shape the development of the Drosophila haltere. Genes & Development, 12: 1474-1482.

Werren, J.H., J. Gadau, L. Beukeboom, C. Desplan, J. Lynch, R. Rivers, S. Richards, L. van de Zande. (2004 white paper). Proposal to Sequence the Nasonia Genome.

Yeates, D.K. & Wiegmann, B.M. 1999. Congruence and controversy: Toward a higher-level phylogeny of Diptera. Annual Review of Entomology, 44:397–428

Yoder, M.J. 2007. Mannomicrus (Hymenoptera: Diapriidae), a new genus of myrmecophilic diapriid, with a digital version of Masner and García's (2002) key to New World Diapriinae and an illustration of digital description and key markup using an ontology. Zootaxa 1439: 47–55.

Zhang, S. & O. Bodenreider. 2005. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc. 2005; 2005: 864–868.