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Re: ontology specs for self-publishing experiment

From: Tim Clark <twclark@nmr.mgh.harvard.edu>
Date: Thu, 6 Jul 2006 15:23:42 +0200
Message-Id: <440F67FE-E706-415C-BB8E-F7C385F579A5@nmr.mgh.harvard.edu>
Cc: Eric Neumann <eneumann@teranode.com>, AJ Chen <canovaj@gmail.com>, w3c semweb hcls <public-semweb-lifesci@w3.org>, SWAN Team <swan-team@mind-informatics.org>
To: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>
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
>
Received on Thursday, 6 July 2006 13:35:35 GMT

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