Thanks PatC
We should ask the folks to start making it available online
then PatH could use his cmap tools to create the visualisations
wouldnt that be neat? (01)
also, I cc the person ontology team, re-using existing ontologies and
starting from the
top (the head) could be good head start form that too..
cheers
PDM (02)
On Dec 19, 2007 12:56 AM, Patrick Cassidy <pat@xxxxxxxxx> wrote:
> More about brain ontologies:
>
> [Pat Hayes responded to PDM]
>
> >>(ontology for the brain link?)
>
> > [PH] link? An ontology for all of brain science would be huge. I would
> have no idea how to even start such a giant project.
>
> There has been a start - just a start, in the BIRN collaborative effort.
> They are making an attempt to (among other things) represent neural
> structure and processes. It's still a young project, and the ontology part
> of BIRNlex (to represent metadata about images of brains) is not yet well
> developed, but when I saw it a year ago it looked like a competent effort.
>
> The rest of this note is detail only for those really wanting to know what
> BIRN is. I can't find the actual ontology on-line, but there is a pointer
> to contact information below.
>
> PatC
>
> --------------- tear line
> --------------------------------------------------
>
> Their site: http://www.nbirn.net/research/index.shtm
> A few introductory paragraphs:
> "The Biomedical Informatics Research Network (BIRN) is a geographically
> distributed virtual community of shared resources offering tremendous
> potential to advance the diagnosis and treatment of disease.
>
> "BIRN enhances the scientific discoveries of biomedical scientists and
> clinical researchers across research disciplines.
> * hosts a collaborative environment rich with tools that permit uniform
> access to hundreds of researchers, enabling cooperation on
> multi-institutional investigations.
> * synchronizes developments in wide area networking, multiple data
> sources, and distributed computing.
> * designs, tests, and releases new integrative software tools that
> enable researchers to pose questions and share knowledge across multiple
> animal models (mouse, human, and non-human primate).
> * receives funding from the National Institutes of Health's National
> Center for Research Resources (NCRR), established in 2001.
>
> Their ontologies: ( http://www.nbirn.net/research/ontology/index.shtm )
> . . . include only one "ontology" (NeuroNames) pertaining to neural
> structure and processes, but it is, as they admit, not an ontology:
> "NeuroNames, the nomenclature component of the software called BrainInfo, is
> not really an ontology. It is a collection of about 15000 terms, 2000 of
> which are acronyms. It allows a complete description of the primate brain in
> terms of about 900 structures (approximately 580 primary volumetric
> structures, 130 superstructures and 180 superficial structures). These terms
> form a hierarchy defined by a "volumetric substructure" relationship."
>
> However, the BIRNlex ontology is more like a real ontology (can't find a
> download location, but contact info is at:
> The BIRNlex (
> http://neurogateway.org/catalog/query.do?expID=BIRN-nif-6434&format=html&gen
> ericXSL=true )
> " BIRN's unique lexicon (BIRNLex) is a controlled vocabulary designed
> for annotating BIRN data sources. These sources may include complex image
> databases, such as data from structural and functional magnetic resonance
> imaging (MRI) on human subjects involved in studies on Alzheimer?s disease
> or schizophrenia. The BIRNLex is a specialized vocabulary utilized by BIRN
> scientists in the context of their research, including common terms for
> neuroanatomy, molecular species, subject information, behavioral and
> cognitive processes, experimental practice and design, and the associated
> elements of primary data provenance required for large-scale data
> integration across disparate experimental studies.)"
>
> They say that they want to be consistent with the OBO foundry of medical
> ontologies ( http://www.obofoundry.org/ )
>
> For some brain images they find interesting: (Mouse BIRN)
> http://www.nbirn.net/research/function/index.shtm
>
> PatC
>
> Patrick Cassidy
> MICRA, Inc.
> 908-561-3416
> cell: 908-565-4053
> cassidy@xxxxxxxxx
>
> > -----Original Message-----
> > From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx [mailto:ontolog-forum-
> > bounces@xxxxxxxxxxxxxxxx] On Behalf Of Pat Hayes
> > Sent: Tuesday, December 18, 2007 4:07 AM
> > To: paola.dimaio@xxxxxxxxx
> > Cc: [ontolog-forum]
> > Subject: Re: [ontolog-forum] brainwaves (WAS: to concept or not to
> > concept, is this a question?)
> >
>
> > >Pat
> > >
> > >>>>> Wait: neural paths aren't waves.
> > >
> > >right observation
> > >
> > >
> > >( from relative ignorance - this is not my direct field so I don't
> > >have the literature at hand darn)
> > >and following up on an earlier post which said there are no brainwaves
> >
> > The waves are revealed in EEGs, which are instruments which measure
> > electrical potentials on the surface of the scalp. I believe it is
> > known that these are in fact induced by a global preponderance of
> > neural activity in the cortex, but the EEG is a very coarse view of
> > the actual activity of the brain itself. (for one thing, there is a
> > bony skull between the brain and the skin.) More recent techniques,
> > notably MRI scanners, can 'see' regions of increased neural activity
> > in 3-D inside the actual brain, but what they detect directly is the
> > increased oxygen use from the blood supply to the brain, which is (a)
> > fairly coarse: it only gets you to the nearest 1000 neurons or so;
> > and (b) somewhat delayed, being about a second after the actual
> > neural event. Nevertheless, it shows very localized patterns of
> > neural activity in many circumstances. With nonhuman subjects (cats,
> > monkeys, mice), direct readings can be taken from fine needle
> > electrodes inserted into individual neurones, and most of the
> > detailed knowledge of functional brain anatomy has been discovered
> > this way, eg the visual cortex's arrangement into columns. As this
> > technique usually (though not always) involves killing the animal,
> > its not encouraged on human subjects.
> >
> > >
> > >I guess it depends on 'classification'
> > >
> > >(ontology for the brain link?)
> >
> > link? An ontology for all of brain science would be huge. I would
> > have no idea how to even start such a giant project.
> >
> > >
> > >brain activity
> > >frequency
> > >signal
> > >wave
> > >neural path
> > >other motion that can be detected?
> > >
> > >define and establish the relationships between them
> > >then we talk again
> > >
> > >
> > >1) according to commonly cited classification (I studied psychology
> > >one year), there are brainwaves and they have also names
> > >(alpha, beta etc)
> > >http://www.web-us.com/brainwavesfunction.htm
> >
> > Right, those are the EEG-detected waves.
> >
> > >They have been studied to some extent, but the subject may be more
> > >interdisciplinary than research is prepared to stretch to
> >
> > There has been a great deal of work on them and they are very well
> > understood. They are used in clinical diagnostic medicine, for
> > example. In fact, the local university here has one of the leading
> > labs in this area, which involves using very special equipment,
> > highly electrically screened to pick up very small changes in the
> > potentials. One needs a special building to do it in.
> >
> > >(personal
> > >view)
> > >
> > >2) Again, I am working on something else now but
> > >here is the reasoning
> > >
> > >>get definition and measurement
> >
> > I was presuming that you were referring to the 'paths' formed by the
> > synaptic connections between neurones. This is a well-defined notion.
> > Im not sure what you mean by 'measurement' though.
> >
> > >for 'neural path' (my springerlink is
> > >not responding)
> > >>>compare with definition and measurement for for brainwave as above
> > >>>> establish correlation, if any
> >
> > There isn't any. For one thing, the whole cortex seems to be quite
> > closely connected in the synaptic-path sense: every neuron (there are
> > about 14 trillion of them, far more than the number of people on
> > earth) is only about 7 synaptic links from every other neuron, on
> > average. But the EEG 'waves' pass through this connected network in
> > fairly regular rhythms, which are much slower than single neuron
> > firings. Heres an analogy: a huge crowd or people all talking to one
> > another and moving about. For some reason, when you watch this crowd
> > from high above, you can see that some of them are pointing in the
> > same direction, and at any given moment there is a preponderance of
> > people all looking north, say, forming a kind of vague 'stripe' in
> > the crowd, and that this 'stripe' (which you will call a
> > direction-wave) moves through the crowd slowly and regularly. At one
> > time, all the people *there* are looking north, then a bit later all
> > the people *there* (slightly to the south of the first place) are
> > looking north, and so on. The people don't move south, but the
> > preponderance of north-lookers "moves" in a southerly direction, like
> > a wave passing through the ocean. You can time it, in fact, and draw
> > a graph of it, and it seems to have a definite 'beat', with a
> > definite frequency, which is much slower than the rate at which the
> > people themselves move and talk. Nobody really knows why this
> > happens, but it often does. EEG waves are like that.
> >
> > >My entire speculative and relative ignorant guess is that the wave is
> > >a spatial representation of
> > >some electrical signal
> >
> > More like an aggregate of a very, very large number of signals, which
> > are in fact electrochemical rather than electrical. (Neural signals
> > operate by a 'wave' of sodium and potassium ion transfer through the
> > cell membrane; synaptic connections are done by the release of
> > chemicals called neurotransmitters, of which there are a large
> > number. Antidepressant drugs often work by stimulating the creation
> > of more neurotransmitter.) The electrical part of this is very weak
> > electricity, nothing like an electrical machine like a computer.
> > There is no way a brain could generate enough of an electrical field
> > to be picked up at a distance, in case you were wondering about that.
> >
> > Nobody really knows what the alpha and beta EEG rhythms are for.
> > There are several ideas about it which sound plausible, but nobody
> > has any way to test them directly.
> >
> > Pat
> >
> > >
> > >correct me please
> > >pdm
> > >
> > >
> > >On Dec 18, 2007 2:28 PM, Pat Hayes <phayes@xxxxxxx> wrote:
> > >> >On Dec 18, 2007 7:57 AM, Pat Hayes <phayes@xxxxxxx> wrote:
> > >> >
> > >> >> . Even if one were given a complete
> > >> >> (dead) mammalian brain, there is no conceivable
> > >> >> way to reconstruct all the neural connections in
> > >> >> it, since the total cross-section of a neuron's
> > >> >> end branchings greatly exceeds that of its axon,
> > >> >> and these neurons are tightly packed in the
> > >> >> cortex. Any way to 'take it apart' to find all
> > >> >> the neurons, therefore, would of necessity
> > >> >> involve breaking the connections which hold them
> > >> >> together. Put another way: its impossible to
> > >> >> assemble (or disassemble) a brain; it has to be
> > >> >> grown.
> > >> >
> > >> >This is precisely why I think the brain should be studied as a
> > whole, and
> > >> >not in its puree or minced form.
> > >>
> > >> Well, everyone agrees with that, of course. The
> > >> problem is knowing how to start describing a
> > >> whole brain. BTW, it is definitely known that
> > >> different parts (areas) of the brain perform
> > >> distinct functions, even though they mostly look
> > >> similar under a microscope.
> > >>
> > >> > Thats the only way the neural paths (folk. 'brainwave') can be
> > observed,
> > >>
> > >> Wait: neural paths aren't waves. Waves are
> > >> rhythmic patterns of activity across the whole
> > >> brain, like movements in a flock of birds. These
> > >> are only a tiny fraction of the total brain
> > >> activity, though, most of which seems to not be
> > >> 'waves' at all, more like flashes or bursts.
> > >>
> > >> >
> > >> >I hate to think like Frankenstein , but I bet you can induce some
> > >> >level of passive activity in a coma brain by passing some tiny
> > >> >frequencies.
> > >>
> > >> You can stimulate neurons in an awake brain by
> > >> small electrical impulses along a needle. The
> > >> person in the brain experiences some very odd
> > >> stuff, depending on where you do this to.
> > >>
> > >> > (not ac/dc I guess)
> > >> >I ll have to remember to do that experiment next time I come
> > across a coma
> > >>
> > >> Well, speaking as an ex-epileptic, I'd rather you didn't.
> > >>
> > >> Pat :-)
> > >>
> > >> >
> > >> ><grin>
> > >> >
> > >> >PDM
> > >> >
> > >> >>
> > >> >>
> > >> >
> > >> >
> > >> >
> > >> >--
> > >> >Paola Di Maio
> > >> >School of IT
> > >> >www.mfu.ac.th
> > >> >*********************************************
> > >> >
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> > >--
> > >Paola Di Maio
> > >School of IT
> > >www.mfu.ac.th
> > >*********************************************
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School of IT
www.mfu.ac.th
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