Opinions on comments as part of the content
Joe Krahn krahn at niehs.nih.govThu Mar 8 17:32:14 GMT 2007
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Brian McMahon wrote: > A lot of good stuff in this discussion. One thing it brings out > is the dichotomy between the "simple" approach - stick a CIF in vi, > memorise the CIF dictionaries, stick in a few comments to remind > other readers why we've done something that way and the "formal" > approach of mechanise all i/o with reference to dictionaries > and/or stylesheets. CIF sits astride both camps, albeit somewhat > awkwardly. The editorial staff at the IUCr can edit and manipulate > small-molecule CIFs pretty well, and a generation of Acta C/E > authors can also do so, with varying levels of proficiency. The > editorial staff at RCSB can even do it with mmCIFs, but the > complexity of a full structure description in an mmCIF stretches > people to the limit, and in collections of data sets, whether > coreCIF or mmCIF, we really do need formal validation mechanisms. > > There are clear similarities between the hand-edited HTML pages > of the early web, and the schema-driven content management systems > of today's big Web applications. And perhaps, as on the Web, one > needs to be able to support both approaches. > > It may be that the next cycle of major CIF development will > be able to produce a cleaner implementation that is essentially > fully dictionary-driven: but there will still need to be legacy > support for the archival CIFs (or a major effort to remediate > all existing CIFs to a cleaner form). My feeling is that the simple approach is important. It is the main advantage of a plain text format. If you cant hack it with vi, why not just use a binary format? Even the Web uses JPEG/GIF binary for 'visual array data'. The point of CIF, I thought, is to keep things human readable. > > Enough philosophy - but it's relevant to my next comment. Joe wrote: > >> I know that global_ is not part of CIF, but neither is this hack for >> using data_global. CIF says global_ is reserved for possible future use. >> Obviously people want a global_, so let's include it. > > If you read Chapter 5.2 of International Tables G carefully, > you will see that the semantics of global_ inheritance in STAR are > actually rather subtle (especially if you also have save_frames > in a STAR file). Although one thinks one knows how to use global_, > I suspect it would be very easy to introduce unexpected inheritances > or context faults, particularly in typical FORTRAN programs or in > manual vi editing. Among other things, it breaks the ability to easily > re-order data blocks. Peter's probably correct that the implied semantics > of data_global are dangerous (although everything should work OK in > Acta CIFs, since care is taken to partition the data names between > blocks in a way that should circumvent collisions of data name). I > still think it would be better to resolve this dilemma by formally > relating the purpose of distinct data blocks in an AUDIT_... category, > rather than by opening the doors to the elegant, but rather dangerous, > global_ block. My view is that is is more sensible to redefine GLOBAL_ than to add on a new hack for data_global. Either way, the rules have to change. I am assuming that nobody else uses the STAR format, so that redefining GLOBAL_ does not break anything, but I could be wrong. If you want to actually define some sort of scope inheritance, why limit it to a single magic data block? Wouldn't it make more sense to have some sort of scoping directive within a data block (i.e inherit data-block XXX). Of course, I am thinking in terms of CIF being mostly self-described, and not completely dependent on a dictionary. Joe
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