Hi John et al.,
I think it's a great idea. Do you have some more information (e.g.,
meeting location and draft meeting agenda) about the Neurocommons
meeting you mentioned which Bill and I (and possibly others) can share
with the neurosceintists we're working (have worked) with to see what
they think?
Best,
-Kei
John Wilbanks wrote:
All,
I've been following the discussion here with interest the last two
weeks - with the Neurocommons project, Science Commons is taking on
both issues of intellectual property (on ontologies and databases) and
the semantic web in neuroscience. We're text mining the open content
and indexing with public ontologies with a focus on autism and
epilepsy; draft RDF release is planned in the november time frame.
For what it's worth...we were planning on holding a Neurocommons
meeting in the late fall / early winter and I'd be happy to expand
that meeting to more of a global "meeting of the minds" between SWeb
and Neuro, if that's of use. Let me know...
jtw
kc28 wrote:
Hi Bill,
Thanks for your passionate response. When I said "outreach", I did
imply to establish a mutually beneficial relationship between the
semantic web and neuroscience communities. I agree with you that such
a relationship would help bring scientific/techological advances to
both communities. I also agree that it's an excellent idea to have a
face-to-face meeting with the neuroscientists you listed. However, it
could be a challenge to get all of them agree to come and show up at
the same meeting. I don't mean we shouldn't try. I think we should
try even if we can only get some but not all of them. Also, I think
we should also invite folks from NCBO and MGED to join if possible.
In addition to the face-to-face meeting, I think we can still try to
invite these neuroscientists (as well as some of the NCBO/MGED folks)
to participate in some of future telconf's to establish an ongoing
interaction. For your suggestions on the BioRDF wiki pages (I think
they are very good suggestions), I suggest that we set it as one of
the agenda items to discuss in our BioRDF telconf call. Other folks
may also have other suggestions.
Cheers,
-Kei
William Bug wrote:
I do run on, sometimes, don't I, Kei?
I emphatically agree with the general tenor of your suggestion.
I would word it a bit differently.
I wouldn't call this outreach so much as going to the "customer"
and asking them to help us - the technology experts - to define
their user requirements. I would word it this way to the
technologists, at least. The Neuroscientists should be pitched
using "civilian" colloquialisms, but the point is I believe the
onus is on those developing and applying the technology to stay in
sync with the needs of the neuroscientists.
I realize many of us on this list are in fact trained biomedical
and/ or computer science researchers. I myself was originally
trained as a molecular biophysicist studying neuromodulation of
presynaptic, Voltage-dependent, Ca++-channels using single-channel
and whole-cell electrophysiological techniques. That places us at
the extremely valuable nexus where we possess specific insight into
the information needs of broader community of neuroscientists we
hope will benefit from the technological resources we develop,
while also possessing the technological insight required to
determine what is practical.
My sense is it's important to develop credibility on both sides of
this equation - the technology developers need to clearly
demonstrate they're sensitive the needs of "bleeding edge"
researchers. They are developing tools to revolutionize a
scientist's ability to perform their research tasks effectively and
efficiently - transform them from 19th century cottage scientists
where all knowledge mining must be done laboriously and with very
limited scope by their lonely brain into 21st century
informaticists where large scale, data/knowledge mining against the
evolving "World Brain" (H.G. Wells term - http://
sherlock.berkeley.edu/wells/world_brain.html) is a routine practice.
The scientists also need to demonstrate they recognize the value
provided by the technologists. This will again derive from clear
demonstrations of the value the technological solutions can provide
to the researcher. This latter issue is often a hard one to get
across, but its lack of such recognition/trust that can lead the
technologists to go at it on their own out of frustration (Kei,
Don, and others who attended the Human Brain Project meeting in
April can attest to the fact that I am just as subject to this
frustration as any other bioinformatics developer - :-) ).
Along these lines, I'd suggest:
1) Presentations by neuroscientists who have done seminal work in
neuroinformatics:
I think Kei's suggestion is an excellent. However, I'd suggest
a F2F meeting, where these folks are invited as speakers. It will
be hard to get the full effect of what they have to say on a phone
or video conference. They are likely to take a talk at a meeting
more seriously and a greater level of commitment is likely to
derive from it.
I would suggest there be a session of neuroinformatics
presentations by neuroscientists, and also a session of semantic
web technology presentations by participants of this group. The
focus should be on neuroinformatics projects using semantic web
technology with one intro talk on semantic web technology applied
to biomedical informatics to provide a context for those
neuroscientists who've not yet got the take home message.
My suggestion for neuroscientists would be - in no particular
order of importance:
1) Gordon Shepherd (SenseLab) - integration of various
modalities of neuro-data with a focus on the olfactory system
2) Doug Bowden (NeuroNames) - unified, mammalian
neuroanatomical lexicon
3) Maryann Martone (CCDB, SMART Atlas, & BIRN) /Mark
Ellisman (BIRN)/ Jeff Grethe (BIRN infrastructure) - broad-field,
neuroimaging- centric neuroinformatics infrastructure
4) Rolf Kütter (CoCoMac) - literature informatics
("bibliomics") system with a focus on neuro-connectivity
5) Rob Williams (GeneNetwork/WebQTL/Mouse Brain Library) -
genetic variability and brain phenotypes from molecules through
anatomy and behavior
6) Peter Hunter (CellML and parametric spatial modeling of
the brain)
6) Dan Gardner (BrainML) - XML schema for neuroscience data
There are other folks, but I believe this core of people cut across
a variety of neuroscientific sub-domains and levels of technical
complexity. I'd also recommend someone from the field of 3D
digital brain atlasing (atlas data set/computer vision
algorithm/atlas tool development), but as I'm in this field myself,
I don't feel it's appropriate for me to suggest which of the
several researchers would be the most appropriate. I would only
say it's important to recognize the distinction between
spatially-based, neuroscience data sets (GENSAT, Allen Brain Atlas,
Desmond Smith's "voxelized" microarray data sets) and the use of
brain atlases to provide a canonical coordinate space and
algorithmic tool set via which one can perform large-scale
integration & atlas mapping of spatially-based, neuroscience data
sets. This task - integration of spatially-mapped neuroscience
data sets - is obviously one for which semantic web technologies
will be a critical catalytic factor.
2) The BioRDF Wiki page:
I'd suggest this focus on semantic web applications in the
neuroscience. There is already a link to a list of projects (e.g.,
SWAN, Semantic Synapse, NeuroCommons). Rather than place
substantive info on these 3 projects 3 clicks away, I'd suggest you
list them right there on main BioRDF Wiki along with a 1 - 2
sentence summary of each project. This will guarantee the widest
possible recognition/ visibility for these efforts.
I'd also suggest that in listing of "other" neuroscience
resources on the web, rather than creating an ad hoc collection of
a few projects (which can effect general credibility - e.g., "Where
are all those neuroscience resources I think are important - why
just BrainML & GENSAT?" - I'd point to the several consortia
and/or registries/"yellow pages" already compiled - e.g., the
Society for Neuroscience's Neuroscience Database Gateway
(http://big.sfn.org/NDG/ site/), David Kennedy's Internet Analysis
Tools Registry (mainly neuroscience tools, though this scope is
expanding - http://
www.cma.mgh.harvard.edu/iatr/display.php?spec=all), fMRI Tools
(http://www.fmritools.org/), The Neuroinformatics Portal Pilot
(http://www.neuroinf.de/), etc.
3) Licensing:
To say one final thing about licensing, I completely agree with Don
that it is a hideous, unworkable mess. Go back to the single
statement in Article 8 of the U.S. Constitution, and you clearly
get the sense of what was originally intended by establishing
copyright and patent law as a legal entities
(http://www.archives.gov/national-
archives-experience/charters/constitution_transcript.html):
"The Congress shall have Power...To promote the Progress of Science
and useful Arts, by securing for limited Times to Authors and
Inventors the exclusive Right to their respective Writings and
Discoveries;"
It was recognized even 200 years ago the creative commons is of
great value to society. For this value to be realized, these
resources must be a part of the commons and available to all -
including latter day inventors, artists, and scientists seeking to
build on what came before. This need, however, must be balanced
again the desire of the artist, scientists, inventor to make a
productive living from the fruits of their labor (otherwise, the
creation stops).
I'd guess most folks on this list would certainly agree with the
need to establish this right. Where the founders went wrong was in
the statement "The Congress shall have Power To...", as this left
the door wide open for Congress to redefine what copyright was all
about. As most of you probably know, the balance began to shift
from the "...Authors and Inventors (and scientists)..." to
publishers (those solely in business to make $$$ off the efforts of
the creative persons) starting in the late 19th Century with the
proliferation of pirated sheet music. This trend worsened through
the last century, but really took a significant, qualitative leap
away from the original intentions as outlined in Article 8 above
with the DMCA. Given how significant a driver IP is for the
engines of the economy (and greed), I'm still uncertain how we can
over turn this trend and get back to the original principles. The
work sponsored by the CreativeCommons - and specifically The
ScienceCommons - will certainly help to get us there**. This is the
case despite the extremely clear detriment the current trend has
toward society as a whole*** and to the communication amongst
scientists in particular.
Though still problematic, I actually endorse the use of licensing
by the NeuroNames folks (as you might have been able to gather
already), as I see their application going right back to that
original statement in the U.S. Constitution. It's one thing to
bulk download sequence records and "cleanse" their semantic content
in order to promote powerful knowledge mining efforts. When it
comes to highly curated, knowledge resources, the onus is on the
user to be careful both to clearly understand the original
intentions and limitations of the resource, as well as to work to
protect the integrity of the resource. It does none of us any good
to create a "better" or more "open" NeuroNames, if that just
becomes another version of NeuroNames. If we are not ALL using the
same NeuroNames (or at least using compatible and consistent
versions), then we defeat the purpose of using NeuroNames for
large-scale data integration and semantic mining.
What is needed is for there to be an established authority to
arbitrate when issues of curation and usage of a knowledge
resources come into conflict. Here again, I'd suggest going to
NCBO for help. Not that they have an infinite supply of resources
and can solve all the problems, but at least they understand this
complex issue from both sides - that of the curation authority and
of the biomedical informatics scientist trying to make productive
use of the resource - and have some resources and authority to
grease the wheels of science in this domain.
Again - just my $0.02. I hope this helps to clarify what I've been
trying to communicate in this thread.
Cheers,
Bill
** I expect it's a bit superfluous to mention here, but I'd suggest
checking out the SC info resources, if you've not already at http://
sciencecommons.org/resources.
***see the excellent article by Richard Nelson posted by John
Wilbanks on the Science Commons weblog a few months back [http://
sciencecommons.org/weblog/archive/2006/02/15/richard-nelson-on-the-
scientific-commons] for an excellent treatment of how this directly
impedes the pursuit and accumulation of scientific knowledge.
On Jun 6, 2006, at 7:42 PM, kc28 wrote:
Hi Bill,
You really can write faster than I can read :-). Actually, we
have discussed in a previous telconf about how to outreach to
the neuroscience community. I think this represents a good
opportunity to try to get people like Doug Bowden involved, as we
are interested in converting Neuronames into RDF/OWL. I wonder if
it's possible to invite neuroscientists like Doug Bowden and
Gordon Shepherd (and possibly more) to talk about their work in
our future BioRDF/Ontology telconf. This will foster more
interaction between the semantic web community and neuroscience
community. I wonder how this sounds to other semantic web folks.
Cheers,
-Kei
William Bug wrote:
Dear Matthias,
I would strongly recommend you contact Doug Bowden and colleagues
at NeuroNames before you undertake this task - or at least take
a look at the NeuroNames specifics I list in my previous
email. I'd be glad to answer any questions you may have about
statements I made. Doug and his collaborators are extremely
collegial and make a very sincere effort to work with those
interested in making effective - or novel - use of NN.
The other person you should contact is Daniel Rubin at NCBO, who,
for all I know, is lurking on this thread. Others in the thread
appeared to be addressing Daniel. This is a topic actively
under investigation both by NCBO and by the BIRN.
As I mentioned in my post to this thread, Doug & colleagues have
been working for the last year with Jack Park of SRI to express
NN in XTM format. A lot of effort needs to go into vetting this
"remapping" to make certain none of the assertions in the
hierarchy - explicit or implicit - are invalidated - as well as
ensuring no new assertions are unwittingly introduced. You may
want to work from this version of NN to create an RDF/OWL
version. As I mentioned in the previous post, there has been
some substantive effort to examine the differences and
similarities between XTM & RDF - and there may even be
translators or XSL instances that can get you most of the way.
Doug also distributes the entirety of NN on CD with all of the
latest work they've done in the past year to incorporate rat &
mouse neuroanatomical terminologies - an added dimension
absolutely critical to those of us interested in collating
microarray, in situ & IHC expression studies in mouse brain with
neuroimaging data sets and 3D digital brain atlases.
There is definitely a need for an open source, RDF/OWL version
of NeuroNames (and the neuroanatomical portion of RadLex for
that matter - http://www.rsna.org/RadLex/ - if you are
interested in human, radiological imaging of the brain).
I believe we must do our best to work with the
curators/developers on these various knowledge resource
projects, given the biological complexity embedded in these
resources.
As far as the licensing goes, Doug realizes this is a thorny
issue. The initial license was merely put in place to avoid
others downloading this highly curated knowledge resource,
modifying it, then repackaging it as "NeuroNames." As I
mentioned, this was not a paranoid fear. The license was
imposed in response to someone actually having done this with
NN. Knowledge resources like this - even when they are just
terminologies - require careful curation, and uncontrolled
dissemination and modification can ultimately degrade the
usefulness of the resource.
Of course, closed, proprietary licensing can also degrade its
usefulness, so there is a delicate balance that must be struck.
This is an issue I believe NCBO can help us all to resolve.
They won't have all the answers, but may be able to sponsor a
means to derive an effective solution to this problem.
My recommendation is a statement be sent by the W3CSW HCLSIG -
maybe the BioRDF & BIOONT groups collectively - informing Doug
of the need as they see it. He will not be surprised by the
nature of your request, but will be very surprised and pleased
to see this need emerging from the semantic web community. I
don't believe he reads this list. I know he will be happy to
work with participants on the W3CSW HCLSIG to get us what we
have all identified as essential - an open source, unified
neuroanatomical terminological (and in association with FMA - as
Neuro-FMA - ontological) resource all formal annotation efforts
can make shared and productive use of.
Just my $0.02 on the topic.
Cheers,
Bill
On Jun 6, 2006, at 3:38 PM, Matthias Samwald wrote:
Hi Kei,
I am under the impression that the neuronames ontology available
on their website (as an Excel file...) is different from the
version that is licensed as part of the UMLS. I guess the
version that is online is a newer version of the one
incorporated in UMLS. However, this might be seen as a
derivative work, so it might still be restricted. In that case,
it would seem like people of the neuronames group are violating
the licence restrictions themselves (by making it available on
the internet). I will write them and ask about that.
kind regards,
Matthias
Hi Matthias,
Thanks for doing that, but do we still have the licensing issue as
stated by Olivier?
Cheers,
-Kei
Matthias Samwald wrote:
I will convert the neuronames - ontology to SKOS (an OWL ontology
used for the representation of taxonomies / theasauri). It will
be added to the extension of the bio-zen ontologies framework
[1]. I will keep you updated.
kind regards,
Matthias Samwald
[1] http://neuroscientific.net/index.php?id=download
On Mon, 05 Jun 2006 21:17:55 -0400, kc28 wrote:
For more up-to-date information about neuronames and related
tools, please visit: http://braininfo.rprc.washington.edu/.
While building our own open neural anatomy is one option,
getting the neuroscientist (e.g., braininfo people) involved if
possible may be another option (outreach to the neuroscience
community?).
Bill Bug
Senior Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
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Bill Bug
Senior Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
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This email and any accompany attachments are confidential. This
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