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Meeting Notes 12.02.2021

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Casper Welzel Andersen edited this page Feb 12, 2021 · 1 revision

Participants:

  • Casper Andersen
  • Francesca Bleken
  • James Hester
  • Stuart Chalk
  • Saulius Grazulis
  • Emanuele Ghedini
  • Rickard Armiento
  • Joana Morgado
  • Jesper Friis

Going over the work outlined in issue #16. Emanuele explained how we created the first diagram. Rickard: How about CIF 2? James: The main difference is the addition of extra data types: list and tables (key: value "hash-table"). Loops within loops are not allowed (even though it’s part of the STAR* format, from/on which the CIF data format is derived/based).

Generating the "EMMOnized" CIF ontology from the CIF dictionaries: The goal is to "import" the CIF data dictionaries into our ontology, which can then be referenced and mapped to in a more general "outer" ontology. The general/generic ontology will act as a “catch-em-all” for various ontological concepts for the similar thing. E.g., we can have the concept of a "unit cell", which can be linked to different descriptions of unit cell by different languages like CIF, ASE, etc. Emanuele: We are ontologizing the data, not the CIF syntax.

James: Updated CIF dictionaries in the GitHub repository COMCIFS/cif_core. Python software that understands CIF dictionaries old and new: pip install pycifrw. Development repository for pycifrw: https://bitbucket.org/jamesrhester/pycifrw/src/development/

How do we describe units for different concepts and CIF keys? The latter part of the meeting was spent discussing this subject in-depth. Emanuele: Don’t use EMMO quantities in the CIF language. Jesper: Define units/quantities in the “outer” ontology. Emanuele: Due to CIFs different way of writing quantities (unit-less number), don’t use EMMO quantities, which are based on number+unit (SI). Saulius: The way of writing number values without units is a syntax issue, not semantical issue.

For further reading on crystallographical concepts in general, we recommend:

  • International tables for Crystallography Volume G dedicated to crystallographic ontologies and syntax it.iucr.org/g
  • Fundamentals of Crystallography edited by C. Giacovazzo.
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