- From: John Wilbanks <wilbanks@creativecommons.org>
- Date: Thu, 08 Jun 2006 09:31:52 -0400
- To: kc28 <kei.cheung@yale.edu>
- CC: William Bug <William.Bug@DrexelMed.edu>, public-semweb-lifesci@w3.org
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 - William.Bug@DrexelMed.edu
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 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 - William.Bug@DrexelMed.edu
>>
>>
>>
>>
>>
>>
>>
>> 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
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>>
>
>
>
--
..................................................................
John Wilbanks
Executive Director
Science Commons
http://sciencecommons.org
wilbanks@creativecommons.org
..................................................................
Received on Thursday, 8 June 2006 13:32:10 UTC