[Gusdev-gusdev] phenotype data

[Christiane Hertz-F. <ch...@sa...>]

Hi,

further to recent conversations re. phenotype data, here is the kind of
Trypanosoma data I was envisaging capturing (This is all very much based
around RNAi, there's little "classical genetics" in tryps and due to the
diploid nature of tryps, researchers are using RNAi extensively. Also, one
of the functional genomics projects is based on RNAi - with the possibility
of GeneDB housing data in years to come):

1. type of experiment: 	RNAi (double stranded)
2. construct:		targets coding region
3. developmental stage the experiment is carried out in:	(covered by life
cycle ontology)
4. effect on expression of other proteins
5. phenotype (first thoughts going on what has already been published):
	A. (no) growth (cell proliferation) or morphological [e.g. cytoskeleton,
kinetoplast mitochondrial DNA)] phenotype in a particular life cycle stage
	B. (no) differentiation defect
	C. cell cycle block, cytokinesis block, RNA editing block
	D. mitochondrial defect, Golgi/endocytic pathway defect, motility (i.e.
non-motile, reduced motility)

The types of data generated by the RNAi project are graphs, video clips and
microscopy images.

Arnaud pointed out during discussions today, that the allele tables probably
won't be the right place to store this information. Discussions are
continuing ...

Christiane