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Re: Advice on COMCIFS policy regarding compatibility of CIFsyntaxwith other domains. .

Dear James,

   I am glad we are getting closer, but now please consider what
you have written, and what it really means in practical terms:

> Preamble: The CIF syntax describes a human-readable, syntactic
> container for scientific data.

The word syntactic is misplaced here, and the "human-readable"
constratint was lost years ago with the creation of mmCIF.  As
we have just agreed, the semantics is an important part of the language, 
Also, in practice, one of the most important contributions
of CIF to our science has been the controlled vocaubulary it has
provided, independent of the form of expression:  tag-value, XML,
HDF5, etc.  In addition, for the PDB, the important issue is _not_
the human readability, but the preservation of all the essential
information of a scientific experiment, and, if you glance throught
some Acta C entries, you will see that even for small molecules,
the days of human readable CIFs are far behind us.   When we 
make a change, we need to bear all of that in mind.

I would recommend starting with a clearer expression of what CIF is:

===================
CIF is a language for the management of scientific data.  If combines
a controlled vocuabulary with a simple, human-readable form of expression
(the CIF syntax) backed by rules clarifying the meaning of the language
(the CIF semantics).  The overarching goal of CIF is to ensure that
the data of the relevant domains can be generated, transformed, 
transmitted and archived in ways that facilitate doing the science
involved in ways that both serve the individual scientific domains and
ensure that different domains can share information reliably.
=================
> CIF syntax aims to be as simple as
> possible.  The domain dictionaries are the primary location of
> semantic information in the Crystallographic Information Framework.
> In the following, the phrase 'dictionary level' refers either to the domain
> dictionaries, the DDL language in which the domain dictionaries are
> written, or the CIF2 common semantic features specification which
> imposes minimum requirements on the semantics specified by dictionaries
> and DDLs.

Given that much modified goals, this next paragraph becomes an
inappropriate strait jacket, misallocating responsibilies.  I
would suggest we return to what the real practice has been:

============
The CIF language tries for an appropriate balance between simplicity
and sufficient expressive ability to meet the needs of the scientific
domains involved, and changes to the existing syntax and common semantics
should only be made for good reason.  If it is possible to make a
needed change by simply defining a new term in the controlled vocabulary,
in one of the domain dictionaries, then that option whould be considered
first, especially because the controlled vocabulary is used in
other forms of expression, such as XML and HDF5.  This is what we
will call a change "at the dictionary level".  However, there are
times, e.g. with the introduction of a new dictionary definition
langauge, when changes are needed in the common syntax and semantics
that apply to all domains.
================
>
> 1. A feature should only be added to CIF syntax if all of the
> following are satisfied:
>
> (i) Implementation of the desired behavior by
> changes at the dictionary level rather than to CIF syntax
> is not feasible, or else such changes, while feasible, would
> significantly reduce human readability;

Then I would suggest the following version of this guideline, recognizing
the current division of labor.

==========

1. a. A feature should only be added to or changed in the the common 
syntax and semantics of the CIF language if implementation of the desired 
behavior by changes in the controlled vocabulary at the dictionary level 
is not feasible, or such changes, while feasible, would make it 
significantly more difficult for either people or software systems to work 
with the data effectively than when done by a change in the vocabulary; 
and

1. b. A feature should only be added by changes in the common syntax
of the CIF language if implementation of the desired behavior by
changes in the common semantics is not feasible, or such changes, while
feasible, would make it significantly more difficult for either people 
or software systems to work with the data effectively than when done
by a change in the syntax.

==============

-- Herbert
=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya@dowling.edu
=====================================================

On Wed, 16 Mar 2011, James Hester wrote:

> Hi Herbert,
>
> I agree that there is an in-principle need for a common semantic
> features document, and I thank you for directing our attention to this
> issue.  John B has suggested a 'base semantics' document to accompany
> the 'base syntax' document.  This seems like a workable approach to
> me, and we would call the 'base semantics' document 'common semantic
> features' in keeping with CIF1.  I would further suggest we hold off
> on developing the 'common semantic features' document until we have
> finished the syntax.
>
> Below find a redrafted version of the Preamble and point 1(i) to make
> the existence of the common semantic features document clear.
>
> ===========================================================
> Principles guiding development of CIF syntax
> -----------------------------------------------------------------
>
> Preamble: The CIF syntax describes a human-readable, syntactic
> container for scientific data.  CIF syntax aims to be as simple as
> possible.  The domain dictionaries are the primary location of
> semantic information in the Crystallographic Information Framework.
> In the following, the phrase 'dictionary level' refers either to the domain
> dictionaries, the DDL language in which the domain dictionaries are
> written, or the CIF2 common semantic features specification which
> imposes minimum requirements on the semantics specified by dictionaries
> and DDLs.
>
> 1. A feature should only be added to CIF syntax if all of the
> following are satisfied:
>
> (i) Implementation of the desired behavior by
> changes at the dictionary level rather than to CIF syntax
> is not feasible, or else such changes, while feasible, would
> significantly reduce human readability;
>
> (end of changes)
>
> On Wed, Mar 16, 2011 at 11:44 AM, Herbert J. Bernstein
> <yaya@bernstein-plus-sons.com> wrote:
>> Dear James,
>>
>>  I am not objecting to Brian's document.  I think we should keep
>> as much of it as possible for CIF2.  The only problem is that it
>> is a "semantic" document and your policy according to you and
>> John B. seems to want to relegate all semantic issues to the
>> dictionaries.  It is that relegation to which I am objecting.
>> Most features consist of both syntactic and semantic components,
>> and I find it much less confusing to deal with a feature in
>> its entirety than to deal with just the syntax.
>>
>>  Until this discussion, I had thought the intent of the dictionaries
>> was to deal with the tag definitions particular to certain domains
>> and that both the syantax and semantics of CIF was a global concern.
>> I find the relegation of the semantics of CIF2 to the dictionaries
>> surprising and recommend against it.  I want to keep Brian's
>> document a global document.
>>
>>  Regards,
>>    Herbert
>>
>> =====================================================
>>  Herbert J. Bernstein, Professor of Computer Science
>>   Dowling College, Kramer Science Center, KSC 121
>>        Idle Hour Blvd, Oakdale, NY, 11769
>>
>>                 +1-631-244-3035
>>                 yaya@dowling.edu
>> =====================================================
>>
>> On Wed, 16 Mar 2011, James Hester wrote:
>>
>>> Dear Herbert,
>>>
>>> Please explain why you think that the latest version of the guiding
>>> principles is at variance with the 'Common Semantic Features' document
>>> and approach.  For example, what would prevent us from adopting a
>>> similar CSF document for CIF2?  It would help if you quoted particular
>>> points from the guidelines in your reply.
>>>
>>> James.
>>>
>>> On Wed, Mar 16, 2011 at 3:59 AM, Herbert J. Bernstein
>>> <yaya@bernstein-plus-sons.com> wrote:
>>>>
>>>> Dear Colleagues,
>>>>
>>>>   I would suggest that people review Brian's excellent common
>>>> semantic features document for CIF 1.1.  I think keeping those
>>>> sort of semantic decisions couple to the syntax decisions for
>>>> CIF has worked well, and I do not think the sharp departure
>>>> now proposed for handling CIF2 will work as well for the
>>>> reasons I stated previously.  It ain't broke.  Why are
>>>> we fixing it?  New feautures involve a mix of syntax and
>>>> semantics depedending on the feature.  I believe we should
>>>> be focusing on features rather than the bin within which
>>>> they fit for presentation purposes.
>>>>
>>>>   Regards,
>>>>      Herbert
>>>> =====================================================
>>>>  Herbert J. Bernstein, Professor of Computer Science
>>>>    Dowling College, Kramer Science Center, KSC 121
>>>>         Idle Hour Blvd, Oakdale, NY, 11769
>>>>
>>>>                  +1-631-244-3035
>>>>                  yaya@dowling.edu
>>>> =====================================================
>>>>
>>>
>>>
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>>
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>
>
>
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