@article {124,
	title = {The caudal skeleton of the catfishes, order Siluriformes. American Museum novitates; no. 2398},
	year = {1969},
	month = {1969/00/01},
	abstract = {49 p. : ill. ; 24 cm.. Includes bibliographical references (p. 47-49).. "To achieve a better understanding of the evolution of , comparative studies of single character complexes throughout the entire order is believed to be a rewarding approach. A survey of the of},
	url = {http://en.scientificcommons.org/18021295},
	author = {Lundberg, John G and Baskin, JN}
}
@article {274,
	title = {Lacantunia enigmatica (Teleostei: Siluriformes) a new and phylogenetically puzzling freshwater fish from Mesoamerica},
	volume = {1000},
	year = {2005},
	month = {2005/00/01},
	pages = {1 - 24},
	author = {Rodiles-Hern{\'a}ndez, R and Hendrickson, DA and Lundberg, John G and Humphries, JM}
}
@article {189,
	title = {A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences},
	volume = {41},
	year = {2006},
	month = {2006/00/01},
	pages = {636 - 662},
	publisher = {Elsevier},
	author = {Sullivan, JP and Lundberg, John G and Hardman, M}
}
@article {211,
	title = {Discovery of African roots for the Mesoamerican Chiapas catfish, Lacantunia enigmatica, requires an ancient intercontinental passage},
	volume = {156},
	year = {2007},
	month = {2007/00/01},
	pages = {39 - 53},
	publisher = {BioOne},
	author = {Lundberg, John G and Sullivan, JP and Rodiles-Hern{\'a}ndez, R and Hendrickson, DA}
}
@article {207,
	title = {Phenex: Ontological Annotation of Phenotypic Diversity},
	volume = {5},
	year = {2010},
	month = {2010/00/01},
	pages = {e10500},
	publisher = {Public Library of Science},
	abstract = {Background: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Methodology/Principal Findings: Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Conclusions/Significance: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.},
	url = {http://www.plosone.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pone.0010500},
	author = {Balhoff, James P and Dahdul, Wasila M and Kothari, Cartik R and Lapp, Hilmar and Lundberg, John G and Mabee, Paula M and Midford, Peter E and Westerfield, Monte and Vision, Todd J}
}
@article {206,
	title = {Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature},
	volume = {5},
	year = {2010},
	month = {2010/00/01},
	pages = {e10708},
	publisher = {Public Library of Science},
	abstract = {Background: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies.Methodology/Principal Findings: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators.Conclusions/Significance: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.},
	url = {http://www.plosone.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pone.0010708},
	author = {Dahdul, Wasila M and Balhoff, James P and Engeman, Jeffrey and Grande, Terry and Hilton, Eric J and Kothari, Cartik R and Lapp, Hilmar and Lundberg, John G and Midford, Peter E and Vision, Todd J and Westerfield, Monte and Mabee, Paula M}
}
