[ome-devel] on omero, pytables and genotypes

[Gianluigi Zanetti]

Hi Kristen.

Here at CRS4, we are using omero + omero tables (omero pytable wrapping)
for exactly the same purpose. We have added a set of models to Omero and
a certain amount of syntactic sugar written in python to simplify usage.

We are currently using this modified version of Omero to support two
population studies, with order of 20k individuals enrolled and large
amounts/types of data connected to each individual both experimental and
clinical.

To handle genotype data, we are using the following scheme: we directly
model markers as, basically, their defining sequence mask in illumina
top format; maintain per marker alignment information to reference
genomes; define specific genotyping assays, e.g., Affymetrix 6.0,
Illumina Human1M, ad hoc TqMan assays, re-sequencing results, as ordered
collection of markers (SNPMarkersSet in the examples below); map
genotyping results as floating point arrays on top of the SNPMarkersSet,
essentially we are keeping track of homozygous alleles probabilities and
confidence in the, per snp, result.

As a side remark, to be able to have consistent marker information,
e.g., comparison between Illumina and Affy results, we had to develop a
tool, based on the projection to a common reference genome, for unique
(well, at least as far as the given reference genome is concerned :-))
marker identification and, when possible, link to dbSNP known markers. 

To give you a general idea, I am attaching some example python scripts
with inlined  documentation. They are taken from the current
documentation draft, and they are probably missing context information,
but I hope that something useful could be gleaned from them. They should
be read in the following order: create_individuals.py;
create_markers_sets.py; data_blocks.py.

There is much more, e.g., a sort of LIMS support, specialized handling
of Electronic Health Record data by mapping OpenEHR structures to
pytables, galaxy interfaces to support data import and query, ...

We are in the process of cleaning up what we have, and our idea was to
make a public release of the software sometime before the end of the
year. However, if you feel brave, we will be happy to send you snapshots
of the current state of affairs. 

--gianluigi



On Fri, 2011-10-21 at 13:45 -0700, Kristen Eisenberg wrote:
Hi there!
> 
> We are currently trying to move our genotype data description from a
> one-file per genotype to pytables, since it appears to be an efficient
> way to handle simple by-column and by-row operations.
> 
> Now, what we are trying to understand is how this can best fit inside
> Omero. Are you supporting an array omero.grid Column type in
omero.grid.table? It should be
> able to handle medium size (i.e., up to 8M elements float) arrays.
> 
> Attached is a python file with a somewhat more detailed discussion of
> what we would like to do.
> 
> An ugly alternative, more or less what we are already doing, is to
have
> Omero keep track of DataObject(s) (and how they have been obtained)
and
> then to have another layer of software that knows how to resolve an
> hdf5/pytable url to a record.
> 
> 
> Kristen Eisenberg
> Billige Flüge
> Marketing GmbH
> Emanuelstr. 3,
> 10317 Berlin
> Deutschland
> Telefon: +49 (33)
> 5310967
> Email:
> utebachmeier at
> gmail.com
> Site:
> http://flug.airego.de - Billige Flüge vergleichen
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: create_individuals.py
Type: text/x-python
Size: 2974 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20111022/3713e7d1/attachment.py>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: create_markers_sets.py
Type: text/x-python
Size: 5894 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20111022/3713e7d1/attachment-0001.py>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: data_blocks.py
Type: text/x-python
Size: 4759 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20111022/3713e7d1/attachment-0002.py>