Difference between revisions of "Links"
From phenoscape
(→Software) |
(→Bibliography) |
||
| Line 44: | Line 44: | ||
* Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) [[Media:Caroreprint.pdf|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. | * Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) [[Media:Caroreprint.pdf|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 ( | + | * Mabee PM et al (2007a). [[Media:TREE Mabee.pdf|Phenotype ontologies: the bridge between genomics and evolution.]] Trends Ecol Evol <cite>mabee2007a</cite> |
| + | * Mabee PM et al (2007b). [[Media: JEZ Mabee.pdf|Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish.]] J Exp Zoolog B Mol Dev Evol. <cite>mabee2007b</cite> | ||
* Schulz et al (2007). [http://www.biomedcentral.com/1471-2105/8/134 Spatial location and its relevance for terminological inferences in bio-ontologies.] BMC Bioinformatics 2007, 8:134 [http://dx.doi.org/10.1186/1471-2105-8-134 doi:10.1186/1471-2105-8-134] | * Schulz et al (2007). [http://www.biomedcentral.com/1471-2105/8/134 Spatial location and its relevance for terminological inferences in bio-ontologies.] BMC Bioinformatics 2007, 8:134 [http://dx.doi.org/10.1186/1471-2105-8-134 doi:10.1186/1471-2105-8-134] | ||
===References=== | ===References=== | ||
<biblio> | <biblio> | ||
| − | # | + | #mabee2007a pmid=17416439 |
| + | #mabee2007b pmid=17599725 | ||
#rosen1974 Rosen DE. 1974. ''[http://hdl.handle.net/2246/606 Phylogeny and zoogeography of salmoniform fishes and relationships of Lepidogalaxias salamandroides].'' Bulletin of the American Museum of Natural History 153:267-325. | #rosen1974 Rosen DE. 1974. ''[http://hdl.handle.net/2246/606 Phylogeny and zoogeography of salmoniform fishes and relationships of Lepidogalaxias salamandroides].'' Bulletin of the American Museum of Natural History 153:267-325. | ||
#finkfink1981 Fink SV, Fink WL. 1981. ''Interrelationships of the ostariophysan fishes (Teleostei)''. Zoological Journal of the Linnean Society 72(4):297-353. | #finkfink1981 Fink SV, Fink WL. 1981. ''Interrelationships of the ostariophysan fishes (Teleostei)''. Zoological Journal of the Linnean Society 72(4):297-353. | ||
#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. | #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> | </biblio> | ||
Revision as of 16:44, 23 August 2007
Contents
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
Fish resources
Morphology image database resources
Software
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 (2007a). Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol mabee2007a
- Mabee PM et al (2007b). Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol. mabee2007b
- 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>
- mabee2007a pmid=17416439
- mabee2007b pmid=17599725
- 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.
- finkfink1981 Fink SV, Fink WL. 1981. Interrelationships of the ostariophysan fishes (Teleostei). Zoological Journal of the Linnean Society 72(4):297-353.
- 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>
