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Re: [ddlm-group] DDLm aliases (subject changed). .. .. .. .. .

OK, now to the specifics of this item.  I will interpolate my remarks
into David's message with "***" flags. -- 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 Mon, 31 Jan 2011, David Brown wrote:

> Not having done any programming for many years and not being familiar with
> the current jargon, I find keeping up with the rapid-fire discussion on
> _aliases requires some effort on my part and the discussion has usually
> move on before I havc a chance to comment.
> 
> However, being incommunicado on weekends, I took Herbert's draft home where
> I could sit down without distraction and see what eactly what was
> proposed.  The errors and ambiguities in the draft did not help me get my
> heasd around the proposal, but I made some progress, and here are my
> comments.  First the general comments, then particular comments interleaved
> in the draft.
> 
> 1. _identifier_set:  What does this set identify?  The _id seems to flag
> arbitrary groups aliases.  'alias_set' would be a better name for this
> category, or even just 'set'.  What's in a name?  It sets certain switches
> in the brain, and if these are misset by the dataname, it may take a lot of
> work to get them reset.  Not conducive to instant communication. 
>
*** Yes, for maximal generality, a set is an arbitrary grouping.  We
have been through many alternative names for these groupings, and so far
"set" is the only one to which there has not (yet) been strong objection
on grounds of confusion with other, existing aggregational terminology.
The only (weak) point in favor of "_identifier_set" rather than
"_alias_set" is that the primary save frame name/tag/identifier
can appear in the list.  I would be just as happy with "set", but
then I assume sombody will have been deprived of some future use
of some other set aggregation scheme, so to avoid appearing to
hog a very useful name, it probably should be qualitied in some
way.  Does "tag_set" appeal to people?

> 2. Why do we need both _alias and _alias_identifier_set categories?  They
> have indentical information (if the datanames (Syd's word) or tags
> (Herbert's word) are any indication).  I suppose (though this is no where
> spelled out) that _identifier_set would have its own save frame in the
> dictionary and would not be an attfibute of a datanmae.  If this is a
> correct interpretation it would provide a place whare all the alias
> datanames in the dictionary could be listed within a single loop).  This
> seems redundant, but I cannot speak from programming experience.  If
> alias_identifier_set does not appesr in its own save_ frame, how does it
> differ from 'alias'?

*** We do not need both an _alias and and _alias_identifier_set category,
and more than we need both an _atom_site and an _atom_site_aniso_U
category (well perhaps a both more).  It is just an organizational
convience to all both the flatter, very denormalized DDL1 style
of presentation as well as the more normalize DDL2 style of
presentation.  It does have the side advantage of allowing
one to pull our a separate list of tags by set.

> 
> 3. If my supposition in 2. is correct, we would appear to have a problem. 
> We will now have a variety of flavours of CIF dictionaries, each expressing
> a particular programmer's preferences for grouping the aliases.  This will
> make no difference to the CIFs themselves as these groupings are irrelevant
> once a CIF has been written, but if, for example, I am given a program
> written by Herbert and different program written by either of the Johns, I
> might need a different mmCIF dictionary for each of these two programs,
> dictionaries that differ only in the way the aliases are gouped.  When I
> load my CIF it cannot give instructions on which dictionary to call up
> because is will have no knowledge of the idiosyncrasies of the program I
> have chosen to use.  A possible solution would be to use the _import
> feature to create a virtual dictioanry at run time.  Thus the
> _identifier_set information would be held in a local dictionary that would
> be imported into the authorised CIF dictioanry at run time.  However, there
> are limitations on what can be imported.  The _identifier_set category
> could be imported but it would be impossible to import the
> _identifier_set_id into the alias loop by this mechanism.  Since I am not
> sure that I understand how Herbert intends to use this feature, I do not
> feel competent to suggest a way in which this problem could be handled. 
> Having programs that used different dialects of CIF dictionaries does not
> seem to be in line with the traditional development of CIF, particularly
> for a feature that is unlikely to be much used, even if they do not affect
> the CIFs themselves.  We should think carefully about the implications of
> this move.
>  

*** The main reason I am trying to bring this to COMCIFS is that we
very much seem headed in the direction of multiple, conflicting
interpretations of our standards, and dictionaries that will
not fit together.  Without this, we seem headed towards having,
for example, at least three distinct and possibly conflicting
core dictionaries in simultaneous use (the current core, the one
in mmCIF and the new DDLm core), and at least three and possibly
four mmCUF dictionaries (the official IUCr DDL2 mmCIF, the PDB's
DDL2 pdbx mmCIF, and 2 more DDLm versions of each of those).

> 4. My detailed comments follow the feature they comment on below:
> 
> 
> 
> save_definition.xref_code
>        _definition.id             '_definition.xref_code'
>        _definition.update           2011-01-26
>        _definition.class            Attribute
>        _description.text
> ;
>         Code identifying the equivalent definition in the dictionary
>         referenced by the DICTIONARY_XREF attributes.
>
>         Use of _definition.xref_code is deprecated in favor of
>         use of _alias.xref_code
> ;
>        _name.category_id            definition
>        _name.object_id              xref_code
>        _type.purpose                Identify
>        _type.container              Single
>        _type.contents               Code
>         save_
> 
> 
> This item is deprecated.  It should be deleted.   The  alias and xref
> iitems have never been tested and it is clear from the current DDLm that
> thay are placeholders that are awaiting development.  If there are any
> programs that make use of the items they can only have been written by
> members of this group.  The current xref defintiions inadequate and
> unworkable. .The is no excuse for leaving this item in if we don't need it.

*** See my general remarks on communicating with the unknown users
of what has been posted since 2007.

> 
> save_ALIAS
>
>        _definition.id               alias
>        _definition.scope            Category
>        _definition.class            List
>        _definition.update           2011-01-26
>        _description.text
> ;
>         The attributes used to specify the aliased names of definitions.
>         Every tag has an implicit alias to itself with a null
>         _alias.xref_code to allow use of the primary tag in
>         the ALIAS_IDENTIFIER_SET category.
>
>         The use of _alias.identifier_set_id in the key of
>         this catgeory is provide a placeholder for the
>         to conform the key of the parent ALIAS category
>         to the key of the child ALIAS_IDENTIFIER_SET
>         for automatic joins.  It is not intended that
>         _alias.identifier_set_id should be used in the
>         ALIAS category when no join is being done.
> 
>
> This last paragraph would be easier to undestand if all the words were
> present and the sentences grammatical..  In any case it should appear under
> _alias,identifierr_set, not here.  If I am right in thinking alias is an
> attribute and alias_identifier_set is not,  how does one join a
> non-attribute to an attribute?


*** This stray item has to do with being able to have both the
denormalized flat presentation and the normalized presentation
via a join.  If we stay with just the normalized presentation,
it is not necessary.  I apologize for my typos.  I should have
said "is to provide" instead of "is provide".  Discussing the
key of a category in the category definition seems appropriate
because the key is defined here (see just below).

>
> 
> ;
>        _category.parent_id          ddl_attr
>        _category_key.primitive      ['_alias.definition_id',
>                                      '_alias.xref_code',
>                                      '_alias.identifier_set_id']
>         save_
> 
> 
> save_alias.definition_id
>        _definition.id             '_alias.definition_id'
>        _definition.class            Attribute
>        _definition.update           2006-11-16
>        _description.text
> ;
>         Identifier tag of an aliased definition.
> ;
>        _name.category_id            alias
>        _name.object_id              definition_id
>        _type.purpose                Key
>        _type.container              Single
>        _type.contents               Tag
>         save_
> 
> save_alias.deprecated
>        _definition.id             '_alias.deprecated'
>        _definition.class            Attribute
>        _definition.update           2006-11-16
>        _description.text
> ;
>         Specifies whether use of the alias is deprecated
> ;
>        _name.category_id            alias
>        _name.object_id              definition_id
> 
> 
> .object_id should be the second part of the _definition.id, i.e.,
> 'deprecated'.  This needs correcting in many places.

*** thanks for spotting that 
>
>        _type.purpose                STATE
>        _type.container              Single
>        _type.contents               YesorNo
>        _enumeration.default         No
>         save_
> 
> 
> save_alias.dictionary_uri
>        _definition.id             '_alias.dictionary_uri'
>        _definition.update           2011-01-26
>        _definition.class            Attribute
>        _description.text
> ;
>         Dictionary URI in which the aliased definition belongs.
>         _alias.dictionary_uri is deprecated in favor if
>         _alias.xref_code
> ;
>        _name.category_id            alias
>        _name.object_id              dictionary_uri
>        _type.purpose                Identify
>        _type.container              Single
>        _type.contents               Uri
>         save_
> 
> 
> This item should be moved to the _dictionary_xref category.  The xref.id 
> is sufficient link.  Again, the fact that it may appear in the draft
> dictionaries should not prevent it being deleted in DDLm since the draft
> dictionaries are just drafts and will be chaniged once we have sorted out
> how to do the aliases.

*** I donlt disagree on the objective.  I just disagree on whether
the ghost of tags past needs to remain here to haunt its old abode.

>
> 
> save_alias.identifier_set_id
>        _definition.id   '_alias.identifier_set.id'
>        _definition.class  Attribute
>        _definition.update 2011-01-26
>        _description.text
> ;
>        A code identifying an identifier_set of related tags.
>        This linked item is provided in the ALIAS category to
>        ensure that the key of the ALIAS category is
>        conformed to the key of the ALIAS_IDENTIFIER_SET
>        category.  The alias has not been joined with
>        ALIAS_IDENTIFIER_SET, _alias.identifier_set_id
>        it is not intended that  _alias.identifier_set_id
>        in the ALIAS category.
> 
> 
> I cannot make much sense of the last sentence.  Perhaps there are missing
> words?

*** Thanks.  I'll try to clean up the words.

>
>
>        This is a pointer to _identifier_set.id
> ;
>        _name.category_id alias
>        _name.object_id   code
> 
> 
> See above.  'code' is not the proper .object_id
*** thanks.  you are right

>
>        _name.linked_item_id         '_identifier_set.id'
>        _type.purpose     Key
>        _type.container   Single
>        _type.contents    Code
>        _enumeration.default  .
>       save_
> 
> 
> save_alias.xref_code
>        _definition.id             '_alias.xref_code'
>        _definition.update           2011-01-26
>        _definition.class            Attribute
>        _description.text
> ;
>         Code identifying the dictionary containing the primary
>         definition of the dictionary as given in the
>         DICTIONARY_XREF category.
> 
> ;
>        _name.category_id            definition
>        _name.object_id              xref_code
>        _name.linked_item_id         '_dictionary_xref.code'
>        _type.purpose                Key
>        _type.container              Single
>        _type.contents               Code
>         save_
> 
> 
> save_IDENTIFIER_SET
>
>      _definition.id      identifier_set
>      _definition.scope   Category
>      _definition.class   List
>      _definition.update  2011-01-27
> ;
>       Data items used to describe the identifier_set identifiers
>       used in this dictionary.  Data items in this category
>       are NOT used directly as attributes of individual data items.
>       See linked item _alias_identifier_set.identifier_set_id
>       for such uses.
>
> 
> ;
>       _category.parent_id ddl_attr
>       _category_key.generic  '_identifier_set.id'
>
>       save_
> 
> save_identifier_set.id
>        _definition.id   '_identifier_set.id'
>        _definition.class  Attribute
>        _definition.update 2011-01-27
>        _description.text
> ;
>        A code identifying an identifier_set of related tags.
>        The coverage of an identfier_set may conform precisely
>        to the set of tags in a particular dictionary,
>        or to tags drawn from multiple dictionaries or
>        to a subset of tags from a single dictionary.
>
>        The same tag may belong to multiple identifier
>        sets, and a given tag may not belong to any
>        identifier set, in which case the only associated
>        identifier set is a null value.
> 
> 
> Presumably the second line should read 'need not belong to any'.  The
> wording above is ambiguous.
> The last line should read 'identifier set id' and its default value should
> be given explicitly.  What is nul?
> Possible nul values are 'nul', '0', ' ', '?', '.', etc.

*** I was thinking of "." and "?"

>
>        To help ensure that dictionaries can be merged,
>        each code should either begin with an IUCr-registered
>        prefix or, if not prefixed, have been approved
>        by COMCIFS.  The special prefix 'local_' may be
>        use for purely internal purposes of an organization.
> 
> 
> I assume these are not datanames that appear in the dictionaries but a list
> of COMCIFS  enumerations, some of which might appear in a non-exclusive
> enumeration list.  What happens if someone chooses 'joeblow' as an id?

If COMCIFS approved joeblow, then so be it, but the idea is that
COMCIFS would approved and control the use of set identifiers such
as say DDL1, DDL2, DDLm, core, and mmCIF, but that the PDB, which
has registered the pdbx_ prefix, would control the use of set
identifiers such as pdbx_mmCIF or pdbx_EM, and that somebody who
is doing something purely local, migh just use local_joeblow without
consulting anybody.
> 
> ;
>        _name.category_id identifier_set
>        _name.object_id   code
>        _type.purpose     Key
>        _type.container   Single
>        _type.contents    Code
>
>       save_
> 
> save_identifier_set.description
>        _definition.id   '_identifier_set.description'
>        _definition.class  Attribute
>        _definition.update 2011-01-27
>        _description.text
> ;
>        A description of the identifier_set
> ;
>        _name.category_id identifier_set
>        _name.object_id   code
>        _type.purpose     Describe
>        _type.container   Single
>        _type.contents    Text
> 
>
>       save_
> 
> save_ALIAS_IDENTIFIER_SET
>
>       _definition.id      alias_identifier_set
>       _definition.scope   Category
>       _definition.class   List
>       _definition.update  2011-01-27
> ;
>        The attributes used to specify the identifier_set of
>        tags to which a given tag belong.
>
>        A given tag may belong to multiple identifier_sets
>        and may be cited against multiple dictionaries.
>
>        Note that _alias_identifier_set.identifier_set_id is a
>        component of the key of ALIAS_IDENTIFIER_SET.  If the
>        denormalized join presentation is used to bring the object
>        ids of this child category up into the parent
>        ALIAS category, then _alias.identifier_set_id will
>        we used as an implicit addition to the key of
>        the denormalized ALIAS category.
>
>        Until DDLm can be formally revised to automatically
>        handle the necessary promotion of child catgeory keys
>        in denormalized joins, a place-holder
>        _alias.identifier_set_id has been defined in the
>        ALIAS catgeory.
> 
> ;
>       _category.parent_id  alias
>       _category.parent_join  Yes
>       _category_key.primitive  ['_alias_identifier_set.identifier_set_id',
>                                 '_alias_identifier_set.definition_id',
>                                 '_alias_identifier_set.xref_code']
>        save_
> 
> save_alias_identifier_set.definition_id
>        _definition.id   '_alias_identifier_set.definition_id'
>        _definition.class  Attribute
>        _definition.update 2011-01-27
>        _description.text
> ;
>        Together with _alias_identifier_set.xref_code, identifies
>        an alias belonging to an identifier_set.  An alias may
>        belong to any number of identifier_sets, including zero.
> 
> ;
>        _name.category_id alias_identifier_set
>        _name.object_id   definition_id
>        _name.linked_item_id  '_alias.definition_id'
>        _type.purpose     Key
>        _type.container   Single
>        _type.contents    Tag
>         save_
> 
> save_alias_identifier_set.identifier_set_id
>        _definition.id   '_alias_identifier_set.identifier_set_id'
>        _definition.class  Attribute
>        _definition.update 2011-01-27
>        _description.text
> ;
>        Identifies an identifier_set to which the alias
>        identified by _alias_identifier_set.definition_id
>        and _alias_identifier_set.xref_code ) belongs.
>
>        A pointer to _identifier_set.id
> ;
>        _name.category_id alias_identifier_set
>        _name.object_id   code
>        _name.linked_item_id  '_identifier_set.id'
>        _type.purpose     Key
>        _type.container   Single
>        _type.contents    Code
>
>       save_
> 
> 
> save_alias_identifier_set.xref_code
>        _definition.id   '_alias_identifier_set.xref_code'
>        _definition.class  Attribute
>        _definition.update 2011-01-21
>        _description.text
> ;
>        A code identifying the actual dictionary,
>        virtual dictionary or other logical grouping
>        to which the identifier tag belongs.
> 
> 
> What is this identifier tag - '.definiton_id' or '.definiton_set_id'?
>
*** They are just pointers, see the primary definitions at
the _name.linked_item_id linked tags.  But for clarity, I
will repeate them locally in the next pass.
> ;
>        _name.category_id alias_identifier_set
>        _name.object_id   code
>        _name.linked_item_id  '_dictionary_xref.code'
>        _type.purpose     Key
>        _type.container   Single
>        _type.contents    Code
>         save_
> 
>
> 
> 
> We also need to refined the _dictionary_xref category.  '.uri; should be
> added, '.format' should be better derfined or deleted.  Perhaps '.version'
> should also be added.  Definining the dictionaries is just as important as
> definiting the definition_sets

*** I'll try to propose something on the next pass, probably on Wednesday
during the next storm.


> 
> David
> 
>
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