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Re: [ddlm-group] Proposal to update dREL, part II

  • To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
  • Subject: Re: [ddlm-group] Proposal to update dREL, part II
  • From: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
  • Date: Wed, 19 Sep 2018 18:11:36 +0000
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Dear DDLm group,


With respect to proposal 3, I agree in principle that the proposed syntax extension seems to yield an improvement, but the details are not completely clear to me.  Specifically,


- May the _category.key_id be used in the expanded syntax?  Including if it is not named as a _category_key.name?

- More generally, which attributes are permitted to be used to index a category?  Must they be among those whose names are listed in the category’s own _category_key.name attribute, or is this to become a more general facility?

- Is it necessary to specify a complete key when this syntax is used for a category with a compound natural key?

- In the proposed syntax, are the key names given as simple attribute names or as full CIF item names?




With respect to proposal 4, I agree with the general idea that dREL should prefer to avoid requiring method implementations to explicitly express category keys that can reliably be determined from context.  How that applies here depends to some extent on proposal 3, however.


Additionally, before considering going forward with this proposal, I think we need to describe more formally the cases in which the key values can be conveyed implicitly.  For example, the description remarks that “this short cut is not possible where more than one data name is linked to the same category key”, but I’m not confident that I know how to recognize all such cases programmatically.


Also relevant: are we assuming that linked items are always [components of] their categories’ keys?  Does anything break under this proposal if non-key attributes are linked?








John C. Bollinger, Ph.D.

Computing and X-Ray Scientist

Department of Structural Biology

St. Jude Children's Research Hospital


(901) 595-3166 [office]





From: ddlm-group [mailto:ddlm-group-bounces@iucr.org] On Behalf Of James Hester
Sent: Monday, September 17, 2018 5:39 PM
To: ddlm-group <ddlm-group@iucr.org>
Subject: [ddlm-group] Proposal to update dREL, part II


It appears that after preparing part II I completely forgot to send it to the group.  The marked-up version of this second proposal is available at https://github.com/COMCIFS/dREL/blob/master/drel_changes_2.rst


Proposed changes to dREL, part II






dREL is a machine-actionable language describing data relationships

and designed to be embedded in DDLm dictionaries. The language is

defined both explicitly in the dREL publication [1] and implicitly by

the dREL code appearing in the DDLm core CIF dictionary. Note that

the code in the core CIF dictionary significantly expands the language

presented in the paper, for example, by adding category methods.


The present changes were foreshadowed in the discussion about allowing

set methods to become looped [2].  They are aimed at removing the

current dREL-imposed requirement that all categories must have a

single data name that acts as a key.


Proposal 3: compound key specification



dREL as published permits a particular row in a loop to be specified

by providing the value of the key for that loop using the syntax

``<category>[keyvalue]``, so for example, ``atom_site['O1']`` would be the

row in the atom_site loop for which ``_atom_site.label`` (the key data

name for category ``atom_site``) is 'O1'.  We propose expanding

this syntax to allow multiple key values to be specified:

``<category>[name1=value1,name2=value2]`` would specify the row of

``<category>`` for which category objects ``name1`` and ``name2`` take

values of ``value1`` and ``value2`` respectively.





The current core CIF dictionary treats multi-key categories by

defining a synthetic data name for each such category. These synthetic

data names are currently just a list of the values of the multiple

keys. Having such single-dataname keys allows the dREL syntax to

be unambiguous for all Loop categories.


This approach is suboptimal because:

(1) The synthetic data names have no scientific relevance

(2) A considerable amount of DDLm machinery has been developed simply

    because of the resulting inhomogeneous lists. Without

    these synthetic data names, there would be *no* need in the current

    core dictionary for ragged and nested dimensions and multiple

    data types within a single list, and therefore no requirement

    for DDLm and dREL implementors to cope with such structures.

(3) dREL methods wishing to index into a multi-key category have to

    construct the synthetic keys from the individual values; the new

    syntax would save that line of boilerplate

(4) If a set category becomes looped, a number of looped categories

    will acquire a new key data name. If single-key loops remain a

    dREL requirement, previously single-key loops will require a new,

    synthetic data name to be created. Note that it could be argued

    that this is the way the system was designed to work.


The previous syntax will still be acceptable in those situations where

there is a single key, or where the values of the remaining keys are

unambiguous in context (see next proposal).


This proposed syntax has been included in the example EBNF for dREL

and the transformation to Python code implements the proposed semantics.


Proposal 4: elide keys where they are clear from context



If category A contains data names which are parents or children of key

data names in category B, dREL methods in category A do not need to

explicitly specify the key values of category B when accessing rows of

category B.





If b.k1 and b.k2 are the keys of category B, and data names A.a1 and

A.a2 are linked through ``_name.linked_item_id`` DDLm declarations to

those keys, then any dREL method in category A can simply write ``b.d3``

to access a specific value of dataname ``d3`` in category ``b``.  This is

equivalent to writing ``b[k1=a.a1,k2=a.a2].d3`` under proposal 3.


Note that this short cut is not possible where more than one data name

is linked to the same category key, for example, in ``geom_bond``

two data names are linked to ``atom_site.label``.


Note that partial resolution of data names is also possible, so that

key references that are missing from the original form may be resolved

using linked data names.





The net result of the above two proposals is to make looping Set

categories relatively painless. A dREL reference like ``cell.vector_a``

may remain untouched when multiple cells are present, as long as the

category within which the dREL method appears has only a single

data name that is a child of the single key data name of ``cell``.


However, in situations where the ``<category>[value]`` syntax has

been used and ``<category>`` acquires a new key data name because

some other category has become looped, dREL methods will need

to be rewritten to explicitly specify the key data name that

``value`` corresponds to.  Going forward, the ``[key=value]``

syntax should be preferred to minimise the need to rewrite

methods in advanced looping applications.


We should also be aware the dREL methods in our dictionaries are

curated, and therefore we can apply style guidelines to prefer the

explicit notation of proposal 3 as we see fit.


[1] Spadaccini et. al,

(2012) *J. Chem. Inf. Model.* **52**(8) pp 1917-1925





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