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Re: Microarray Experiment Context

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 17 Dec 2009 15:25:06 -0500
To: Satya Sahoo <sahoo.2@wright.edu>
Cc: HCLS <public-semweb-lifesci@w3.org>, jun.zhao@zoo.ox.ac.uk, mdmiller <mdmiller53@comcast.net>, Helena Deus <helenadeus@gmail.com>, Matthias Samwald <samwald@gmx.at>
Message-id: <4B2A93A2.3010008@yale.edu>
Hi Satya, Jun et al,

I added to the list of provenance terms another a list of terms 
extracted from the abstracts of the 4 microarray experiments listed in 
[1].  The terms were automatically extracted from the abstracts using 
the NCBO Annotator (http://bioportal.bioontology.org/annotator) with 
NIFSTD being the ontology (one can also input multiple ontologies). We 
can prune this list and combine with your list and to see what sort of 
relationships exist among them. We can also go deeper into each paper to 
see what additional terms/relationships we can find (e.g., at the level 
of gene list). Based on these terms and relationships, we can start to 
explore the type of semantic queries that can be answered as part of the 
next step.

I found a couple of interesting issues using the Annotator.

1. It picked up the term "neurofibrillary tangle" but not its plural 
form "neurofibrillary tangles". So it would be nice to include synonyms 
even if these synonyms may not be included in the input ontology.
2. It didn't pick up "temporal and prefrontal cortex" even though 
"temporal cortex" and "prefrontal cortex" are defined in NIFSTD

I wonder if tools like atag can help address these issues (what happens 
if atags are applied to the abstracts). There are terms like "dopamine 
neuron" that doesn't seem to be found in NIFSTD. I'll need to look into 
it more and may check with the NeuroLex group on this.



[1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2

Kei Cheung wrote:
> Hi Satya et al,
> Thanks for creating the wiki page. I think it's a good start. I hope 
> our use case can help facilitate some of the ontology alignment 
> effort. You already listed a few to start. Other might include: 
> NIFSTD, SenseLab, SWAN, TMO, etc. You can also add my name to the 
> contact for the page if you want.
> Cheers,
> -Kei
> Satya Sahoo wrote:
>> Hi all,
>> I have created a wiki page to collect provenance related terms 
>> describing experiment conditions and protocols used to generate 
>> microarray data [1]. The page also lists a set of queries that rely 
>> on the provenance information associated with gene expression data.
>> Please add additional terms required to better describe the 
>> experiment context, such as the statistical tools or process used to 
>> obtain gene list (published in literature) from raw experiment data.
>> -- thanks to Jun for the wiki page edit rights :)
>> cheers,
>> Satya
>> Kno.e.sis
>> http://knoesis.wright.edu/researchers/satya
>> [1] 
>> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext 
Received on Thursday, 17 December 2009 20:40:43 UTC

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