- From: kei cheung <kei.cheung@yale.edu>
- Date: Thu, 08 Jun 2006 10:24:14 -0400
- To: wilbanks@creativecommons.org
- Cc: William Bug <William.Bug@DrexelMed.edu>, public-semweb-lifesci@w3.org
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 - 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 for your cooperation.
>>>
>>
>>
>>
>
Received on Thursday, 8 June 2006 14:24:34 UTC