Difference between revisions of "Phenotype Reading List"
m (Reverted edit of Googlefans, changed back to last version by Alexskr) |
|||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | + | =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/ | |
| − | |||
| − | [http://www. | + | ===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 | ||
| + | |||
| + | |||
| + | [[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST) | ||
Latest revision as of 17:24, 11 August 2006
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
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:
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)