Difference between revisions of "Phenotype Reading List"
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This list is very fly-centric. If someone can contribute zebrafish and | This list is very fly-centric. If someone can contribute zebrafish and | ||
human clinical genetics pointers that would be great. | human clinical genetics pointers that would be great. | ||
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| + | ===EBI Introduction to cell biologists=== | ||
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| + | This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist | ||
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| + | http://www.ebi.ac.uk/microarray/biology_intro.html | ||
===Drysdale R: Phenotypic data in FlyBase=== | ===Drysdale R: Phenotypic data in FlyBase=== | ||
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virtually no biology, but I'd still highly recommend it. Covers fly, | virtually no biology, but I'd still highly recommend it. Covers fly, | ||
zebrafish and other major model organisms. | zebrafish and other major model organisms. | ||
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| + | ===Other books=== | ||
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| + | Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994 | ||
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| + | Lewin B: Genes VII, New York, Oxford University Press, 2000 | ||
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===THE ART AND DESIGN OF GENETIC SCREENS=== | ===THE ART AND DESIGN OF GENETIC SCREENS=== | ||
Revision as of 17:19, 6 December 2005
Phenotype readling list
I have some of these in my endnote library, but endnote is terrible for collecting non-bio references. I'm guessing the CS and logiv people use Latex? If so, if they post their bibtexes here I can compile both an endnote and a bibtex library.
Intro to phenotypes for non-biologists
This list is very fly-centric. If someone can contribute zebrafish and human clinical genetics pointers that would be great.
EBI Introduction to cell biologists
This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist
http://www.ebi.ac.uk/microarray/biology_intro.html
Drysdale R: Phenotypic data in FlyBase
Brief Bioinform 2001,2(1):68-80.
This is an ideal intro for folks familiar with biological databases looking to make the first step into genetics and phenotypes.
Essential Developmental Biology
by J. M. W. Slack
I found this to be a really useful and accessible introduction to developmental biology. Remember, most of the phenotypes we're dealing with will be developmental. It may be challenging for those with virtually no biology, but I'd still highly recommend it. Covers fly, zebrafish and other major model organisms.
Other books
Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994
Lewin B: Genes VII, New York, Oxford University Press, 2000
THE ART AND DESIGN OF GENETIC SCREENS
This is actually a whole collection of reviews in Nature Reviews Genetics coverisg zebrafish, mouse, etc. Go to their website and search on the above:
Here's the one on zebrafish http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4
These are highly recommended for the tools developers
The Making of a Fly: The Genetics of Animal Design [BOOK]
http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&n=283155
May be hard going for those without any knowledge of genetics
Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]
aka the grey book http://www.cshlpress.com/default.tpl?action=full&cart=1133810703113928&--eqskudatarq=467&newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition
Everything you ever wanted to know about Drosophila genetics but were afraid to ask Michael. This may be a little overwhelming for the CS folks
Formal ontology and logic
References on formal ontology and logic and qualities that are tied to qualities
A formal theory of substances, qualities, and universals.
Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.: Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS Press (2004) 49–59
Available from: http://ontology.buffalo.edu/bfo/SQU.pdf
This paper may be heavy-going for those without a background in logic, but I would still highly recommend the first couple of pages to everyone involved in this project.
Stanford Encyclopedia of Philosophy
Entry on properties: http://plato.stanford.edu/entries/properties/
I think properties here are used in the sense that Fabian Neuhaus and I would use "quality", rather than in the looser sense that a CS or OWL person may use the term.
Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/
I was hesitant about adding this one. Inquiring minds may want to check this out. Determinate vs determinable roughly corresponds to value vs attribute
Data modeling
Basic properties for biological databases: character development and support
in Math. Comput. Modelling 25 (1997), 109-127.
Required reading for everyone in the project. 1997, but it anticipated many of the problems we are facing. This has more of a systematics focus, but really the design of ontologies for phenotypic characters should be independent of whether we are applying this to genetic screens or to phylogenetic classisification.
Papers by George
George gets his own section here. The GB is paper is a good introduction to the EAV model as it was originally formulated in 2003.
Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.
Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.
Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM: CRAVE: a database, middleware and visualization system for phenotype ontologies. Bioinformatics 2005, 21(7):1257-1262.
Cjm 12:03, 5 December 2005 (PST)