- From: mdmiller <mdmiller53@comcast.net>
- Date: Fri, 23 Oct 2009 08:15:18 -0700
- To: "Kei Cheung" <kei.cheung@yale.edu>, "Helen Parkinson" <parkinson@ebi.ac.uk>
- Cc: "HCLS" <public-semweb-lifesci@w3.org>, "Tony Burdett" <tburdett@ebi.ac.uk>
hi all, on a different HCLS thread i saw this proposal from jeni tennison for specifying a generic dataset, it might be a useful way to encode a list of differentially expressed genes. it looks like one could do this encoding on the fly, so that the data itself at the source could be in whatever format is natural. http://sw.joanneum.at/scovo/schema.html cheers, michael Michael Miller mdmiller53@comcast.net ----- Original Message ----- From: "Kei Cheung" <kei.cheung@yale.edu> To: "Helen Parkinson" <parkinson@ebi.ac.uk> Cc: "HCLS" <public-semweb-lifesci@w3.org>; "Tony Burdett" <tburdett@ebi.ac.uk> Sent: Wednesday, October 14, 2009 7:03 PM Subject: Re: Action Items from call today > Thanks, Helen. > > To make it more concrete. I've been thinking about some example queries > that I hope can be answered by the RDF data once converted. I wonder if > the following example quereis can be answered: > > Retrieve a list of differentially expressed genes between different brain > regions (e.g., hippocampus and entorhinal cortex) for normally aged human > subjects. > > Retrieve a list of differentially expressed genes for the same brain > region of normal human subjects and AD patients. > > Using these lists of genes one can issue (federated) queries to retrieve > addtional information about the genes for various types of analyses (e.g., > GO term enrichment). > > Just a thought. > > Cheers, > > -Kei > > > > Helen Parkinson wrote: > >> Hi >> >> here are my action items from the call today >> >> 1. MAGE-TAB->RDF, Lena requested details. >> >> Code here: https://sourceforge.net/projects/limpopo/ >> >> Java Parser for MAGE-TAB developed by EBI, used by several groups. >> Contact Tony Burdett tburdett@ebi.ac.uk for details. Tony estimates for a >> simple RDF dump a few days work. Lena if you are interested in working on >> this java code please contact Tony as he's already designed with rdf >> export in mind >> >> 2. MAGE-TAB->MAGE-ML - code from Junmin Liu at UPenn >> >> https://sourceforge.net/projects/tab2mage/files/ - see mage2tab >> Pretty much all public MAGE-ML comes from AE and is available from >> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's >> mage-ml importer, and non public data >> >> >> 3. EBI experimental factor ontology (EFO) slides, attached >> see also www.ebi.ac.uk/efo >> >> 4. Noted that an RDF dump of atlas data and triple store access will be >> useful, we'll announce when these are available >> >> thanks >> >> Helen >> >> >> > > >
Received on Friday, 23 October 2009 21:08:38 UTC