Links

Links relevant to the project

Ontologies

National Center for Biomedical Ontology

• Ontologies from NCBO
• Ontology of Zebrafish Anatomy and Development
• Common Anatomy Reference Ontology (CARO) (also available in OWL format)
• Maintaining inter-ontology relations between species specific anatomy ontologies and CL/GO/CARO
• OBD Phenotype file formats - Includes standards and schemas for PhenoSyntax and PhenoXML

Data typed using phenotype ontology

• OBD data and schema downloads

Fish resources

• Zebrafish Information Network (ZFIN)
• DeepFin
• Digital Fish Library
• Catalog of Fishes
• FishBase

Morphology image database resources

• Morphbank
• MorphoBank
• Digimorph
• Morphster

Software

• Phenote
• OBO-Edit

Bibliography

We also maintain a list of references on Connotea, using the tag "phenomap". This list may be more up-to-date than the bibliography below.

Anyone can easily recommend references (and in fact any site or resource) to us simply by tagging it with "phenomap" in Connotea.

Reprints

• Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) CARO - The Common Anatomy Reference Ontology. In: Albert Burger, Duncan Davidson and Richard Baldock (Editors): Anatomy Ontologies for Bioinformatics: Principles and Practice. ISBN 978-1-84628-884-5.
• Mabee PM et al (2007). Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol mabee2007
• Schulz et al (2007). Spatial location and its relevance for terminological inferences in bio-ontologies. BMC Bioinformatics 2007, 8:134 doi:10.1186/1471-2105-8-134

References

<biblio>

1. mabee2007 pmid=17416439
2. rosen1974 Rosen DE. 1974. Phylogeny and zoogeography of salmoniform fishes and relationships of Lepidogalaxias salamandroides. Bulletin of the American Museum of Natural History 153:267-325.
3. finkfink1981 Fink SV, Fink WL. 1981. Interrelationships of the ostariophysan fishes (Teleostei). Zoological Journal of the Linnean Society 72(4):297-353.
4. finkfink1997 Fink, S.V. and W.L. Fink. 1997. Interrelationships of the Ostariophysi. In: Interrelationships of Fishes, M. Stiassney, L. Parenti and D. Johnson (Eds). Academic Press, 209-249.

</biblio>