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Glycan and molecule structure improvements #829

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LucieLamothe opened this issue May 10, 2022 · 0 comments
Open
1 of 7 tasks

Glycan and molecule structure improvements #829

LucieLamothe opened this issue May 10, 2022 · 0 comments
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concept/term addition Request for a new concept(s), or change(s) to existing concept(s) polishing Does not extend the content or functionality, but improves other qualities

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@LucieLamothe
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  • Add regex for the ID, which is a natural number starting from 1 (at the moment they are max 5 digits, but that may change at some point(how soon?))

done in PR #783

  • Add format for the LINUCS notation (under something like Carbohydrate (sequence/Glycan) format?)
  • Add the citation https://doi.org/10.1016/S0008-6215(01)00230-0 in the format, remove from the LINUCS ID. Perhaps the same with the fully spelled-out synonym.
  • Maybe a comment in the ID, noting the fact about the LINUCS notation
  • Revise all the "Carbohydrate" & "Glyc.." concepts in EDAM (incl. Glycoinformatics😊). For example there is "Carbohydrate structure" which is defined only as 3D structure (not TODO in 2021😉)
  • GlycosciencesDB has 4 formats for "2D" structure: CarbBank, LINUCS, GlycoCT_condensed, GlycoCT_xml. And maybe some of the visualisations should be added? (Not sure)
  • Part of the revision: "Protein" 3D structure formats are usually generic for any molecules, incl. glycans. Revise accordingly.
@matuskalas matuskalas changed the title Molecule strcuture Glycan and molecule structure improvements May 10, 2022
@matuskalas matuskalas added concept/term addition Request for a new concept(s), or change(s) to existing concept(s) polishing Does not extend the content or functionality, but improves other qualities labels May 10, 2022
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concept/term addition Request for a new concept(s), or change(s) to existing concept(s) polishing Does not extend the content or functionality, but improves other qualities
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