Structuring Metadata

As mentioned in Structuring Datasets, the atbrepo.yaml file in each dataset directory contains the metadata necessary to describe the dataset in the ACSC database. This metadata must be provided by the user in YAML format according to the following template:

title: "This will appear as the title of the simulation on the ACSC website. Should be enclosed in quotation marks."
notes: "This will appear as a description of the simulation on the ACSC website. Should be enclosed in quotation marks.  If the data is related to a publication, the DOI of the publication can also be included in this field."
program: The name of the program used to carry out the simulation run. Currently supported values are AMBER, GROMACS, and GROMOS.  Only one program name per dataset should be provided.
organization: The organization the uploading user is affiliated with, as outlined in "Contribution Prerequisites".  Currently supported values are bernhardt, chalmers, deplazes, krenske, malde, mduq, omara, smith, and yu.
tags: Freeform text tags for the simulation, prefixed with a hyphen. Note that some tags are prefixed with "item-", as shown below
    - replicate-[number] of [total number]
    - protein-[name of protein]
    - peptide-[name of peptide]
    - lipid-[name of lipid]
    - PDB-[pdb code]
    - solvent-[name of solvent]

A few example metadata files are included for reference:

title: 'D6PC lipid bilayer'
notes: 'A lipid bilayer consisting of 512 D6PC molecules. Initiated from a smaller 128-lipid DLPC equilibrated bilayer with trimmed tails. Pore spontaneously form during the simulation.'
program: GROMACS
organization: mduq
tags:
    - lipid-D6PC
    - lipid bilayer
    - GROMOS
    - 54A7
    - solvent-H2O

title: 'Hen egg-white lysozyme'
notes: "Hen egg-white lysozyme protein with GROMOS 54A7 in AMBER (replicate 1 of 3).  Initial structure obtained from the Protein Data Bank (PDB). PDB ID - 1AKI, URL -  https://www.rcsb.org/structure/1AKI "
program: AMBER
organization: mduq
tags:
    - GROMOS
    - 54A7
    - solvent-H2O
    - replicate-1 of 3
    - PDB-1AKI
    - protein-hen egg-white lysozyme
    - protein

title: 'Alpha-helical peptide AP'
notes: 'Alpha-helical peptide AP with GROMOS 54A7 in GROMOS (replicate 1 of 3).'
program: GROMOS
organization: mduq
tags:
    - GROMOS
    - 54A7
    - solvent-H2O
    - replicate-1 of 3
    - peptide-alpha-helical peptide AP
    - peptide