Re: ontology specs for self-publishing experiment

Dear Tim,

I think this is an excellent idea - and comes at a very propitious time.

I would suggest including participants on the FuGO, PaTO, and EXPO  
projects as well.

Cheers,
Bill

On Jul 6, 2006, at 9:23 AM, Tim Clark wrote:

> Michael
>
> The FuGE project may have some interesting overlaps with SWAN.   
> Current phase of SWAN is focused on construction of annotation and  
> publishing tools for semantically characterized hypotheses, claims,  
> findings, counterclaims, etc on digital resources in neuromedicine,  
> at the community level.  This is planned to be followed by a  
> complementary phase involving management and characterization of  
> laboratory results using an extension of the same ontology.
>
> I propose we arrange mutual presentations and discussions to see if  
> any synergies exist such that we might take advantage or each  
> others' work.
>
> Best
>
> Tim
>
> ---------------------------------------------------------------------- 
> --------
> Tim Clark	617-947-7098 (mobile)
>
> Director of Research Programs
> Harvard University Initiative in Innovative Computing
> 60 Oxford Street, Cambridge, MA 02138
> http://iic.harvard.edu
>
> Director of Informatics
> MassGeneral Institute for Neurodegenerative Disease
> 114 16th Street, Charlestown, MA 02129
> http://www.mindinformatics.org
> ---------------------------------------------------------------------- 
> --------
>
>
>
> On Jul 5, 2006, at 7:38 PM, Miller, Michael D (Rosetta) wrote:
>
>> Hi Eric,
>>
>> Just wanted to point out how this overlaps with the current FuGE  
>> (http://fuge.sourceforge.net/) and FUGO (http:// 
>> fugo.sourceforge.net/) efforts.  These are focused on systems  
>> biology and are intended to provide the underpinnings of reporting  
>> gene expression, gel, mass spec, and -omics experiments/ 
>> investigations.
>>
>> The goal of FuGE (Functional Genomic Experiments) is for the most  
>> part to provide:
>>
>> "a. Publishing Protocols
>> b. Publishing Regants and Products
>> c. Stating the Hypothesis (and model using RDF) that is being  
>> tested by the experiment; this includes which citations are  
>> supportive or alternative to ones hypothesis
>> d. Publishing Experimental Data (possibly as RDF-OWL aggregates  
>> and tables)
>> e. Articulating the Results and Conclusions; specifically, whether  
>> the experiment refutes or supports the central Hypothesis (most of  
>> us agree we cannot 'prove' a hypothesis, only disprove it)"
>>
>> But it is a UML based model that will then have an equivalent XML  
>> Schema generated.  The advantage, I think, this approach has over  
>> a pure ontology representation is that it better captures the  
>> actual work-flow of these experiments for the interchange of data  
>> and annotation.  That being said, the UML model incorporates a way  
>> to annotate the class objects with ontology Individuals with a  
>> reference to the Individual's RDF class and its ontology.  The UML  
>> model adds the additional semantics of identifiers (typically  
>> expressed as LSIDs) that allows tying reference elements generated  
>> in the XML Schema to the full definition of an object.  So a  
>> biological sample can be fully described in one document then  
>> referenced by a treatment that incorporates it into a prep.
>>
>> So, for instance, typically a hypothesis is specific to the  
>> particular experiment/investigation.  In FuGE, it is simply a  
>> Description class with a text attribute associated by a Hypothesis  
>> association to the Investigation class.  But in the XML document,  
>> this specific Description can be annotated by references to  
>> ontologies that allow hypothesis to be translated to RDF upon  
>> import.  We used the OMG Ontology Definition Metamodel  
>> specification mapping of Individuals from OWL/RDF to UML so that  
>> these could then be mapped back to an OWL/RDF representation for  
>> reasoning (http://www.omg.org/ontology/ontology_info.htm#RFIs,RFPs).
>>
>> FUGO is intended to become part of the OBO ontologies and FUGO's  
>> goal is to provide general annotation terms for these type of  
>> experiments.
>>
>> cheers,
>> Michael
>> Michael Miller
>> Lead Software Developer
>> Rosetta Biosoftware Business Unit
>> www.rosettabio.com
>>
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb- 
>> lifesci-request@w3.org] On Behalf Of Eric Neumann
>> Sent: Monday, July 03, 2006 6:57 AM
>> To: AJ Chen
>> Cc: w3c semweb hcls
>> Subject: Re: ontology specs for self-publishing experiment
>>
>>
>> AJ,
>>
>> This is a great start, and thanks for taking this on! I would like  
>> to see this task force propose a conceptual framework within the  
>> two months. It does not have to be final, but I think we need to  
>> have others on the list review the ontologies (http://esw.w3.org/ 
>> topic/HCLS/ScientificPublishingTaskForce? 
>> action=AttachFile&do=get&target=SPE_Specs.html) and requirements  
>> (http://esw.w3.org/topic/HCLS/SciPubSPERequirements) you have  
>> proposed, ask questions about them, and adjust/expand as needed.
>>
>> I think there has been good discussions on this topic in the past,  
>> and I would also refer folks to the SWAN paper by Gao et al.   
>> http://www.websemanticsjournal.org/ps/pub/2006-17 . This work is  
>> inline with with what Tim Clark has been proposing to the group,  
>> and I think it is a useful model to consider. Perhaps we can  
>> combine these efforts and propose a workable (demo anyone?) by the  
>> end of summer...
>>
>> In terms of gathering more Scientific Publishing of Experiments  
>> (SPE) requirements, I wanted to list some items that appear to be  
>> inter-related and relevant:
>>
>> 1. By Publishing experiments, one must also consider (i.e.,  
>> include in the ontology):
>> a. Publishing Protocols
>> b. Publishing Regants and Products
>> c. Stating the Hypothesis (and model using RDF) that is being  
>> tested by the experiment; this includes which citations are  
>> supportive or alternative to ones hypothesis
>> d. Publishing Experimental Data (possibly as RDF-OWL aggregates  
>> and tables)
>> e. Articulating the Results and Conclusions; specifically, whether  
>> the experiment refutes or supports the central Hypothesis (most of  
>> us agree we cannot 'prove' a hypothesis, only disprove it)
>>
>> 2. Hypotheses should be defined in terms of authorship (ala DC),  
>> what the proposed new concepts is, and what (experimental) fact  
>> (or claim) is required to support it. It should also refer to  
>> earlier hypotheses either by:
>> a. extension of an earlier tested and supported hypothesis:  
>> refinement
>> b. similarity or congruence with another untested hypothesis:  
>> supportive
>> c. being an alternative to another hypothesis, that will qualify  
>> itself through the refutation of the earlier one: refutation
>> This would allow one to define rules and queries that can traverse  
>> the lineage of hypotheses (forwards and backwards, similar to  
>> citations), and how one papers work can be related to ongoing work  
>> on different fronts that have branched.
>>
>> 3. "Publication" should be a specific concept in SPE, that would  
>> serve to be the hub of DC metadata as well as the above  
>> experimental data and hypotheses. Different non-disjoint  
>> Publication "Roles" could be defined, such as  Peer-Reviewed,  
>> Electronically-Published, Topic Review, and Follow-up Data. I  
>> would also invite the folks interested in Clinical Publications to  
>> specify what requirements they feel should be included, (e.g.  
>> regulatory applications, Common Technical Document).
>>
>> I also think it would be useful if we could add a Concept Map  
>> graphic for the proposed SPE ontology (class relations mainly).  
>> Sometime ideas can get expressed faster to the larger community  
>> using images.
>>
>> cheers,
>> Eric
>>
>>
>>
>>
>>> From: AJ Chen <canovaj@gmail.com>
>>> Date: Sun, 25 Jun 2006 16:00:23 -0700
>>> Message-ID:  
>>> <70055a110606251600m469b7d63t405579e7a61e7ef8@mail.gmail.com>
>>> To: public-semweb-lifesci@w3.org
>>> I added the first draft of specs for the ontology being developed  
>>> for
>>> self-publishing experiment. see the link on the task wiki page -
>>> http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce
>>>
>>> This specs document and the requiremnets document are meant to be  
>>> only the
>>> starting point for discussion.  I truly hope more people in this  
>>> group will
>>> participate in this open development process, making comments or  
>>> providing
>>> changes to the documents.
>>>
>>> While the ontology is being developed by this community, I am  
>>> going to
>>> develop a self-publishing tool that implements the ontology,  
>>> which allows
>>> you to try this new way of sharing research information. With  
>>> easy-to-use
>>> tools to demonstrate the benefits of sharing and searching  
>>> experiment
>>> information in semantic data format, it will help attract more  
>>> people to
>>> contribute to the development of the ontology as well as the tools.
>>>
>>> Best,
>>> AJ
>>
>>
>>
>> Eric Neumann, PhD
>> co-chair, W3C Healthcare and Life Sciences,
>> and Senior Director Product Strategy
>> Teranode Corporation
>> 83 South King Street, Suite 800
>> Seattle, WA 98104
>> +1 (781)856-9132
>> www.teranode.com
>>
>

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







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