Phenotype Reading List

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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.

Genetics of Development

Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.

http://www.learner.org/channel/courses/biology/units/gendev/

EBI Introduction to cell biology

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


Cjm 12:03, 5 December 2005 (PST)