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Re: [ddlm-group] Objectives of CIF2 syntax discussion. .

Alas, no, I can't support it until I can see that it actually solves a
problem.  But I do agree with the general philosophy of finding
solutions to problems by working with DDLm and domain dictionaries.

On Thu, Jan 20, 2011 at 8:49 AM, Herbert J. Bernstein
<[email protected]> wrote:
> Dear David,
>
> �Inasmuch as we agree on the style tag, there is no need
> to argue about the import tag. �I am happy with your
> better solution.
>
> �Hopefully James will support us in this minor but
> useful addition to DDLm.
>
> �Thank you for your help.
>
> �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
> � � � � � � � � [email protected]
> =====================================================
>
> On Wed, 19 Jan 2011, David Brown wrote:
>
>> Dear Herbert,
>>
>> I suggested earlier that we could easily add the style tag you suggest.
>> In some cases where an earlier dataname has
>> already been superceded by a second dataname it would be necessary to
>> indicate which is the proper (i.e., later) name
>> that should be used on writing since all datanames that have ever been
>> approved must appear in the alias list.� With the
>> style tag the _alias_uri would not be as important and could be omitted.
>>
>> There are a number of reasons why your import scheme would have made life
>> considerably more complicated.� The first is
>> that the old tags do not conform to CIF2 syntax and therefore would have
>> to be insulated within the routines that
>> manipulates the data under DDLm CIF-dictionary control.� The second is
>> that DDLm has a much tighter heirarchical category
>> structure that is desinged to simplify the merging and updating of the
>> dictionaries.� This was introduced to overcome
>> some of the weaknesses of the earlier file structures.� Allowing the DDL1
>> and DDL2 datanames to be defined in save frames
>> within the DDLm dictionary would lead to incompatibilities that would
>> prevent many of the newly introduced features in
>> DDLm being used.� For example in DDLm the category and object parts of the
>> datanames are defined independently and
>> represent the two components out of which the dataname is constructed at
>> run time.� The dataname in the save_ statement
>> is, by convention, a composite of these two components, but it is not the
>> definition of the name.� Since it is not
>> possible with the older datanames to separate them into a catagory and
>> object component without in some cases misnaming
>> the category, their presence would effectively mean that the tighter
>> features of DDLm could not be used either in
>> programming or in updating and merging.� One should not try to put new
>> wine into old wine skins.
>>
>> Anyway it sounds as if we have agreement on at least something. and
>> knowing that DDLm can achieve compatibility with the
>> earlier archive by using the aliases on reading and writing, and proper
>> DDLm names otherwise, should simplify the
>> discussions on syntax.
>>
>>
>>
>> Herbert J. Bernstein wrote:
>> � � �Dear David,
>>
>> � � �� That was very helpful.� You want to maintain one dictionary that
>> will dynamically act as a DDL1, DDL2 or
>> � � �DDLm dictionary. Fair enough.� But then shouldn'e the information on
>> what alias is intended for what style of
>> � � �output simply be in the alias tags.� It is not really a matter of
>> which dictionary it come from, but of which
>> � � �of several alternate styles of tags it conforms to.
>>
>> � � �� Right now the alias category has 2 tags,
>>
>> � � �� _alias.definition_id
>> � � �� _alias.dictionary_uri
>>
>> � � �We could both do what we need to do without conflicting if there were
>> a third tag
>>
>> � � �� _alias.tag_style
>>
>> � � �which would simply be a character string, such as DDL1, DDL2, DDLm,
>> my_new_style, ... which could be used to
>> � � �tie together the style of tags to be used for a particular dictionary
>> use, both for validation of input and
>> � � �for generation of output.� If no particular style had been specified,
>> the save frame name would win.� This
>> � � �would bring the data on which are DDL1 names and which are DDL2 names
>> for the core values neatly together on
>> � � �one core dictionary without having to know if any other dictionaries
>> were DDL1 style and which are DDL2
>> � � �style.� The DDLm dictionary would have all the information right
>> there and would not even need to refer to
>> � � �the older dictionaries on most cases to work with DDL1 and DDL2 data
>> files.
>>
>> � � �� For my work, this would be just as effective as the import ... as
>> ... or my method_alias suggestion in
>> � � �allowing me to use CIF1 tags that are illegal under CIF2 without
>> requiring us to allow those names as valid
>> � � �tags in DDLm dictionaries.
>>
>> � � �� Could you accept _alias.tag_style, and perhaps allowing
>> _alias.dictionary_uri to be omitted when not really
>> � � �needed?� This would be a big help to me in then making a DDLm imgCIF
>> dictionary that could not only replace
>> � � �the DDL2 dictionary, but could also, for the first time provide a
>> DDL1 version of all imgCIF tags.� I could
>> � � �even then automatically produce valid DDL1 and DDL2 dictionaries from
>> the DDLm dictionary source, making thr
>> � � �DDLm dictionary the only version that I would have to maintain.
>>
>> � � �� Thank you again.� That was really very helpful.
>>
>> � � �� 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
>> � � ����������������� [email protected]
>> � � �=====================================================
>>
>> � � �On Wed, 19 Jan 2011, David Brown wrote:
>>
>> � � � � � �Herbert,
>>
>> � � � � � �I have copied below the DDLm entry for the item you suggest.
>> Notice that
>> � � � � � �it has a different name in the DDLm CIF-dictionary.� The input
>> file
>> � � � � � �includes all the information needed to calculate this item but
>> � � � � � �_diffrn_standards.decay_% is not present in the input and we
>> require to add
>> � � � � � �it.� The values we need in the input file are read in and
>> associated with
>> � � � � � �the new DDLm datanames (is this what you call a tag?).� The
>> user must make
>> � � � � � �some decision what information he requires and must emter this
>> into the
>> � � � � � �program in the form of a dataname.� There are many ways this
>> could be done,
>> � � � � � �but this is a programming decision, not a dictionary one.� The
>> information
>> � � � � � �mau be supplied as '_diffrn_standards.decay_percent' or
>> � � � � � �'_diffrn_standards.decay_%'.� Either way the instruction is
>> converted (via
>> � � � � � �the alias) to '_diffrn_standards.decay_percent' which is the
>> name that
>> � � � � � �would be used in the method.� Note that changing a dataname
>> does not
>> � � � � � �require any change in the value of the item.� After execution
>> of the method
>> � � � � � �this item would be populated.� The user must also decide what
>> output is
>> � � � � � �needed, say mmCIF (i.e. a CIF2 datafile).� The program locates
>> the correct
>> � � � � � �output name� '_diffrn_standards.decay_%' in the alias list and
>> writes the
>> � � � � � �mmCIF file using this name.� Note that the name
>> '_diffrn_standards.decay_%'
>> � � � � � �does not correspond to the CIF2 syntax, but the input and
>> output parts of
>> � � � � � �the program recongnize when it is working with CIF1 syntax.
>>
>> � � � � � �The reason this is cleaner is that only one method is needed
>> since all
>> � � � � � �manipulations between reading the input and writing the output
>> are carried
>> � � � � � �out using the DDLm CIF-dictionary including the DDLm
>> CIF-dictionary tags.
>> � � � � � �If we need different methods for different standards we would
>> end up with
>> � � � � � �three different dictionaries and we would loose the abitlity
>> e..g., to read
>> � � � � � �in a CIF1 data file and write out a CIF2 datafile.� Writing,
>> and more to
>> � � � � � �the point maintaining, the kind of dictionary you envision
>> would be a
>> � � � � � �nightmare.
>>
>> � � � � � �Best wishes
>>
>> � � � � � �David
>>
>> � � � � � �------------------------------------------
>>
>> � � � � � �save_diffrn_standards.decay_percent
>> � � � � � ���� _definition.id
>> '_diffrn_standards.decay_percent'
>> � � � � � ���� _definition.update���������� 2008-06-09
>> � � � � � ���� _description.text
>> � � � � � �;������������� The percentage decrease in the mean
>> � � � � � ��������������� intensity of the set of standard reflections
>> measured at the
>> � � � � � ��������������� start of the measurement process and at the
>> finish.� This
>> � � � � � �value
>> � � � � � ��������������� usually affords a measure of the overall decay
>> in crystal
>> � � � � � ��������������� quality during the diffraction measurement
>> process.
>> � � � � � �Negative
>> � � � � � ��������������� values are used in exceptional instances where
>> the final
>> � � � � � ��������������� intensities are greater than the initial ones.
>> If no
>> � � � � � ��������������� measurable decay has occurred, the standard
>> uncertainty
>> � � � � � �should
>> � � � � � ��������������� be quoted to indicate the maximum possible value
>> the decay
>> � � � � � ��������������� might have.� A range of 3 standard uncertainties
>> is
>> � � � � � �considered
>> � � � � � ��������������� possible.� Thus 0.0(1) would indicate a decay of
>> less than
>> � � � � � ��������������� 0.3% or an enhancement of less than 0.3%.
>> � � � � � �;
>> � � � � � ���� _description.common�������� 'DiffrnStandDecay%'
>> � � � � � ���� _name.category_id����������� diffrn_standards
>> � � � � � ���� _name.object_id������������� decay_percent
>> � � � � � ���� _type.purpose��������������� Measured
>> � � � � � ���� _type.container������������� Single
>> � � � � � ���� _type.contents�������������� Real
>> � � � � � ���� _enumeration.range���������� :100
>> � � � � � �loop_
>> � � � � � ���� _description_example.case
>> � � � � � ���� _description_example.detail
>> � � � � � ������������������ '0.5(1)'
>> � � � � � �;������������������� represents a decay between 0.2% and 0.8%
>> � � � � � �;
>> � � � � � ������������������� '-1(1)'
>> � � � � � �;�������������������� the change in the standards lies between
>> a decay of
>> � � � � � ������������������������������� 2% and an increase of 4%'
>> � � � � � �;
>> � � � � � ������������������� '0.0(2)'
>> � � � � � �;�������������������� the change in the standards lies between
>> a
>> � � � � � ������������������������������� decay of 0.6% and an increase of
>> 0.6%.
>> � � � � � �;
>> � � � � � �loop_
>> � � � � � ����������� _alias.definition_id
>> � � � � � ����������� _alias.dictionary_uri
>> � � � � � ����������� '_diffrn_standards_decay_%'������ cifdic.c91
>> � � � � � ����������� '_diffrn_standards.decay_%'������ cif_mm_1.0.dic
>> � � � � � ����� save_
>>
>>
>>
>>
>>
>> � � � � � �Herbert J. Bernstein wrote:
>>
>> � � � � � �Let's take a concrete example:� Suppose we want to use a DDLm
>> method to populate
>> � � � � � �_diffn_standards.decay_% in an mmCIF dictionary from the actual
>> measured reflections (or, more
>> � � � � � �elegantly as a long-term goal directly from the data in a scan
>> of image frames).
>>
>> � � � � � �That tag cannot be used directly in a dREL method. Under David
>> and John's proposed use of the
>> � � � � � �alias mechanism, what aliases would have appear where and to
>> what should be method itself refer,
>> � � � � � �and in what save frame would it be defined.� Ideally, we would
>> like to be able to have this all
>> � � � � � �gathered into one dictionary, and the dictionary merge
>> mechanism allows us to do that, so
>> � � � � � �whatever we propose should not depend on the name or type of
>> the dictionary.
>>
>> � � � � � �I can see how the alias mechanism can be used to validate the
>> value.� I don't yet see how it can
>> � � � � � �be used to generate the value using the illegal tag. If I
>> understand the DDLm docuemnt correctly,
>> � � � � � �to generate a value for a tag, the method has to be in the same
>> frame defining that tag, but we
>> � � � � � �seem to have barred this tag from being the name of a save
>> frame in a CIF2-style DDLm
>> � � � � � �dictionary.� If we were to go back to allowing all the valid
>> CIF1 tags as tags in DDLm
>> � � � � � �dictionaries, then this particular problem would go away with a
>> little jiggering either of the
>> � � � � � �alias mechsnism or by adding the import ... as ... to the
>> methods. I think the import is cleaner,
>> � � � � � �but I msay be wrong and look forward to seeing the alias
>> solution. I am not sure I see any simple
>> � � � � � �solution if we don't relax the tag restriction back to CIF1
>> rules, but again, I may be wrong.
>>
>> � � � � � �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
>> � � � � � ������������������ [email protected]
>> � � � � � �=====================================================
>>
>> � � � � � �On Wed, 19 Jan 2011, Bollinger, John C wrote:
>>
>>
>>
>> � � � � � �On Wednesday, January 19, 2011 7:37 AM, Herbert J. Bernstein
>> wrote:
>>
>>
>>
>> � � � � � �If the CIF1 interoperability with DDLm is an absolute given, we
>> should be a
>> � � � � � �ble to work things out.� That may or may not require changes in
>> CIF2, but I
>> � � � � � ��am fairly sure it will require some new hooks in dREL and DDLm
>> to be able to work fully with
>> � � � � � �CIF1 tags.� Perhaps I've missed those hooks.
>>
>>
>> � � � � � �I trust those here having more practical experience with DDLm
>> and dREL to c
>> � � � � � �orrect me where I am wrong, but as far as I can tell, DDLm's
>> alias system p
>> � � � � � �rovides all the needed hooks.� Here are some implied details
>> that might cla
>> � � � � � �rify matters:
>>
>> � � � � � �1) Each dREL method appearing in a DDLm data dictionary refers
>> to CIF items
>> � � � � � ��exclusively in terms of those items' data names (not aliases),
>> as defined in the dictionary in
>> � � � � � �which the referenced items and the method's item all a
>> � � � � � �ppear.
>>
>> � � � � � �2) Where necessary, DDLm aliases bind the data names actually
>> used in input
>> � � � � � ��data CIFs to the corresponding names defined in the
>> dictionary.� This alia
>> � � � � � �sing is transparent to dREL methods and to data validation
>> procedures.
>>
>> � � � � � �3) When needed, a DDLm-based system can automatically select an
>> output data
>> � � � � � ��name for an item, based on the name of the dictionary in which
>> the user ex
>> � � � � � �pects the output name to be defined.� If the chosen dictionary
>> is not the D
>> � � � � � �DLm dictionary itself then the given dictionary name is used to
>> select the appropriate alias from
>> � � � � � �among those defined for the item in question.� This activity
>> also is transparent to dREL, if not
>> � � � � � �outside dREL's scope altogethe
>> � � � � � �r.
>>
>> � � � � � �All of that depends heavily on the content of the dictionary,
>> but it appear
>> � � � � � �s fully supported by DDLm and dREL as presently defined. None
>> of those oper
>> � � � � � �ations inherently depend on details of CIF syntax.
>>
>>
>> � � � � � �It is possible that part of the problem here is a disagreement
>> over the mea
>> � � � � � �ning of "CIF1 interoperability".� The above description
>> explains CIF1 inter
>> � � � � � �operability over the full breadth of DDLm / dREL design goals
>> as I perceive
>> � � � � � ��them, but Herbert has expressed an interest in embedding
>> script in data fi
>> � � � � � �les, and perhaps his concerns arise from that direction.� As
>> far as I can t
>> � � � � � �ell, that would be outside dREL's design parameters, but dREL
>> could conceiv
>> � � � � � �ably still be applied in such a context.� Details and any
>> semantic differen
>> � � � � � �ces would need to be defined in the appropriate data
>> dictionary, however, n
>> � � � � � �ot in that dictionary's DDL (whether DDLm, DDL2, or DDL1).� As
>> stimulating as a discussion of
>> � � � � � �that topic might be, I think at the moment it would go r
>> � � � � � �ather too far afield.
>>
>>
>> � � � � � �Regards,
>>
>> � � � � � �John
>>
>> � � � � � �--
>> � � � � � �John C. Bollinger, Ph.D.
>> � � � � � �Department of Structural Biology
>> � � � � � �St. Jude Children's Research Hospital
>>
>>
>> � � � � � �Email Disclaimer:� www.stjude.org/emaildisclaimer
>>
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