- From: kc28 <kei.cheung@yale.edu>
- Date: Thu, 08 Jun 2006 09:20:49 -0400
- To: William Bug <William.Bug@DrexelMed.edu>
- Cc: public-semweb-lifesci@w3.org
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,
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>>> notify us immediately by returning this message to the sender and
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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)
>
>
> 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
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> of this email communication by others is strictly prohibited. If you
> are not the intended recipient please notify us immediately by
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>
Received on Thursday, 8 June 2006 13:25:35 UTC