Difference between revisions of "Phenotype Reading List"

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-=Phenotype readling list=
+<div id="nolabel" style="overflow:auto;height:1px;">
-I have some of these in my endnote library, but endnote is terrible
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-people use Latex? If so, if they post their bibtexes here I can
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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)

Difference between revisions of "Phenotype Reading List"

Revision as of 05:15, 6 July 2006

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