Re: BioRDF [Telcon]: slides for the UMLS presentation

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  
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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 
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Received on Thursday, 8 June 2006 13:25:35 UTC