OK. I will be traveling most of the rest of the month for
non-Neurocommons related work. But I'll return to this end of June and
start gathering some forces. I'll also get in touch with Karen Skinner.
I'd been thinking about early December as a time frame and Boston as a
location. I'll need to shift the planning up a notch, since if we're
going to have a bigger group I can't host it at MIT as planned.
The meeting will be free as in beer and free as in speech but I won't be
able to cover travel costs - just the hotel and the lunches. If we're
going to get a group like this together, I'd also like to have some
hacking. The Neurocommons RDF draft release will be out before the
meeting and I'd like to have at least a piece of the time be focused
around getting the users and the coders wired together on some problems,
use cases, and more.
jtw
William Bug wrote:
Ditto, John!
I'd also suggest including NCBO folks on this (specifically Daniel
Rubin and Barry Smith), as I see an obvious convergence of needs and
focus here - despite the fact some see the top-down ontological
approach and the bottom-up SW approach as being difficult to reconcile.
Cheers,
Bill
On Jun 8, 2006, at 10:24 AM, kei cheung wrote:
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)
Please Note: I now have a new email - [EMAIL PROTECTED]
This email and any accompany attachments are confidential. This
information is intended solely for the use of the individual to
whom it is addressed. Any review, disclosure, copying,
distribution, or use of this email communication by others is
strictly prohibited. If you are not the intended recipient
please notify us immediately by returning this message to the
sender and delete all copies. Thank you for your cooperation.
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)
Please Note: I now have a new email - [EMAIL PROTECTED]
This email and any accompany attachments are confidential. This
information is intended solely for the use of the individual to
whom it is addressed. Any review, disclosure, copying,
distribution, or use of this email communication by others is
strictly prohibited. If you are not the intended recipient please
notify us immediately by returning this message to the sender and
delete all copies. Thank you for your cooperation.
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)
Please Note: I now have a new email - [EMAIL PROTECTED]
This email and any accompany attachments are confidential. This
information is intended solely for the use of the individual to whom it
is addressed. Any review, disclosure, copying, distribution, or use of
this email communication by others is strictly prohibited. If you are
not the intended recipient please notify us immediately by returning
this message to the sender and delete all copies. Thank you for your
cooperation.
--
..................................................................
John Wilbanks
Executive Director
Science Commons
http://sciencecommons.org
[EMAIL PROTECTED]
..................................................................
