- From: William Bug <William.Bug@DrexelMed.edu>
- Date: Thu, 8 Jun 2006 00:37:19 -0400
- To: Jack Park <jack.park@sri.com>
- Cc: public-semweb-lifesci@w3.org, Peter Karp <pkarp@AI.SRI.COM>
Many thanks for weighing in directly on this discussion, Jack. I should have cc'd you myself on this. Clearly the presentation you sight discussion the following issue is one of great relevance to biomedical semantic web projects: "Where ontological entities carry information resources that speak to the same subject, then those entities are merged into a single subject map entity -- a subject proxy -- regardless of conflicts between messages conveyed." Such a capability will be critical to merging the top-down (ontological) and bottom-up (SW) approaches to KR. Terminologies - and TMRM - clearly play a critical role in the intervening layers uniting these approaches. Cheers, Bill On Jun 7, 2006, at 1:21 PM, Jack Park wrote: > > Brief comment regarding the topic mapping work Bill mentions here. > > Doug Bowden recently participated in a workshop on "Ontology > Federation" here at SRI. We had several speakers from both the > topic mapping world, and bioinformatics: Douglas Bowden and Peter > Karp, and Steve Newcomb, Patrick Durusau, and myself. Vinay > Chaudhri opened the workshop and participated. Richard Fikes spoke > from the perspective of the KR community. KR lies, of course, at > the roots of the work products we all create. > > We are moving away from the XTM topic mapping specification, and > into the TMRM [1] topic maps reference model, the product of which > we now call "subject maps" to distinguish topic maps from a > slightly different paradigm. Subject maps are no longer constrained > by a preselected ontology (XTM) and can be implemented using key/ > value properties of the author's choice. This permits authors to > create subject maps that can mimic any frame-like language chosen, > including, I suppose, OWL. > > There exists a necessary and important tension between the use > cases of traditional KR and those for which the topic mapping > paradigm has been created and shown useful. When Bill mentions > "more semantic web compliant", I would ask questions derived from > two important use cases. The two use cases do not circumscribe the > entire field of KR, but they serve as place holders to delimit a > useful discussion between ontologists and subject mappers. I will > argue that both ontologies and subject maps are valuable, and they > can serve users together. The two use cases about which I speak are: > 1- accurately answering questions according to some authority > 2- understanding some universe of discourse, even where > conflicting world views exist > > Use of authoritative ontologies is clearly the domain of question > answering. Understanding some universe of discourse is also rightly > the domain of ontologies, but here, subject maps offer the > opportunity to "federate" disparate world views into a unified > framework organized around subjects. Where ontological entities > carry information resources that speak to the same subject, then > those entities are merged into a single subject map entity -- a > subject proxy -- regardless of conflicts between messages conveyed. > There are benefits to be derived from such merging operations. > Patrick Durusau and I spoke to this topic in a teleconference to > the Ontolog community [2], and slides and an mp3 of the talk are > available. There will be other papers released soon on these > opportunities. > > It was in the spirit of this federation opportunity that Doug > Bowden and I first spoke. To be "semantic web compliant", it is > always possible for our subject map portal to carry plenty of RDF > metadata. It remains to be answered whether the goal of such > metadata is to accurately answer specific questions, or to just > advertise the presence of world views. > > Bioinformatics, in all of its many manifestations, I strongly > believe, will benefit from collaborations between ontologists and > subject mappers. > > Jack > [1] http://www.isotopicmaps.org/tmrm/ > [2] http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_04_27 > > William Bug wrote: >> >> Hi All, >> >> Sorry - I'd thought I'd already subscribed to this list, but >> apparently not - until now. >> >> The need for a mereotopologically-sound, neuroanatomical ontology >> is quite pressing across the community of neuroscientists involved >> in neuroinformatics projects most of which include a neuroimaging >> component. Generally there is only one thing neuroscientists are >> interested in when analyzing images at whatever resolution from >> the macromolecular (EM) on up to the macroscopic - i.e., >> identifying biologically relevant shapes. In order for these >> shapes to have any meaning in a context where one attempts to pool >> data and perform relevant data reduction operations, the shapes >> must exist within a shared coordinate space of some sort. For >> instance, if two separate labs are examining the change in the >> size of the Substantia Nigra during the course of Parkinsonian >> neurodegeneration, in order for them to compare their >> observations, they require several data integration/semantic >> frameworks: >> - a shared neuroanatomical terminology >> - a shared coordinate space (to place the shapes from their >> images in a comparable coordinate framework) >> - a shared, well-founded anatomical ontology which >> encapsulates mereotopological knowledge about shapes in - at least >> - 3D space. >> Other knowledge resources can be helpful in supplementing this >> array of tools, but, generally, these are the absolute minimum. >> >> [NOTE: the Wikipedia has a moderately clear definition of >> mereotopology (http://en.wikipedia.org/wiki/Mereotopology). >> Basically, it combines a formal, ontological theory of shapes and >> boundaries (mereology) with the mathematics of topology with the >> goal of providing a computational formalism to support applying >> logical operations to objects in space. As has been pointed out >> by others, a great deal of the work in this field of applied >> biomedical mereotopology derives from related work in the GIS >> field. Use of mereotopology by geographers has been going on for >> quite some time and is much more advanced. Work from GIS can be >> adapted for use in the biomedical domain, but it must be done with >> great care, as many of the assumptions behind the way researchers >> represent space and manner of information being represented can >> differ significantly across these disciplines.] >> >> The same is true as you scale this problem up to field-wide >> projects such as BIRN or The NeuroCommons. >> >> As several have mentioned in this thread, there are already >> existing resources that can begin to fill this need. >> >> 1) NeuroNames >> Kei, Olivier, Peter Mork, and others have already given sufficient >> references on NeuroNames in this thread, so that others can dig in >> deeper to the specifics if they like. >> >> Having worked with Doug Bowden, Mark Dubach, and their colleagues >> over the last year or so in an advisory capacity on the specific >> issue of use of NeuroNames for semantically-based, neuroanatomical >> data set integration, I can add a few important qualifying points: >> a) Doug et al. have been working on the extremely difficult >> task of unifying neuroanatomical terminologies across mammalian >> species for 20 years now. Embedded in Neuronames & Braininfo, >> there is a wealth of hard won empirical knowledge related to how >> one achieves this end. I think it would be ill-advised to try to >> duplicate their effort, as the myriad scientific problems related >> to this effort would surely present themselves again and only need >> to be worked out once one. >> b) Doug et al. are extremely collegial and quite receptive to >> feedback and collaboration - within the bounds of their limited >> resources. >> c) NeuroNames is a terminological resource - not a well- >> founded, spatial ontology of brain anatomy capable of supporting >> mereotopological reasoning. As with most research-based >> terminologies, there are many semantically-based relations >> embedded in the NeuroNames graphs, but as the primary goal of NN >> is to disambiguate and integrate across the neuroanatomical >> lexicon, the embedded semantic information can often lead to a >> logical dead end. For instance, many neuroanatomical terms >> critical to specifying location in the rodent brain have been >> placed in the NN category "ancillary terms," as they don't fit >> into the core hierarchy in an unambiguous way. This can make use >> of NN for annotating mouse brain gene & protein expression >> patterns (e.g., GENSAT, the Allen Brain Atlas, various BIRN >> projects) extremely problematic. >> d) The NN primary structures (http:// >> braininfo.rprc.washington.edu/indexabout.html) provide the closest >> thing to an ontology in NN. As Peter Mork pointed out, there has >> been an effort in the past to unite this core NN hierarchy with >> the FMA, which does provide a mereotopologically sound framework >> for anatomy. Barry Smith (formal ontologist who has worked for >> over a decade on problems in biomedical ontology - most >> especially, though hardly exclusively, in the area of >> mereotopological reasoning) and his colleagues have worked closely >> with the Cornelius Rosse and his colleagues at the FMA project to >> create in association with the work started in the FMA a >> foundational ontology for biomedicine (the Ontology of Biological >> Reality) that is becoming increasingly important to all of the >> ontologies being monitored by NCBO and incorporated into the OBO >> site and the emerging OBO Foundary (http://obofoundry.org/). >> e) Doug and his colleagues have worked closely with Jack Park >> (a consulting scientist to SRI's AI Center - http:// >> www.ai.sri.com/) to represent NN as a TopicMap (XTM). As many on >> this list may know, there has been a moderate amount of effort to >> integrate and/or reconcile XTM with RDF here at the W3C (search on >> "TopicMaps" at the main RDF page - http://www.w3.org/RDF/). I'm >> not certain how this effort will ultimately make NN more "semantic >> web" compliant, but the bottom line is a great deal of effort has >> already been expended to express NN in a semantically well- >> grounded formalism. >> f) Though - as Don points out - neuroanatomical >> representations are likely to significantly evolve over the coming >> decades, as the number of large scale gene & protein expression >> characterization studies focussed on the brain continue to >> accumulate. Having said that, the "conventional" view of >> neuroanatomy will likely remain relevant for a long while to come, >> not only because it has been used to characterize findings in the >> literature for the last 125+ years, but also because it did derive >> from a wealth of empirical observation which is likely to remain >> valid in many domains of neuroanatomical study. I would also >> modify Don's well informed comment regarding the derivation of >> "conventional" views of neuroanatomy. To a large extent they are >> related to functional studies of the brain - as well as lesion >> based studies of functional deficits dating back to the 19th >> century (think "Broca's Area"), but they are also very much based >> on a study of the morphology of the brain - both the external >> surface morphology (sulci, gyri, and lobes), as well as >> histological examination of internal structures. Many of these >> studies of structure in space are likely to stay with us for some >> time to come (and are well-founded in reality), though as Tim >> Clark & Don have pointed out in this thread, nomenclature is still >> a very significant problem even in this very "old" field. >> g) licensing of NN - Doug et al. formerly had a completely >> open policy to distributing NN. The only a reason a license was >> instituted was at some point about 5 years back another group >> sucked down the entirety of NN, reworked a lot of what was there - >> probably with very practical goals directed toward making NN more >> "correct" and effective in their problem domain - then >> "republished" their product as "NeuroNames". This lead to a great >> deal of confusion. The fact they chose to do this on sly also >> meant the work they did was not necessarily compatible with the >> work done by Doug et al.. In order to avoid this happening again, >> it was decided a license would be established to discourage this >> sort of behavior. As anyone who has developed a terminology and/ >> or ontology, it is absolutely essential there remain a single >> curating authority, if the value of the resource is to remain in >> tact. The "vetting" performed by the central authority - as is >> extensively done by the curators of the Gene Ontology, for >> instance - is absolutely essential to the guaranteeing the >> integrity of the knowledge resource. This is not a "closed" or >> proprietary process, just a highly controlled one. Unfortunately, >> Doug Bowden's resources are MUCH MUCH smaller than those available >> to the curators/developers of GO, so the NN curation effort >> necessarily moves at a slower pace. >> >> 2) Working with the Neuroscience community >> As Kei, Don, and others have stated, it would be unwise to proceed >> in creating an "open source" neuroanatomical ontology without >> interacting with the researchers who've already put a lot of >> effort into this problem over the past decade or so. With this in >> mind, I have several suggestions: >> a) The 5 ways of knowing neuroanatomy: >> This is a pitch I've been making which I think helps to >> sum up the current ways various sub-fields have attempted to >> identify/label/collate brain morphology >> i) Terminlogies - e.g., NN, BrainLex >> ii) Ontologies - e.g., Neuro-FMA (the project Peter Mork >> referred to) >> iii) Literature Informatics (CocoMac, BrainMap, >> NeuroScholar, BAMS, ArrowSmith, etc.). >> These are very mature projects. Some include their >> own mereotopological reasoning systems (e.g., CocoMac and >> BrainMap) in order to be able to pool and compare the relatedness >> of structures and connectivity across different studies in the >> literature. The goal in this category is to perform large-scale >> semantic mining of the literature to confirm/refute current >> knowledge and uncover new correlations - very much along the lines >> of what The NeuroCommons Project expects to achieve via use of >> semantic web technologies. Some researchers in this category are >> actually participating in The NeuroCommons Project (i.e., Gully >> Burns, who developed NeuroScholar). >> iv) voxel/pixel analysis: >> This approach applies computer vision algorithms to >> automatically - or semi-automatically - identify 2D & 3D shapes in >> digital anatomical images. This field is also extremely mature, >> though there are many significant caveats to exactly how much of >> this work can be effectively automated. >> v) parameterized models: >> Often these are derived from - or used to drive - the >> voxel/pixel based analysis described in 'iv' - though the spatial >> modeling is definitely a distinct approach from the pure voxel/ >> pixel approach. >> >> None of studies you'd fit into these categories exclusively focus >> on their technique/tool alone without some aspect of the other >> "ways of knowing neuroanatomy" playing a role in what they do. >> However, it is clear much fundamental work in this area primarily >> focuses on one technique over the others. >> >> Having said that, when the neuroscience community makes use of >> this work to examine a specific biological problem, they will >> often draw significant tools and resources from more than one of >> these domains. >> >> b) NCBO/NCOR sponsored meeting focused on mereotopology in >> neuroanatomy: >> Barry Smith is working to bring together researchers >> working in the 5 domains described above. There is a very >> pressing need in large-scale, field-wide neuroinformatics projects >> such as what is being done in the BIRN project to have these 5 >> domains converge and work more cooperatively. Right now, a lot of >> manual effort has to be put out to bring them together. This is >> something BIRN has been pursuing. In the last 6 months, we have >> received a great deal of support and guidance on this effort from >> NCBO. Daniel Rubin interacts directly with the BIRN Ontology Task >> Force, and the work Barry Smith has been doing with FMA, OBO, >> FuGO, and PATO have very much begun to create a much more well- >> founded and computable path toward performing large-scale >> annotation of neuroimaging data. >> This meeting is on the NCBO/NCOR slate for 2007, but in >> the interim I hope to see more effort invested in the coming year >> across the 5 communities listed above toward the goal of >> integrating across these "ways of knowing" now that the need has >> been recognized. >> 3) Microarrays: >> Just as Don, Kei, Alan R., and others have pointed out, high- >> throughput assays - microarrays, BAC-based IHC, in situ studies >> using the Gene Paint technology employed by the Allen Institute of >> Brain Science to construct the Allen Brain Atlas of gene >> expression in the brain - are going to transform our understanding >> of neuroanatomy over the coming decades. This is just a given. >> There is a pressing need to derive a means to integrate spatially- >> mapped studies of gene & protein expression into a neuroimaging >> setting. The spatial resolution may be very coarse - e.g., "whole >> brain" - but they still provide sufficient spatial information to >> be usable in the context of a neuroanatomical coordinate system. >> We are working in the BIRN project to create a means for >> researchers to integrate these distinct approaches to studying the >> brain. As Alan R. pointed out, FuGO is working to put description >> of microarray experiments on a solid, formal footing, and I would >> expect one aspect of that will be to represent microarray data in >> RDF/OWL. This is not a trivial problem, given as much of the >> available data is merely MIAME-compliant - MIAME not even being a >> data format, but just a collection of minimal data requirements. >> One need only look at the great complexity of the data submission >> process at the NCBI GEO site to get an appreciation for how >> difficult this problem can be. A great deal of effort is being >> invested in the microarray field to come up with a better means >> handle this issue, and the FuGO effort will be a critical >> clearinghouse for this work. The important thing to remember when >> it comes to field-wide data pooling and re-analysis, it may >> sometimes be necessary to get right back to the microarray primary >> image files so as to reapply different criterial when performing >> the statistical tests and reductions on pooled data. Given this >> requirement - one we also see in the neuroimaging domain - I >> believe it is very important to proceed in a well-reasoned manner >> when seeking to integrate across microarray datasets using >> semantic web technologies. Alan R. and myself - possibly others >> too - on this list are on the FuGO Coordinators Committee, so >> hopefully we can help to keep those lines of communication open. >> >> Sorry to go on so, but this is a topic on which I've labored quite >> intensively over the past year. There is a lot being done on this >> issue, and I think all efforts will get much further more quickly >> - and in a way that will carry more street cred with practicing >> neuroscientists - if we all try to work together. >> >> Cheers, >> Bill >> >> 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 > > > 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. 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Received on Thursday, 8 June 2006 04:37:37 UTC