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Re: New features on NeuroLex

From: Kei Cheung <kei.cheung@yale.edu>
Date: Fri, 07 Aug 2009 09:06:14 -0400
To: neurolex@googlegroups.com, Helen Parkinson <parkinson@ebi.ac.uk>, HCLS <public-semweb-lifesci@w3.org>
Cc: Maryann Martone <maryann@ncmir.ucsd.edu>
Message-id: <4A7C26C6.2010803@yale.edu>
Hi Helen et al,

I'm glad that connectivity is not only established between different 
regions within the same brain, but it seems to also occur among 
different brains (e.g., people at EBI and people at NIF).  :-)   Now I'm 
trying to connect with the brains of the people in BioRDF and HCLS as a 
whole (cc'ed to the HCLS mailing list). In BioRDF, we are currently 
developing a use case to do query federation of neuroscience microarray 
data using semantic web. I hope our neurons can all connect eventually 
(the wiki neuron concept is still alive)!

Cheers,

-Kei


Helen Parkinson wrote:
> Hi,
>
> thanks to Kei for introducing me to this group.
>
> Looking at some annotations we have we may also need some cross product 
> terms:
>
> 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
>
> I have mapped all the brain regions either to FMA/NIFSTD, and mapped 
> 'tangles' to NIFSTD p8:sao2409833926 'neurofibriallary tangles', but I 
> couldn't get a map from NIFSTD to the 3 neuron terms:
>
> layer II stellate neurons
> layer III stellate neurons
> layer II stellate island cells
>
> If someone would kindly point me to the correct terms, or if this would 
> be better done using cross products, let me know how these are generated 
> I'd be very grateful,
>
> thanks
>
> Helen
>
>
>
>
>
>
>
>
>
> Maryann Martone wrote:
>   
>> They are meant to be layer III pyramidal cells throughout the cortex.  
>> They could certainly be defined as cross products of specific brain 
>> regions.
>>
>> On Aug 6, 2009, at 9:04 PM, Kei Cheung wrote:
>>
>>     
>>> Thanks, Maryann.
>>>
>>> One thing I forgot to ask is that it says "layer III pyramidal cells" in
>>> the description. I don't know if they are meant for all brain regions
>>> studied in the experiment or some of the brain regions. According to the
>>> mappings reported by Stephen, it might mean that layer III pyramidal
>>> cells are specific to certain brain regions. Anyway, that's all I have
>>> to ask now. Helen and others might have more questions.
>>>
>>> -Kei
>>>
>>> . Maryann Martone wrote:
>>>
>>>       
>>>> We are working with the BAMS group to import their connectivity
>>>> information  into NIF.  Entorhinal cortex and hippocampus are very
>>>> heavily interconnected.  NIF's current nomenclature is based on
>>>> Neuronames, which is based on classical anatomy and explicitly didn't
>>>> use terminology that included a functional designation, e.g., Visual
>>>> cortex.  It does have striate cortex=area 17 of Brodmann, which can be
>>>> identified on structural or cytoarchitectural grounds.  We're working
>>>> a bit with FMA on this, and expect that the representation of these
>>>> areas will be forthcoming soon.
>>>>
>>>>
>>>> On Aug 6, 2009, at 8:05 PM, Kei Cheung wrote:
>>>>
>>>>
>>>>
>>>>         
>>>>> Hi Stephen et al.
>>>>>
>>>>> Thanks for your effort in mapping the brain regions described in the
>>>>> experiment protocol to those defined in Neurolex. While some have
>>>>> identical mapping, others do not (e.g., posterior cingulate vs
>>>>> posterior
>>>>> cingulate gyrus). Primary visual cortex seems to present a challenge.
>>>>> I'm not a neuroscientist, but I find it interesting. Also, I wonder
>>>>> what
>>>>> types of connectivity exist among these brain regions. For example,
>>>>> are
>>>>> hippocampus and entorhinal cortex connected in some way (e.g., memory
>>>>> processing)? If so, does Neurolex capture it?
>>>>>
>>>>> I cc'ed Helen Parkinson who is running ArrayExpress at EBI. She is
>>>>> interested in creating a neuro-altas for mciroarray gene expression
>>>>> data. She is also interested in collaborating with BioRDF within the
>>>>> HCLS, as we are developing a semantic web use case that features
>>>>> semantic integration of neuroscience microarray data. I don't know
>>>>> whether Helen has already been on this list. If not, may I ask
>>>>> permission from the group to add her to the list. The discussion here
>>>>> may help her to curate some data for testing purposes. I hope this can
>>>>> also help faciliate a 3-way collaboration among NeuroLex/NIF, EBI, and
>>>>> BioRDF.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> -Kei
>>>>>
>>>>> Stephen Larson wrote:
>>>>>
>>>>>
>>>>>
>>>>>           
>>>>>> Here's my analysis of your protocol.  I'll include links to the
>>>>>> classes I think correspond to your brain parts and neurons.  Let me
>>>>>> know what you think.
>>>>>>
>>>>>> Thanks,
>>>>>> --Stephen
>>>>>>
>>>>>> On Thu, Aug 6, 2009 at 12:36 PM, Kei Cheung <kei.cheung@yale.edu
>>>>>> <mailto:kei.cheung@yale.edu>> wrote:
>>>>>>
>>>>>>
>>>>>>  Hi,
>>>>>>
>>>>>>  Do we have the brain parts (and possibly layers and neurons with
>>>>>> the
>>>>>>  brain parts) for annotating the following two example microarray
>>>>>>  experiments?
>>>>>>
>>>>>>  (http://np2.ctrl.ucla.edu/np2/viewProject.do?action=viewProject&projectId=433773 
>>>>>>
>>>>>>  <http://np2.ctrl.ucla.edu/np2/viewProject.do?action=viewProject&projectId=433773 
>>>>>>
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> )
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>  We will perform LCM on 6 brain regions with about 14 biological
>>>>>>  replicates per brain region. The brain regions are as follows:
>>>>>>
>>>>>>
>>>>>>
>>>>>>  1) entorhinal cortex
>>>>>>
>>>>>>
>>>>>> http://neurolex.org/wiki/Category:Entorhinal_cortex
>>>>>>
>>>>>>  2) hippocampus
>>>>>>
>>>>>>
>>>>>> http://neurolex.org/wiki/Category:Hippocampus
>>>>>>
>>>>>>  3) medial temporal gyrus
>>>>>>
>>>>>>
>>>>>> http://neurolex.org/wiki/Category:Middle_temporal_gyrus  (??)
>>>>>>
>>>>>>  4) posterior cingulate
>>>>>>
>>>>>>
>>>>>> http://neurolex.org/wiki/Category:Posterior_cingulate_cortex / 
>>>>>> http://neurolex.org/wiki/Category:Posterior_cingulate_gyrus
>>>>>> (??
>>>>>> -- these look suspiciously similar... perhaps they should be merged?)
>>>>>>
>>>>>>
>>>>>>  5) superior frontal gyrus
>>>>>>
>>>>>>
>>>>>> http://neurolex.org/wiki/Category:Superior_frontal_gyrus
>>>>>>
>>>>>>
>>>>>>  and 6) primary visual cortex.
>>>>>>
>>>>>>
>>>>>> Looking for the right one here.
>>>>>>
>>>>>>
>>>>>>  We
>>>>>>  will collect layer III pyramidal cells
>>>>>>
>>>>>>
>>>>>> When in neocortex:
>>>>>>
>>>>>> http://neurolex.org/wiki/Category:Neocortex_pyramidal_cell_layer_2-3
>>>>>>
>>>>>> When in hippocampus:
>>>>>>
>>>>>> http://neurolex.org/wiki/Category:Hippocampus_(CA)_pyramidal_cell
>>>>>> <http://neurolex.org/wiki/Category:Hippocampus_%28CA%29_pyramidal_cell 
>>>>>>
>>>>>>
>>>>>>
>>>>>>  from the white matter in each
>>>>>>  region, isolate total RNA from LCMed cell lysates, and perform
>>>>>> double
>>>>>>  round amplification of each sample for array analysis.
>>>>>>
>>>>>>  (http://np2.ctrl.ucla.edu/np2/viewProject.do?action=viewProject&projectId=110 
>>>>>>
>>>>>>  <http://np2.ctrl.ucla.edu/np2/viewProject.do?action=viewProject&projectId=110 
>>>>>>
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> )
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>  First use laser capture microdissection to select 1000 neurons
>>>>>> bearing
>>>>>>  neurofibrillary tangles and 1000 normal neurons from the layer 2
>>>>>>  stellate island neurons of the entorhinal cortex of 10 mid-stage
>>>>>> AD
>>>>>>  cases. Second, to isolate the RNA from these captured neurons,
>>>>>> perform
>>>>>>  double round linear amplification and hybridize the labeled cRNA
>>>>>> to
>>>>>>  affymetrix U133A arrays. Third, to use paired, permutational
>>>>>>  t-tests to
>>>>>>  analyze the microarray data to select tangle-specific
>>>>>> differences in
>>>>>>  gene expression. For the purposes of submitting this proposal, a
>>>>>> value
>>>>>>  of 1 ug of RNA was entered due to web site constraints on values
>>>>>>  placed
>>>>>>  in that field. However, all samples are from LCM captured cells
>>>>>>  and the
>>>>>>  actual RNA yield is likely closer to 100 pg.
>>>>>>
>>>>>>  Thanks,
>>>>>>
>>>>>>  -Kei
>>>>>>
>>>>>>  Stephen Larson wrote:
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I wanted to highlight some new features in the NeuroLex that
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>  should
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> make its content even more useful.  We have now made it standard for
>>>>>>> all category pages to display lists of other pages that relate to
>>>>>>> them, even if they have not been explicitly asserted on that page.
>>>>>>>
>>>>>>> This means:
>>>>>>>
>>>>>>> * Brain region partonomy: Brain region category pages that have been
>>>>>>> indicated to be "part of" another brain region, display a "part of"
>>>>>>> hierarchy of its sub parts.
>>>>>>> * Neuron location: Brain region category pages display a list of
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>  those
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> neurons that have indicated they are "located in" that brain region.
>>>>>>> * Brain Region connectivity: Brain region category pages will
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>  display
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> inferred projections on their pages from other pages that take
>>>>>>> advantage of the "AfferentProjections" and "EfferentProjections"
>>>>>>> properties
>>>>>>>
>>>>>>> These lists and hierarchies will all be automatically updated and
>>>>>>> populated when users fill in these properties that relate category
>>>>>>> pages together.
>>>>>>>
>>>>>>> Several good example pages to check out include:
>>>>>>>
>>>>>>> http://www.neurolex.org/wiki/Category:Cerebellum
>>>>>>> http://www.neurolex.org/wiki/Category:Telencephalon
>>>>>>> http://www.neurolex.org/wiki/Category:Hippocampus
>>>>>>>
>>>>>>> We hope this makes NeuroLex a more useful digital common grounds for
>>>>>>> collaboratively assembling knowledge in neuroscience!
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>             
>>>>>           
>>>>         
>>>>         
>>>       
>
>   
Received on Friday, 7 August 2009 13:07:09 UTC

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