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With the release of the OandM specification I have been investigating the FreeGs domain with a view to its conformance. This has resulted in the diagrams above and a much better comprehension of both the domain and OandM. I have since realised that FreeGs fits very well within the OandM framework and actually does need to be massaged slightly to work and take advantage of aspects of OandM.

UML Examples

The image below is a first attempt to place the FreeGs concepts into the OandM specification. Initially this was done from the HollowWorld examples with specimens we however, are concerned with abstract concepts rather than real world objects. * Instance UML diagrams for species detail and calculation of the free energy of a species/reaction:


The diagrams demonstrate a work flow case where the result from the Species Detail becomes the featureOfInterest in the Free Energy Calculation.
Free Energy Calculation
The instance example shows both a Species and a Reaction as 'substitutable' features meaning that the instance could be valid for either feature. The information that is missing from this diagram is the input parameters for both a Species and a Reaction. Because these are domain specific features the necessary input parameters would be included and would feed through to the Procedure.

Species Detail
This instance satisfies the current SpeciesDetail information produced by the FreeGs web application. These objects are defined in the InformationModel section.

-- DalePercival - 07 Mar 2007

Within the OandM model context does the overrideActivityModel become a redundant attribute for a Species? Or does it need to remain as a domain specific attribute for modelling purposes? If the attribute remains then it becomes another Procedure which won't work according to the specifications as an Observation may only have on Procedure.

The file below is a first pass instance of the species detail that would satisfy use case 1 of our web service using the OandM specifiication. What hasn't been included yet is information about the model used in the DataSet and the set of parameter/value pairs with uom's. please see SpeciesDiscussion

-- DalePercival - 08 Mar 2007

Model Detail
For the purposes of FreeGs the details of a Model need to contain the parameters that would allow a system to be calculated. This is the set of parameter/value pairs that are displayed in a species data request from the current application. For our purpose the only way to serve this functionality is to provide an xlink:href to the parameter details. We are unable to describe the procedure inline as this only provides for a descriptive summary of the procedure.

-- DalePercival - 11 Mar 2007
Topic attachments
I Attachment Action Size Date Who Comment
SpeciesDetail.xmlxml SpeciesDetail.xml manage 7.3 K 08 Mar 2007 - 11:57 DalePercival Species detail instance document for Quartz.
Species_Instance_UML.PNGPNG Species_Instance_UML.PNG manage 11.5 K 07 Mar 2007 - 12:53 DalePercival Instance UML diagrams for species detail and calculation of the free energy of a species/reaction
Topic revision: r5 - 15 Oct 2010, UnknownUser

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