Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy

Database

Volumn 2015, Issue , 2015, Pages

  Dahdul, Wasila ^a   Dececchi, T Alexander ^a   Ibrahim, Nizar ^b   Lapp, Hilmar ^c   Mabee, Paula ^a  

^a University of South Dakota   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGICAL ONTOLOGY; COMPARATIVE ANATOMY; DATA MINING; FACTUAL DATABASE; HUMAN; INFORMATION PROCESSING; NATURAL LANGUAGE PROCESSING; PROCEDURES;

ANATOMY, COMPARATIVE; ANIMALS; BIOLOGICAL ONTOLOGIES; DATA CURATION; DATA MINING; DATABASES, FACTUAL; HUMANS; NATURAL LANGUAGE PROCESSING;

EID: 84943181375     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav040     Document Type: Article

References (28)

1. Deans, A.R., Lewis, S.E., Huala, E. et al. (2015) Finding our way through phenotypes. PLoS Biol., 13, e1002033.
2. Mabee, P., Balhoff, J.P., Dahdul, W.M. et al. (2012) 500, 000 fish phenotypes: the new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. J. Appl. Ichthyol., 28, 300-305.
3. Mungall, C.J., Gkoutos, G.V., Smith, C.L. et al. (2010) Integrating phenotype ontologies across multiple species. Genome Biol., 11, R2.
4. Balhoff, J.P., Dahdul, W.M., Kothari, C.R. et al. (2010) Phenex: ontological annotation of phenotypic diversity. PLoS One, 5, e10500.
5. Dahdul, W.M., Balhoff, J.P., Engeman, J. et al. (2010) Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoSOne, 5, e10708.
6. Balhoff, J.P., Dahdul, W.M., Dececchi, T.A. et al. (2014) Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. J. Biomed. Semantics, 5, 45.
7. Maddison, W.P. and Maddison, D.R. (2014) Mesquite: a modular system for evolutionary analysis. Version 3.01. http://mesquiteproject.org (5 January 2015, date last accessed).
8. Vos, R.A., Balhoff, J.P., Caravas, J.A. et al. (2012) NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst. Biol., 61, 675-689.
9. Haendel, M.A., Balhoff, J.P., Bastian, F.B. et al. (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J. Biomed. Semantics, 5, 21.
10. Mungall, C.J., Torniai, C., Gkoutos, G.V. et al. (2012) Uberon, an integrative multi-species anatomy ontology. Genome Biol., 13, R5.
11. Maglia, A.M., Leopold, J.L., Pugener, L.A. and Gauch, S. (2007) An anatomical ontology of amphibians. Proc. Pac. Symp. Biocomput., 12, 367-378.
12. Dahdul, W.M., Lundberg, J.G., Midford, P.E. et al. (2010) The teleost anatomy ontology: anatomical representation for the genomics age. Syst. Biol., 59, 369-383.
13. Dahdul, W.M., Balhoff, J.P., Blackburn, D.C. et al. (2012) A unified anatomy ontology of the vertebrate skeletal system. PLoS One, 7, e51070-e51070.
14. Gkoutos, G., Green, E., Mallon, A. et al. (2005) Using ontologies to describe mouse phenotypes. Genome Biol., 6, R8.
15. Dahdul, W.M., Cui, H., Mabee, P.M. et al. (2014) Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J. Biomed. Semantics, 5, 21.
16. Midford, P.E., Dececchi, T.A., Balhoff, J.P. et al. (2013) The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. J. Biomed. Semantics, 4, 34.
17. Day-Richter, J., Harris, M., Haendel, M. et al. (2007) OBOEdit-an ontology editor for biologists. Bioinformatics Appl. Note, 23, 2198-2200.
18. Rubinstein, J.S., Meyer, D.E. and Evans, J.E. (2001) Executive control of cognitive processes in task switching. J. Exp. Psychol. Hum. Percept. Perform., 27, 763-797.
19. Rogers, R.D. and Monsell, S. (1995) Costs of a predictible switch between simple cognitive tasks. J. Exp. Psychol. General, 124, 207-231.
20. Cui, H. (2012) CharaParser for fine-grained semantic annotation of organism morphological descriptions. J. Am. Soc. Inf. Sci. Technol., 63, 738-754.
21. Van Auken, K., Jaffery, J., Chan, J. et al. (2009) Semi-automated curation of protein subcellular localization: a text mining-based approach to gene ontology (GO) cellular component curation. BMC Bioinformatics, 10, 228.
22. Arighi, C.N., Carterette, B., Cohen, K.B. et al. (2013) An overview of the BioCreative 2012 workshop track III: interactive text mining task. Database, 2013, bas056.
23. Burleigh, J., Alphonse, K., Alverson, A. et al. (2013) Next-generation phenomics for the tree of life. PLoS Curr. Tree of Life, Edition 1. doi: 10.1371/currents.tol.1085c1713acafc8711 b1372ff7010a1374b03733.
24. Piwowar, H. (2011) Who shares? Who doesn't? Factors associated with openly archiving raw research data. PLoS One, 6, e18657.
25. Cranston, K., Harmon, L., O'Leary, M. and Lisle, C. (2014) Best practices for data sharing in phylogenetic research. PLoS Curr. Tree of Life, Edition 1. doi: 10.1371/currents.tol.bf1301eff1374a1376b1360ca4825c69293dc59645.
26. Dietze, H., Berardini, T., Foulger, R. et al. (2014) TermGenie-a web-application for pattern-based ontology class generation. J. Biomed. Semantics, 5, 48.
27. Huang, F., Macklin, J.A., Cui, H. et al. (2015) OTO: ontology term organizer. BMC Bioinformatics, 16: 47.
28. Skutschas, P.P. and Gubin, Y.M. (2012) A new salamander from the late Paleocene-early Eocene of Ukraine. Acta Palaeontol. Pol., 57, 135-148.