Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [ddlm-group] Clarification of SU in DDLm dictionaries

I think we are agreed. I will edit this into ddl.dic and submit a pull request as per usual.

On Fri, 29 Jan 2021 at 01:33, Bollinger, John C <John.Bollinger@stjude.org> wrote:
Dear James and Group,

I do not object to changing "must be accompanied" to "should be accompanied".  I carried over the former from the current definition, but I agree that it seems a little heavy handed.  It is not a semantic error to provide a measurand value without its uncertainty, though doing so does have substantial implications.

John

From: ddlm-group <ddlm-group-bounces@iucr.org> on behalf of James Hester <jamesrhester@gmail.com>
Sent: Wednesday, January 27, 2021 9:24 PM
To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
Subject: Re: [ddlm-group] Clarification of SU in DDLm dictionaries
 
Caution: External Sender. Do not open unless you know the content is safe.

Dear John and group, 

I'm generally happy with the wording as John has proposed as it appears that I correctly understood the meaning. The only quibble is the use of the word "must" (The value of a measurand item *must* be accompanied by ...). Does this mean that software must flag an error if the su is missing? I think it would be preferable to use "should" in the meaning of RFC2119 instead (meaning "that there may exist valid reasons in particular circumstances to ignore a particular item, but the full implications must be understood and carefully weighed before choosing a different course.")

thanks,
James.

On Thu, 28 Jan 2021 at 10:48, Bollinger, John C <John.Bollinger@stjude.org> wrote:

Dear James and group,

 

Yes, that was my intention.¬† When the option is exercised to express a value for a measurand‚Äôs SU item ‚Äúintegrated with the measurand value in a manner characteristic of the data format‚ÄĚ, the integrated syntactic value conveys two distinct dictionary values, one for the measurand item and representing only the measured value itself, the other for the SU item and representing only the uncertainty in the measured value.¬† I am open to variations on the wording that are clearer about that.

 

John

 

 

From: ddlm-group <ddlm-group-bounces@iucr.org> On Behalf Of James Hester
Sent: Wednesday, January 27, 2021 5:33 PM
To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
Subject: Re: [ddlm-group] Clarification of SU in DDLm dictionaries

 

Caution: External Sender. Do not open unless you know the content is safe.

 

Dear John and DDLm-group,

 

We need to distinguish between the 'syntactic value' that appears after a 'syntactic data name' in a CIF file, and the 'dictionary value' that is assigned to a dictionary data name by some mapping to DDLm from a data format.  A key distinction between the two types of values is that the dictionary value is substituted as-is into a dREL expression, whereas a syntactic value may require some transformation, for example, removing delimiters or transforming a string to a number. The mapping from a CIF file to DDLm is usually simple - the data name to map to is the one associated with the value, and the value is transformed to the appropriate DDLm type by performing obvious manipulations. This mapping is so transparent for CIF that we often don't separate it out as a separate process. In my SU proposal I essentially proposed a new mapping where the SU of a 'syntactic value' is mapped to the associated SU 'dictionary data name' of the 'syntactic data name' that the 'syntactic value' was associated with.

 

So, I would agree with John's reformulation as long as it is understood that the "dictionary value" associated with the 'Measurand' data name does not include the SU, but that the 'syntactic value' may. I can certainly read it that way, but is that what you intended John?

 

James.

 

On Tue, 26 Jan 2021 at 03:09, Bollinger, John C <John.Bollinger@stjude.org> wrote:

Dear DDLm Group,

 

I am satisfied with items (1) and (2) of the proposal.  I am less satisfied with some details of item (3) and therefore with item (4).

 

I appreciate and accept that one of the objectives is to achieve independence of DDLm and of our data dictionaries from the format of data files.  On the other hand, I would also prefer to avoid loading the CIF serialization format, or others, with implicit dictionary-related semantics.  Thus, if the value presented for a measurand item is permitted to additionally convey a value for that item's associated SU item -- and we need that to support a large volume of existing data -- then that should be expressed by the measurand's definition, presumably as an aspect of its data type.

 

Thus, I suggest that the DDLm definition of measurands be adjusted to be generic with respect to the details of how a measurand value that conveys its own SU is represented, without removing the explicit provision for measurand and su being presented in combined form.  In conjunction with that, the chapter on CIF file syntax should mention the CIF convention for this.  The last bit may be a little tricky from the perspective of separating convention from rule, but as one of the more ardent supporters of maintaining that separation, I think a satisfactory compromise can be reached in that area.

 

The revised DDLm definition for 'Measurand' might then be more like this:

 

```

       Used to type an item with a numerically estimated value
       that has been recorded by measurement or derivation. A 
       data name definition for the standard uncertainty (SU) of this

       item must be provided in a separate definition with

       `_type.purpose` of `SU`. The value of a measurand item

       must be accompanied by a value of its associated SU

       item, expressed either:
         1) integrated with the measurand value in a manner

            characteristic of the data format,

       or
         2) as a separate, explicit value for the associated SU item.

       These alternatives are semantically equivalent.
```

 

That formulation is intended to have the same properties as James's with respect to the questions he presented.  I think the entire discussion he presented applies to this variation on the definition, too.  The most important part to me is the last sentence, which I intend as a foundation for a more explicit specification, as described above, of the CIF syntax details that James's alternative would leave implicit.

 

 

Regards,

 

John

 

 

--

John C. Bollinger, Ph.D., RHCSA

Computing and X-ray Scientist

Department of Structural Biology

St. Jude Children's Research Hospital

 

 


From: ddlm-group <ddlm-group-bounces@iucr.org> on behalf of James Hester <jamesrhester@gmail.com>
Sent: Sunday, January 24, 2021 8:04 PM
To: ddlm-group <ddlm-group@iucr.org>
Subject: [ddlm-group] Clarification of SU in DDLm dictionaries

 

Caution: External Sender. Do not open unless you know the content is safe.

 

Dear DDLm-group,

 

A careful reviewer of the DDLm volume G chapter has noted issues with the way in which we treat standard uncertainties.  I have created a draft proposal for discussion at https://github.com/COMCIFS/comcifs.github.io/blob/master/draft/su_discussion.md (reproduced below). Please provide your comments and once we have come to a resolution I will pass the final result on to COMCIFS for confirmation.

 

thanks,

James.

 

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

# Proposal: treatment of SU in DDLM dictionaries

## Introduction

There is some residual ambiguity around the treatment of su in our
DDLm dictionaries.  Currently, if `_type.purpose` for a data name
is `Measurand`, the DDLm attribute dictionary states:

```
       Used to type an item with a numerically estimated value
       that has been recorded by measurement or derivation. This
       value must be accompanied by its standard uncertainty
       (SU) value, expressed either as:
         1) appended integers, in parentheses (), at the
            precision of the trailing digits,       or
         2) a separately defined item with the same name as the
            measurand item but with an additional suffix '_su'.
```

This raises the following issues:

1. Option (1) presupposes CIF format. DDLm should be agnostic
regarding format

2. Should the `_su` form of the data name be explicitly defined in the
   dictionary?

3. Is it legal to provide both the `_su` form and the parenthetical
form for a data name?

4. Does the value of a `Measurand` data name for the purpose of
dREL include the SU?

5. Can the `_su` suffix be a requirement when the current DDLm
dictionaries contain data names that do not follow this?
(e.g. `_refln.F_sigma`).

The following proposal aims to clarify these questions.

## Proposal

1. That all `Measurand` data names have a corresponding
data name for their SU explicitly defined;

2. That the convention for IUCr dictionaries is that this
data name is formed by adding `_su` to the original data name;

3. That the parenthetical form of presentation of the su value
for CIF syntax is understood as a shorthand assignment of this
su value to the associated SU dataname;

4. That the definition for `Measurand` is therefore rewritten as:

```
       Used to type an item with a numerically estimated value
       that has been recorded by measurement or derivation. A
       data name definition for the standard uncertainty (SU)
       of this item must be provided in a separate definition
       with `_type.purpose` of `SU`.
```

The above questions are then answered as follows:

1. The new definition is format-agnostic

2. Yes, `_su` forms should be defined in the dictionary. Using
`_su` as a suffix is purely an IUCr convention which is not
always followed (e.g. `_refln.F_sigma`) and therefore not
appropriate for the DDLm attribute dictionary to specify.

3. Yes, it is *syntactically* legal to have both forms, as the CIF
syntax can have no embedded understanding of the meaning of the data
names, including `*_su` data names, and therefore duplication cannot
be detected as a syntax error.  It is instead a semantic error in the
same way as a cell volume - cell parameter mismatch would be. Thus
if the two values provided agree, there is no error, and if they
disagree, the software can take steps based on the importance of
the mismatch to the particular computation.

4. No, the value of a `Measurand` data name includes the main
value only.

## Discussion

In order for DDLm to be format-agnostic, each format needs to
associate some location in that format with a data name. The
appearance of a value in a CIF file without the data name appearing as
well (as is being proposed above) is thus not unusual in general,
simply for CIF this association is usually transparent due to the data
name appearing in the format itself.

### Compatibility

#### CIF authoring software

Authoring software remains free to append SU in parentheses.

#### CIF reading software

Legacy CIF reading software will have the same problems that it presumably has
with the new 'dotted' data names, in the sense that a data name that was
unknown at the time of software preparation has been used to provide a value.
This is a cost that we have accepted.

### Other comments

The su of a data item must always have been treated separately in
software, as software must handle the su differently to the main value
due at least to the differences in the way errors are propagated.
The creation of a separate data name captures this fact.

 

--

T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148

 



Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer

_______________________________________________
ddlm-group mailing list
ddlm-group@iucr.org
http://mailman.iucr.org/cgi-bin/mailman/listinfo/ddlm-group


 

--

T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148

_______________________________________________
ddlm-group mailing list
ddlm-group@iucr.org
http://mailman.iucr.org/cgi-bin/mailman/listinfo/ddlm-group


--
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148


--
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
_______________________________________________
ddlm-group mailing list
ddlm-group@iucr.org
http://mailman.iucr.org/cgi-bin/mailman/listinfo/ddlm-group

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.