Discussion List Archives

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

Re: [ddlm-group] Clarification on dREL tables

  • To: James Hester <james.r.hester@gmail.com>, "Group finalising DDLm andassociated dictionaries" <ddlm-group@iucr.org>
  • Subject: Re: [ddlm-group] Clarification on dREL tables
  • From: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
  • Date: Fri, 6 Nov 2020 14:18:26 +0000
  • Accept-Language: en-US
  • ARC-Authentication-Results: i=1; mx.microsoft.com 1; spf=passsmtp.mailfrom=stjude.org; dmarc=pass action=none header.from=stjude.org;dkim=pass header.d=stjude.org; arc=none
  • ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901;h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck;bh=cPM2Q1VMqPqKgmGlbc6bdDObTK1QIlRfJPluBgT2Vwg=;b=XvVTGVrqCNOV39xYTMgyoHIZ7j6Wng8gFirNuD/Uls4Ug5EAaUz4LyGGJSHk799lkgQmbIJimPewr2pvJtCh9X8e52MPsZnNMNMgd+nFZF9ds3NHSxCI0gYMlHqvJBSDCOWR1cIb24MjMH5by100bhdU4OXdi61GkFeEop+3HVOjCSeG95TJo7AAExoFcQhLxJvvqqzyjYUszKEah6aF8PZQj9i+KEHxE95hfrU7V/RcBPYrRamOMqx7Q2M9MXjtxWT+ckBMt4ir2ssqHBVzZ7salbpKgYlFRX5uEn0mjUEBITW/+r7xiasFTffRUiBnRqBkjvrUK0my+v39MM4HSg==
  • ARC-Seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none;b=n21alDNoEpfmT7/oc9GEo13rs4yUvhZWUQ5xEUNThvYLOe+IHUhROJVQTkSALCOenOXmYLJulv95dU2mLv93k1/1pjjQLe3kXpuGwjCWqsI3pKGkyk1sbC4ICANHy3vFVfHVdFxlfYkFF5gPPFgs/oWtKaKdLjONR0h0M4ZmyCz4ivE/ANbO1O+M5cqwWFOGat1saWTNYyTjchY2FOvMZ55LqseKZD60r7x7TpSy6NrXWkGrxyeQ0LUB/XThXXrbTc9Wx/p2g5XW8igwxd5tMgOlsKXPtkcA4O0+5oAuBR904Ue59Oi14vopa7eiVQBOHOEvl7t0GX3NdqRkHSalyA==
  • In-Reply-To: <CABcsX25s9oND1z=N4vSfh85u-j8Va_MA5f_1n7p8hqQ7f24-cQ@mail.gmail.com>
  • IronPort-SDR: JZ0G+KAQozBpu/3BRUVCjq0+K5gzAIK0sBjiTGLVa3PB1x+GXyGKUPogKEL/9EA+HoWEL0ChzdMi1OD3N/CFe64VCosrHKKFqQa6aU9I3r1wWHkawCJvL+jMl+ERlI75bMxdzCJUWeyhAmfSMYODFpjkndGrTLNGC2PRrIwT6vMeU23Drybyly4+3NbaWcr2vP7KKs22eq0GS19xiEcEjTbAjZQLYY8jNJM4BkbtyG8bkp1KJmXP/OEWvGoi+bYLCbHuiuROudGHFmhCc5If41BNs4EQjz1MTcIOag+RqqE=
  • References: <CAM+dB2fbAtdxM_a+xz8sDeZcaSN=TZ+WzvE8hqMpjTtA-fBW0Q@mail.gmail.com>,<CABcsX25s9oND1z=N4vSfh85u-j8Va_MA5f_1n7p8hqQ7f24-cQ@mail.gmail.com>
Dear James,

Do I interpret correctly that the question is about CIF 2 data values of type Table, as opposed to DDLm category keys?  And if I do have that right, then do I further understand correctly that the question is about the data types of the keys themselves, not the types of their associated values?

If I understand correctly on both counts then I have no objection to requiring table keys to be of consistent type.  Moreover, I observe that CIF 2 is apparently more restrictive about the table values it can represent than dREL is about the table values it can work with, because CIF 2 tables must have string keys.



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 Herbert J. Bernstein <yayahjb@gmail.com>
Sent: Friday, November 6, 2020 4:59 AM
To: James Hester <james.r.hester@gmail.com>; Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
Subject: Re: [ddlm-group] Clarification on dREL tables
Caution: External Sender.
Do not click links or open attachments unless you recognize the sender and know the content is safe.

Dear James,
  Why is it necessary or desirable to have a uniform type for keys?  This would seem to bar a lot of uses of 
rather natural mmCIF and imgCIF constructs in which tables can be formed with composite keys some
of which are integers, such as array_id and binary_id and some of which are strings such as entry_id.
This kind of mixture allows us to build useful databases of information culled from multiple entries unless
we completely forbid making databases of rows extracted from tables with integer keys where the data
comes from multiple entries.

On Thu, Nov 5, 2020 at 9:02 PM James Hester <jamesrhester@gmail.com> wrote:
Hi all,

The dREL paper is not explicit on the uniformity of the keys used in dREL tables (associative dictionaries). In the supplementary material it says is that keys can be integers or 'character values'.  It is not explicit about whether these types of keys can be mixed in a single table. I suggest we clarify this point by stating that dREL table keys must be of the same type (the key types would be "cased strings", "caseless strings", or "integers"). I note that values are already constrained to be of the same type, and I believe that this stipulation is consistent with the current usage in the CIF dictionaries.

If there are any concerns about this, feel free to respond, otherwise I will incorporate this clarification into the Vol G dREL chapter.

all the best,
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
ddlm-group mailing list

Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
ddlm-group mailing list

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.