More about brain ontologies: (01)
[Pat Hayes responded to PDM] (02)
>>(ontology for the brain link?) (03)
> [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. (04)
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. (05)
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. (06)
PatC (07)
--------------- tear line
-------------------------------------------------- (08)
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. (09)
"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. (010)
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." (011)
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.)" (012)
They say that they want to be consistent with the OBO foundry of medical
ontologies ( http://www.obofoundry.org/ ) (013)
For some brain images they find interesting: (Mouse BIRN)
http://www.nbirn.net/research/function/index.shtm (014)
PatC (015)
Patrick Cassidy
MICRA, Inc.
908-561-3416
cell: 908-565-4053
cassidy@xxxxxxxxx (016)
> -----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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> >>
> >>
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> >Paola Di Maio
> >School of IT
> >www.mfu.ac.th
> >*********************************************
>
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