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Morphology and DataBases
About two hundred years of morpho-anatomical studies on acanthomorphs have resulted in a large number of diverse and varied works. At the moment, this rich body of "free-text" data is increasingly hard for researchers to manage and analyze. Besides, over the course of authors and times, one anatomical structure can sometimes have been named and/or interpreted differently, thus complicating data comprehension and comparison.
To solve these problems, databases devoted to morphology have been developed. Various projects exist. In a phylogenetic context, it would be useful to computerize these studies, making easier bibliographic searches, but also to standardize these data so as to improve their use in morphological relationships studies.
In this context, our team went into partnership with the american "Phenoscape" project (see the project wiki), which currently develops a morphological database on teleosts as well as bioinformatic tools to process and use these data.
Data standardization and computerization
To compare this large number of heterogeneous data, we must first draw up a common morphological vocabulary. Following the example of genetics, Phenoscape uses ontologies. Ontologies are constrained, structured vocabularies with well defined logical relationships among terms. Ontologies represent the knowledge of a particular discipline and provide not only a mechanism for consistent annotation of data, but also greater interoperability among people and machines.
To homogenize morphological descriptions from ichthyology, Phenoscape and the broader ichthyological community have developed two ontologies: the Teleost Anatomy Ontology (to standardize anatomical structures) and the Teleost Taxonomy Ontology (to standardize taxa), that are used along with several other ontologies to represent systematic characters.
Let us take an example. The orange bone indicated on the opposite figure of acanthomorph's skull was successfully named "pleurinial, pleurinost, lateral occipital, exoccipitali and exoccipital". Thanks to the Teleost Anatomy Ontology, ichthyologists agreed on the use of the "exoccipital" term (other terms are considered as synonyms).
Scientific publications are computerized using combinations of ontology terms and a software especially designed for data curation, the "Phenex" software (see the software wiki).
Nevertheless, notice that ontology terms don't replace terms used by morphologists for accuracy of data could be lost but they are added to them so as to improve data comparison.
Data storage and access
Once data are computerized thanks to the Phenex software, they are stored on a database making use of ontology-based reasoning to link data together. This database is accessible through a public web interface named the Phenoscape Knowledge Base (http://kb.phenoscape.org/). For now, it is a prototype but users can already search for data by anatomical structures, taxa or publications. An updated interface will very soon be available: it will permit multi-criteria searches and will present data in a more complete and practical way.
- Dahdul W.M., Balhoff J.P., Engeman J., Grande T., Hilton E.J., et al. (2010). Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature. PLoS ONE 5(5): e10708.
- Balhoff J.P., Dahdul W.M., Kothari C.R., Lapp H., Lundberg J.G., et al. (2010). Phenex: Ontological Annotation of Phenotypic Diversity. PLoS ONE 5(5): e10500.