- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Thu, 29 Oct 2009 16:43:08 -0400
- To: mdmiller <mdmiller53@comcast.net>
- Cc: Helen Parkinson <parkinson@ebi.ac.uk>, HCLS <public-semweb-lifesci@w3.org>, Tony Burdett <tburdett@ebi.ac.uk>
Hi Michael et al, Thanks for pointing to this generic approach of RDF representation of datasets. A list of differentially expressed genes may be associated with values such as P-values, fold-change, gene symbols, etc. Also, it's important to capture metadata/provenance associated with the gene list. This may include the type of statistical test (e.g., ANOVA) and the array platform employed (e.g., Affymetrix U133A). This may be an interesting discussion topic at the F2F meeting. Cheers, -Kei mdmiller wrote: > 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 Thursday, 29 October 2009 20:43:46 UTC