- From: William Bug <William.Bug@DrexelMed.edu>
- Date: Thu, 8 Jun 2006 10:24:10 -0400
- To: kc28 <kei.cheung@yale.edu>
- Cc: public-semweb-lifesci@w3.org
Hi Kei,
I agree on all points.
As far as getting all of these busy folks together at one time, you
are certainly correct - that is tough. Having said that, they each
represent a category of neuroinformatics researcher, and there are
others, so we could fall back to other folks. To my mind, these are
some of the folks who'd be the preferred speakers, but there are
equally good researchers in the 2nd and 3rd line positions.
Given the pressing need to handle the rapidly expanding universe of
microarray expression data sets, I'd also like to see someone from
the NIH Neuroscience µArray Consortium you cited - the one Karen
Skinner had pointed you to (http://arrayconsortium.tgen.org/np2/
home.do). Effectively integrating neuro-oriented, µarray data in a
semantically relevant manner with the other modalities of data we
need to handle (e.g., in the BIRN project) is becoming a pressing and
quite difficult issue to address.
Given the topic to be discussed, I would say it would be extremely
important to have someone from NCBO attend - and someone from FuGO,
if possible, though there are several direct FuGO participants on
this list already (the FuGO Coordinating Committee membership list -
http://fugo.sourceforge.net/community/community.php - is probably out-
of-date a bit, as there are several recent members who I don't see
listed, including myself). Perhaps Barry Smith or one of his
colleagues could participate in some way as well, possibly via a
video link.
One quick point re: the Wiki. There is a lot of curiosity brewing
amongst the neuroinformatics community right now. I think there is
an excellent opportunity for this group to lead the way in defining
how Semantic Web technologies are specifically relevant to
neuroinformatics. Having a page that strives to keep track of the
various neuro-oriented Semantic Web projects would really be a big
help in clarifying to the larger community what specific value would
come from understanding more about RDF, OWL, et al.. One issue I've
often confronted is why specifically after we put so much effort into
properly utilizing XML do we now need to go one step further and move
to RDF. This is a rather generic question, and obviously the answer
very much depends on what ends you are trying to achieve, but certain
for true "semantically centric" knowledge representation and mining
projects, the gains realized by using RDF are immense. Having some
clear, cogent examples on a W3C SW HCLSIG-associated web site would
really quaff a pressing thirst for knowledge regarding the relevance
of SW technologies to neuroinformatics at this juncture.
Cheers,
Bill
On Jun 8, 2006, at 9:20 AM, 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.
>>
>
>
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 14:24:32 UTC