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rd-alliance / metadata-directory

Prototype metadata directory for the Research Data Alliance:
http://rd-alliance.github.io/metadata-directory/
MIT License
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pdbx-mmcif.md #32

Closed jdwestbrook closed 9 years ago

jdwestbrook commented 9 years ago

This file describes the metadata framework used for archiving macromolecular structure data by the Protein Data Bank.

alex-ball commented 9 years ago

Thanks for your submission. Before we merge it in, please could you look at the following issues:

  1. 'subjects' uses a controlled vocabulary and should be one or more of
    • arts-and-humanities
    • engineering
    • general
    • life-sciences
    • physical-sciences-and-mathematics
    • social-and-behavioral-sciences
  2. 'disciplines' uses a controlled vocabulary. For the terms currently in use, look at _data/disciplines.yaml. Please use the encoded version that comes after /resources/metadata-standards/disciplinary/ in that file, e.g. metabolic-biochemistry. If needed, new terms can be derived from the more granular terms in HESA JACS3.
  3. The link http://mmcif.wwpdb.org/ looks like it should be under website rather than specification_url.
  4. You have a typo: Crystallogarphic
  5. Under mappings and sponsors please use full URLs, i.e. including the initial http://, otherwise they will not work when transformed to HTML.
  6. Under version you do not need to specify "Current Version", this is assumed.
  7. Under description you have a typo: "depositon". Would it be possible to have a little more on mmCIF and what the standard is used for?
alex-ball commented 9 years ago

Please could you also change the name value to pdbx-mmcif to match the file name.

jdwestbrook commented 9 years ago

Please let me know if further changes are required.

alex-ball commented 9 years ago

Thanks for making those changes, much appreciated. Just a few more:

  1. Just today I found that the behaviour of the engine that generates the site has changed, so we have had to change the top level name field (where you have pdbx-mmcif) to be called slug instead. Sorry about that.
  2. The discipline names also have to be in 'slug' format, e.g. physics, structural-chemistry. Perhaps more obscurely, we have abbreviated 'Molecular biology, biophysics & biochemistry' to the slug 'molecular-biology'.
  3. Could you add a little more to the description, explaining about mmCIF and what the standard is used for? Also, it looks like the 'depositon' typo is still there.