Comments on SimulationDM version 1.0 WD

Wed May 11 07:23:35 PDT 2011

Hola Carlos,

thanks for your comments.
I will try to answer some of your comments in the text , and think you 
could upload the ones I do not answer directly on the RFC page for record
in the RFC process.
thanks, Mireille

On 03/05/2011 20:42, Carlos Rodrigo wrote:
> Which document/s are we discussing?
> -----------------------------------
>
> The document that was submitted to the list (and is available in the wiki page), that is,
> the DataModel document, makes reference to other "accompanying documents" very often. For
> instance, it mentions the Appendix many times.
>
> This Appendix is not part of the document and was not submitted to the list together with
> the simDM document.
>
ok, this has been fixe now.
The simulation data model text explains the way the data model covers 
the wide field of simulations , which is a very rich field of metadata.
The details are found in the documentation on Volute:
SimDB.html Specification of the model
  where each data model element is explained.

The graphical overview on the model is given in the UML diagram: 
SimDB_DM.png
> The important question is: What are we revising here? the submitted document or it together
> with the mentioned set of "Accompanying documents"?
yes we need all to understand and implement the details.
> Isn't it too summarized?
same answer as above.
> Punctual comments
> -----------------
> The first thing is again: couldn't we find another word for (experimental) Protocol?? not
> just adding a "(experimental)" in italics before it?
>
> It was very clear at Nara that using this word in a VO context is extremely confusing.
> And, if we are going to continue using it, we should write the "(experimental)" adjective
> everywhere, without exceptions (including figures).
>
> ----
>
> In general, I think that there are too many references to protocols and simDB in the
> document. I understand that some comments must be done because the modeling is done in such
> a way that the data can be accessed. But the data model is about how the data is
> represented/modelled and not about how the data is accessed. And I think that it would be
> better to have as few references to protocols as posible.
>
> Service/Webservice
> --------------------
>
> I've found it quite difficult to understand where the "service" class is located in the
> model (I'm not completely sure that I understand it yet). Looking at figures 1 and 2 I
> assumed at first that a service is specified for each experiment (which would mean that
> there is one service for each run of the code). But looking at figure 3 and section 3, and
> then section 4.8, I see that both "Service" and Experiment (and Protocol and Project) are
> subclasses of Resource. For me this would mean that there is one service for each resource
> (although the resource contains several experiments run under a given protocol) and that
> this service can be used to access the results of all the experiments. Am I right? If so, I
> think that figures 1 and 2 are a little misleading.
>
> ----
>
> Section 2: History
> --------------------
>
> I don't think this section is very important, but given that it is part of the document, I
> would make a couple of small changes.
>
> (a) It is true that some types of simulations (the cosmological ones, for instance) are
> often made in big collaborations. But it is also true that other types of simulations are
> performed by a team of one astronomer plus one student. And, and least, I wouldn't say that
> the first case is more usual. In fact I'm convinced that this is a point that should be
> considered: many (if not most) theoretical simulations are made by small groups.
>
> Thus, I would delete the sentence "and is these days often performed in large collaborations".
>
> (b) When it starts talking about S3 it says: "A recent effort has been"... I don't think it
> is so recent.
>
> The Note is more that two years old and the idea had been already presented in March 2007 at
> the "Astronomical Spectroscopy and the Virtual Observatory." workshop (without the S3 name).
> Actually it was a parallel effort, for microsimulations, when other people were focused on
> 3+1 simulations. I would just change it to "Another effort", "A different approach" or
> something like that. And, by the way, it is not a result of an investigation started at
> Cambridge as we were working in it before Cambridge (and had a first version implemented for
> isochrones and evolutionary tracks, not just theoretical spectra).
>
> "S3 is actually a direct reworking " to "S3 is a generalization ". I don't know what "a
> direct reworking" really means, but I don't think S3 is a direct reworking of TSAP at this
> stage (maybe it was at the end of 2006 when we first implemented it).
>
Sorry I think "generalisation" is not adequate here.
 From my point of view, S3 covers some usecases identified by the VOSpec 
team and
collaborators to distribute theoretical spectra with their metadata.

> (c) We didn't really decided at Victoria that S3 and SimDAP would be merged in a single
> protocol named SimDAL. We decided that it would be nice to do so and that we would
> investigate if it is possible or not. Actually I don't know enough what SimDAP means to be
> able to say how both protocols could be merged, or if they can be merged or if it is a good
> idea to merge them in an only protocol. But, in any case, this is not the subject of this
> document.
>
In every data model specifications there is the need to mention how data 
model fields will be
used and sent to the applications consuming these pieces of metadata .
ex: Photometric calibration is defined in PhotDM and carried on via SSA 
to VOspec or Specview applications ...

So it is important to link data access protocols with  the data model 
specification .
> In fact I think that stating the intentions of the TIG about protocols and so (and what is
> decided or not about that) is out of the scope of a data model document. Even though this is
> the historical introduction, I don't think it is necessary (or even good) to include such
> statements. Thus, better than discussing about it, I would drop the last paragraph.
>

I think if we cannot agree on such expressions like "recent", etc , we 
just stay on facts and
mention the dates when the various documents were issued.
The historical section is interesting for people not involved in these 
efforts to trace back the stream of ideas
from which these documents are originating .
> Section 3.1
> -----------
>
> "and SimDAP has merged with S3 to form SimDAL: a family of access protocols for theory data"
>
> I would change "merged" to "joined" or something like that. At this stage, both things are
> included under the SimDAL concept, but we don't really now yet if they will be an only
> protocol, two protocols, two flavours of the same thing or what. Actually, the word "family"
> seems to imply that there will be more than onw "flavour" and, for me, seems contradictory
> if we say that they are merged.
>
> **************************************************************************
>
> How to use the model
> --------------------
>
> It is quite clear that this datamodel has been made mostly with two ideas in mind:
> cosmological 3+1 simulations and a data base of simulations (mostly of this type).
> This is quite obvious throughout the document (and it's perfectly understable given
> the history).
>
> But, given that this is intended to be THE model for simulations and that I have implemented
> more than 20 services for theoretical data, I have to try to find the correspondence between
> the concepts that I use for those services and the ones in the data model. And I must say
> that it is not easy even for the most simple models. And what worries me is that, if it is
> not easy for me (I'm not an expert in datamodeling, object oriented programming, uml and so,
> but I've been attending talks and discussions about this for a long time), how will it be
> for scientists who have their grid of models and want to make them available in the VO?
>
> I think that we very much need, at least, a simple recipe on how to implement this data
> model for simple cases (let's say: those usually called microsimulations). And probably some
> examples should be included in the document so that data providers have an starting point
> to this complex standard.
>
> And I assume that it is partly my assignment to do such a thing (or at least I would like
> to be able to do it). But I'm still not sure if I am able to figure out how to do it.
>
I fully agree to train on examples : it will clarify the correspondence 
simDM/S3
> A try to make a couple of examples
> ----------------------------------
>
> When writing a votable containing data for a theoretical simulation, I assume that the
> datamodel should be useful to better characterize the content of that votable (concepts and
> relations between them).
>
> Thus, my main exercise has been trying to use this datamodel in a extremely simple case.
> I have a collection of theoretical isochrones and I want to rewrite it adding utypes from
> the datamodel.
>
> And I must say that I'm not sure at all about how to do that.
>
> The main idea to be able to say:
>
> * This is an isochrone
> * It is the isochrone for an star (or set of stars, let's say "star" for simplifying)
> * It has been calculated with the Baraffe et al model
> * The parameter is the star age.
>
> And, even:
>
> * the isochrone is a table with four columns:
> - mass
> - effective temperature
> - logarithm of gravity
> - bolometric luminosity
>
> In a simple model I would imagine something like this:
>
> <PARAM name="model"  utype="SimpleSimDM:model" value="Vandercroft"/>
> <PARAM name="object" utype="SimpleSimDM:targetObject" value="star"/>
> <PARAM name="INPUT:age" value="0.00100" unit="Gyr" ucd="phys.age"
> utype="SimpleSimDM:inputParameter"/>
>
> <TABLE>
> <PARAM utype="SimpleSimDM:product" value="isochrone"/>
> <FIELD name="mass" utype="SimpleSimDM:product.property"/>
> <FIELD name="teff" utype="SimpleSimDM:product.property"/>
> <FIELD name="logg" utype="SimpleSimDM:product.property"/>
> <FIELD name="Lum" utype="SimpleSimDM:product.property"/>
>
> (...)
>
> But this SimDM model is not simple. It is complex and very hierarchical.
> And it is known that this hierarchical structure is not easy to represent in a flat document
> as a votable.
>
> I just try to identify the utypes more adequate for each concept and add relations (by
> grouping) with the semantic labels so that eventually they can be liked to some vocabulary.
>
> And I even get a little lost here. I get confused by the ObjectType, TargetObjectType,
> RepresentationObjectType, ExperimentRepresentationObject, RepresentationObject... I'm not
> very sure what I should use for just saying "this is a star", what for saying "this is an
> isochrone", what for representing the object contained in the isochrone (with its
> properties, mass, logg, etc...). I get the feeling that this is quite a flexible and
> interesting idea, but I don't really understand much about all these classes named *Object*
> without some examples.
>
> Finally:
>
> I have writen two quite simple votables:
>
> - the first one contains one isochrone and I try to use the datamodel in it.
> - the second contains a list of isochrones for a given range of ages.
>
> Could someone tell me (probably Gerard) if they make sense?
>
> (In some cases I have added groups with only one param inside, which is quite unnecessary. I
> do it just to show the idea that something else could be added, if needed, as related to
> that param)
>
> If you make some comments and help me about this, I would try to do something similar for
> the much more complicated case of asteroseismology simulations.
>
> By the way, I don't find in the model any "box" to specify a bibliografic reference. I think
> it would be important to address that too.
>

-- 
--------------------------------------------------------------
Mireille LOUYS          mailto: mireille.louys at unistra.fr

L S I I T&      CDS,
Ecole Nationale Superieure            Observatoire de Strasbourg
de Physique de Strasbourg,            11, Rue de l'Universite
Boulevard Sébastien Brant, BP 10413   67000 STRASBOURG
67412 ILLKIRCH Cedex       	      Tel: +33 3 68 85 24 34
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