Discussion List Archives

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

Re: [ddlm-group] Semantics of whitespace-delimited values


This discussion is becoming rather confusing to me.   So with respect to my understanding and currentPDBx/mmCIF usage:  (1) a dot (.)  and a question mark (?) are treated as special tokens in the grammar for handingnull and missing values, (2) parenthetically appended uncertainties are not used in PDBx (e.g. xxx.xx(xx))rather uncertainties are represented in separated data items, (3) On input we do interpret or otherwise applyany data typing based on the quoting.  All data type interpretation at input is done via the data dictionary.
Regards,
John
On 7/24/15 12:17 PM, Bollinger, John C wrote:> That the BNF in ITVG contains a production for numeric values does not itself make CIF 1.1 numeric typing any less of a convention.> I half wish it did.  The production just provides the details of the conventional format; it does not say that the same value must> be interpreted differently if you put it inside quotation marks.  It doesn’t even really say that values matching that production> must be interpreted as numbers.  It only says, by way of its use in other productions, that a whitespace-delimited string having> that form is a well-formed data value.  In that sense it is superfluous, and it makes the grammar ambiguous (reflecting the genuine> CIF ambiguity that this is all about).>> It therefore does not follow that a strict CIF 2.0 parser, or even a strict CIF 1.1 parser, is required to reject “6.6666(6)” as a> number.  That is conventional, but the usefulness of that convention is in doubt.   It does not even follow that in _atom_site_label> 12, the “12” must be interpreted as a number.>> In any case, I think I’ve failed to make my point, because you (Simon) “agree” with the opposite of my position.  A distinction> between quoted and unquoted data values is a de facto inherent aspect of CIF 1.1 format, else the conventions for ., ?, and numeric> format could not work.  The conventions rely on that distinction to ascribe specific different significance to certain data values> when they are presented unquoted than when they are presented quoted, but the underlying, basic distinction cannot be matter of> convention.  However broadly that inherent distinction applies, I do not want to change it in CIF 2.0.>> It is plausible -- and to me appealing -- to interpret the distinction between quoted and unquoted data values to apply to all CIF> 1.1 values, with the general practice being to ignore it except in certain cases.  That seems to fit more naturally with having the> conventions on top, too.  The main alternative is to say that it applies only to the value data forms explicitly called out in the> conventions.  The only advantage I see in the narrow interpretation is to avoid embarrassment arising from at this point discovering> a new, or at least forgotten, aspect of CIF.  That’s offset for me by the inherent contrivance inherent in interpreting the feature> to exactly fit the convention it supports.>> John>> *From:*ddlm-group [mailto:ddlm-group-bounces@iucr.org] *On Behalf Of *SIMON WESTRIP> *Sent:* Friday, July 24, 2015 9:50 AM> *To:* Group finalising DDLm and associated dictionaries> *Subject:* Re: [ddlm-group] Semantics of whitespace-delimited values>> Upon reflection, I think I've been misleading in referring to numeric typing in CIF1.1 as a 'common semantic feature' (in IntTabs G> the BNF contains a <numeric> rule). So unless this is to be changed, the specification of CIF2 does not necessarily need to change> in this respect (though for completeness and to avoid confusion I still think it ought to be included in the EBNF if possible).>> So I suppose *strictly* a CIF2 parser, like CIF1.1, should not recognize e.g. _cell_length_a "6.6666(6)" as a number, and should> always treat e.g. _atom_site_label 12 as a number? Or perhaps the interpretation is that _atom_site_label 12 could be a number or a> string, but _atom_site_label '12' is definitely a string and cannot be a number?>> I agree "We could (*should*) say that CIF 2.0 removes such distinctions, except for (.) and (?)">>>> Cheers>>>> Simon>> ------------------------------------------------------------------------------------------------------------------------------------>> *From:*"Bollinger, John C" <John.Bollinger@STJUDE.ORG <mailto:John.Bollinger@STJUDE.ORG>>> *To:* Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org <mailto:ddlm-group@iucr.org>>> *Sent:* Friday, 24 July 2015, 15:13> *Subject:* Re: [ddlm-group] Semantics of whitespace-delimited values>> I have no objection to APIs being tolerant of numeric data in this way.>> I see no particular advantage to adding special productions to the EBNF to match unquoted (.) and (?), however, as the current EBNF> already will match them as values just fine.  EBNF is good for describing the language grammar and syntax, but it is not the right> mechanism for expressing semantics.  Putting these explicitly in the EBNF is in any case a secondary issue.  The primary one is> whether the CIF format distinguishes quoted values from unquoted ones generally, or whether it distinguishes only certain special> cases of quoting vs. non-quoting.>> We seem to agree that there’s no good way around the (.) and (?) cases, but I suspect we differ about the more general question.> Even though it is desirable for CIF parsers to be flexible about numbers, the published CIF conventions say to distinguish between> quoted and unquoted values with respect to numeric interpretation.  That’s only a convention, so CIF software is not obligated to> follow it, but following it must be **allowed**, at least in CIF 1.1.  That means that there indeed must be an actionable> distinction between quoted and unquoted numbers.  With that being the case, I am inclined to make it a general distinction, even if> it is one that is typically ignored, rather than a special case.  Moreover, I am inclined to say that there always has been such a> distinction; it just hasn’t been used outside the numeric- and null-value cases.>> We could say that CIF 2.0 removes such distinctions, except for (.) and (?), but I don’t really see the need for another break from> CIF 1.1.>> John>> *From:*ddlm-group [mailto:ddlm-group-bounces@iucr.org] *On Behalf Of *SIMON WESTRIP> *Sent:* Friday, July 24, 2015 7:27 AM> *To:* Group finalising DDLm and associated dictionaries> *Subject:* [ddlm-group] Semantics of whitespace-delimited values>> I agree - indeed the 'less-tolerant' applications in my little survey used third-party APIs to read the CIF so it is probably the> case that the API is being 'intolerant' rather than the application.>> I'd also be happy to see period and question mark in the EBNF - afterall these tokens when white-space delimited should never be> interpreted as the string values "?" or ".", so fundamentally they could be regarded as structural tokens, regardless of any other> semantics associated with them.>> In general, with respect to the imminent introduction of CIF2, the assumption will likely be that the common semantic features of> CIF1 will apply to CIF2, which is fair enough. However, personally I would prefer that such semantics were kept distinctly separate> from the specification. For example, the CIF1 line-folding 'semantics' are now part of the specification that a parser is expected> to be aware of, while the CIF1 character encoding semantics are purely conventions that may be useful in certain domains (the parser> really doesn't need to be aware of them). So if the CIF1 convention with respect to period and question marks is generally thought> to be an inherent part of CIF, then it would be better placed in the specification that parsers should be aware of (i.e. parsers> should be aware of these 'null' tokens and not simply return a "." or "?" with no context)?>> The same applies to numbers - if a parser is expected to unequivocally identify numbers from the syntax, then this is no longer a> 'common semantic feature'. I believe that a parser needs minimally to identify a 'value', which can be interpreted further down the> line.>> So perhaps the question boils down to: which (if any) of the semantic features of CIF1 would we expect a CIF2 parser to be aware of?>> Cheers>> Simon>> ------------------------------------------------------------------------------------------------------------------------------------>> *From:*James Hester <jamesrhester@gmail.com <mailto:jamesrhester@gmail.com>>> *To:* SIMON WESTRIP <simonwestrip@btinternet.com <mailto:simonwestrip@btinternet.com>>; Group finalising DDLm and associated> dictionaries <ddlm-group@iucr.org <mailto:ddlm-group@iucr.org>>> *Sent:* Friday, 24 July 2015, 6:37> *Subject:* Re: [ddlm-group] Semantics of whitespace-delimited values>> Let me take up one of Simon's comments:>> "...we could suggest that CIF applications started to turn to the dictionary rather than syntax to determine the exact nature of a> data item".>> What is not perhaps appreciated is that the application programmer accessing the CIF file searching for a numeric value for a> particular dataname has already consulted the dictionary when writing the program (with the minor exception of e.g. pretty-printers> as noted before).  Consulting the very same dictionary at runtime is pointless as these meanings are never supposed to change. So I> would suggest to Simon that there is no problem nudging *application* programmers to accept the dictionary definitions as they> already have done so in order to write correct calculations, the only problem will be nudging CIF APIs to do their best to return a> number if asked (and your survey would suggest that the majority already do).  My position is very strongly pro application> programmer - if they are asking my API for a number, I am not going to second-guess them unless they have asked me to by providing a> dictionary as well.>> I'd be happy to see period and question mark added to the EBNF as primitive productions, this is a simple change.>> On 9 July 2015 at 07:46, SIMON WESTRIP <simonwestrip@btinternet.com <mailto:simonwestrip@btinternet.com>> wrote:>> Dear all>> I extended the mini survey of current applications a little and looked  closer at some of the less-liberal parsers:>> one of the applications I've looked at did not complain when I included some non-ASCII text in the CIF, while another complained> about a data value constructed as '''z''' (valid CIF1), and one displayed rather quirky behaviour with regard to semicolon-delimited> strings, rejecting the contained 'value' if it had a leading newline but not if it had a leading space ->> all of these particular applications complained about delimited numbers to the extent that the application stopped processing.>> Based on this (albeit limited) survey of some current well- known CIF applications, regarding the introduction of CIF2 it would> definitely be prudent to indicate that 'yes indeed' the interpretation of CIF1.1 wihitespace-delimited values retains significance> in CIF2. However, if possible I think it would be in the interests of flexibility and unambiguity if somehow we could suggest that> CIF applications started to turn to the dictionary rather than syntax to determine the exact nature of a data item (afterall, as I> see it, that's one very strong  motivation for developing CIF2 in the first place - and is the preferred approach in CIF1 too).> Thankfully (from my point of view) this isn't even an issue for the majority of applications I have looked at (they simply grab the> data however they've found it and make use of it if they can, or they carefully validate the data against the dictionary). So what> is challenging me is how we achieve this - i.e. nudging some applications to be a little more flexible (which in my experience is> what many  'users' would most appreciate)., while at the same time maintaining the convention that numbers especially are still> presented in an undelimited (uncluttered) fashion. I've no convincing answer to this yet.>> Regarding the ? and . 'null' values I hesitate to suggest that we could take these out of the issue altogether by making them CIF> key tokens - I hesitate because I suspect that some applications simply ignore their significance anyway and incorrect usage rarely> presents a real problem (and also I haven't yet attempted to see if its actually possible to define them in this way in any case:-)> - so its probably unnecessary and may even seem like a new complication to applications that were not particularly aware of, or> bothered by, the significance of these tokens in the first place.>> Cheers>> Simon>> ------------------------------------------------------------------------------------------------------------------------------------>> *From:*"Bollinger, John C" <John.Bollinger@STJUDE.ORG <mailto:John.Bollinger@STJUDE.ORG>>> *To:* Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org <mailto:ddlm-group@iucr.org>>; SIMON WESTRIP> <simonwestrip@btinternet.com <mailto:simonwestrip@btinternet.com>>> *Sent:* Wednesday, 8 July 2015, 16:21> *Subject:* RE: [ddlm-group] Semantics of whitespace-delimited values>> Thanks Simon, James, and John.  I am uncertain how many distinct parsers are represented by the reports so far, but it seems there> must be at least five.>> I think we agree that parsers and applications should be permitted, if not required, to distinguish between the values . and '.',> and between the values ? and '?'.  We also seem to agree that it is not useful to insist that parsers or applications refuse to> interpret quoted values as numbers, although some CIF 1.1 parsers in fact do so at their own discretion, and some warn instead of> refusing (with even that relying on taking the position that numbers are not supposed to be quoted).>> Not being enamored of special cases, and not wanting CIF 2.0 to rule out CIF interpretation practice that is accepted and common in> CIF 1.1 applications, I find myself favoring CIF 2.0 taking the position that in general, it is permitted but not required to> interpret any string value differently when it is presented in whitespace-delimited form than when it is presented in any of the> other forms.  The conventions for the special values . and ? could then be taken to apply on a domain-wide basis, whereas the> convention for the form of numbers could be taken to apply on a more selective basis (per-DDL, per-dictionary, or even> per-definition). An implication of this position, however, is that whether or not a value is presented whitespace-delimited becomes> a property of that value that a fully general CIF 2.0 parser must make available to its clients.  Moreover, for better or for worse,> future dictionaries could establish additional items or data types whose values are required to be presented unquoted.>> We could perhaps characterize that more specifically, maybe by saying that the exact form of values presented in any of the quoted> forms is significant, or something along those lines, whereas values presented in whitespace-delimited form may afford equivalent> alternative expressions.  That doesn’t exactly fit . and ?, but perhaps some similar statement could do so better.>> John>> -->> John C. Bollinger, Ph.D.>> Computing and X-Ray Scientist>> Department of Structural Biology>> St. Jude Children's Research Hospital>> John.Bollinger@StJude.org <mailto:John.Bollinger@StJude.org>>> (901) 595-3166[office]>> www.stjude.org <http://www.stjude.org/>>>>> -->> T +61 (02) 9717 9907> F +61 (02) 9717 3145> M +61 (04) 0249 4148>> _______________________________________________> ddlm-group mailing list> ddlm-group@iucr.org <mailto:ddlm-group@iucr.org>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/ddlm-group>>>> _______________________________________________> ddlm-group mailing list> ddlm-group@iucr.org> http://mailman.iucr.org/cgi-bin/mailman/listinfo/ddlm-group>
-- John Westbrook, Ph.D.RCSB, Protein Data BankRutgers, The State University of New JerseyDepartment of Chemistry and Chemical Biology174 Frelinghuysen RdPiscataway, NJ 08854-8087e-mail: john.westbrook@rcsb.orgPh: (848) 445-4290 Fax: (732) 445-4320_______________________________________________ddlm-group mailing listddlm-group@iucr.orghttp://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.

Useful links