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HCLS Telecon 

1. ArrayExpress Archive - archival repository of gene expression data - complete data files, meta data in IDF/SDRF format - tab delimited files

2. Atlas of Gene Expression - ranked lists of genes/condition plus p value, relative under/over expression per species. Evidence from multiple experiments. Annotated with EFO - experimental factor ontology, which is mapped into other ontologies. Gene annotation, GO terms, pathways etc for genes are also available from the atlas. MicroRNA data will be added shortly

3. Neuro data has been curated, some additional terms needed for these papers, mapping to NIFSTD is underway. These have been added to NIF and will be mapped in to the AE data

e.g. 

layer II stellate non-tangle bearing neurons from the entorhinal cortex
layer II stellate non-tangle bearing neurons from the entorhinal cortex
layer III non-tangle bearing neurons from the hippocampus (CA1)
layer III non-tangle bearing neurons from the middle temporal gyrus
layer III non-tangle bearing neurons from the posterior cingulate cortex
layer III non-tangle bearing neurons from the superior frontal gyrus
layer III non-tangle bearing neurons from the primary visual cortex
entorhinal cortex layer II stellate island cells bearing tangles 

compositional terms created, will probably be added to EFO, so we can do local queries, as we've not added support for external ontologies to the atlas

Entorhinal cortex layer 2 stellate neuron"has part"  neurofibrillary tangle and Entorhinal cortex layer 2 stellate neuron "lacks" neurofibrillary tangle.  


4. Plan to export the neuro data in AE as triples using http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/ - comments on this?



5. Use cases:

Which genes are always expressed in - 'normal data' normal is a role in the EFO

Which genes are over-under expressed in specific tissues

Which genes are never expressed in neural tissues

Combinatorial queries with other resources - not yet investigated, P-P interaction data is a possibility (e.g. yeast)

How does this community expect to consume these data