Difference between revisions of "Phenotype Reading List"

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=Phenotype readling list=
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I have some of these in my endnote library, but endnote is terrible
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==Intro to phenotypes for non-biologists==
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This list is very fly-centric. If someone can contribute zebrafish and
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human clinical genetics pointers that would be great.
 
  
===Genetics of Development===
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Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.
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===EBI Introduction to cell biology===
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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
 
 
 
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
 
 
 
http://books.google.com/books?ie=UTF-8&hl=en&id=BXfdbKLTiZQC&dq=essential+developmental+biology&prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&lpg=PP5&pg=PP5&printsec=4&sig=FIivE3wd7u_AC9ojAEdW-BpD90A
 
 
 
I found this to be a really useful and accessible introduction to
 
developmental biology. Remember, many 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===
 
 
 
These two are standard texts for molecular biology - this will have a lot of the background material for understanding phenotypes:
 
 
 
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
 
 
 
This may also be useful:
 
 
 
The Shape of Life : Genes, Development, and the Evolution of Animal Form (Paperback)
 
by Rudolf A. Raff
 
 
 
 
 
===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:
 
 
 
http://search.nature.com/search/?sp_a=sp1001702d&sp_sfvl_field=subject%7Cujournal&sp_t=results&sp_q_1=Nature+Reviews+Genetics&sp_x_1=ujournal&sp_p_1=phrase&go.x=0&go.y=0&sp-q=the+art+and+design+of+genetic+screens
 
 
 
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==
 
 
 
===J. Diederich. 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.
 
 
 
==See also an application of the work from this paper in:
 
Diederich, J., R. Fortuner and J. Milton. 1997. Construction and integration
 
of large character sets for nematode morpho-anatomical data. ''Fundam. appl. Nematol.'' 20: 409-424
 
 
 
===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.
 
http://helix-web.stanford.edu/psb04/gkoutos.pdf
 
 
 
Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using
 
ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.
 
http://dx.doi.org/10.1186/gb-2004-6-1-r8
 
 
 
G. V. Gkoutos, E. C. J. Green, A.-M. Mallon, A. Blake, S. Greenaway 1, J. M. Hancock, D. Davidson
 
Ontologies for the description of mouse phenotypes
 
MRC Mammalian Genetics Unit, Harwell, UK
 
http://doi.wiley.com/10.1002/cfg.430
 
 
 
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.
 
http://www.bioinformatics.oupjournals.org/cgi/doi/10.1093/bioinformatics/bti147
 
 
 
 
 
[[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)
 

Revision as of 05:15, 6 July 2006

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