Molecule metadata schema

Molecular metadata is described in the template SchemaValidation/Schema/metadata_template.yaml which is distributed with the package.

##################################################################################
## Mandatory fields for the metadata template.
# This template is used to describe the metadata of a molecule metadata.yaml file
# in a standardized way.
##################################################################################
NMRlipids:
  id: string
  name: string
  charge: integer # The charge of the molecule, e.g. 0 for neutral, -1 for anionic, +1 for cationic

# Chemical identifiers for the molecule serving as a unique identifier
  # The identifier.org prefix is used to look up the identifier in the 
  # identifiers.org database.
  # The value is the unique identifier for the molecule in that database
  # For example, pubchem.compound: 5497103 means that the molecule can be 
  # found at https://identifiers.org/pubchem.compound/5497103
  # The identifiers are used to link the molecule to other databases and resources
  # All identifier fields are optional, but at least one should be provided.
sameAs:
  #key names must correspond to the identifier.org prefix
  # test lookup at https://identifiers.org/[prefix]/[value]
  pubchem.compound: integer
  ChEBI: string
  lipidmaps: string
  metabolights: string
  slm: string
  pdb.ligand: string
  unii: string
  cas: string

# Bioschema properties for the molecule
# These properties are used to describe the molecule in a standardized way
# and are used by the Bioschemas community to improve discoverability
# and interoperability of molecular data.
# The properties are based on the Bioschemas Molecule schema
# https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE
bioschema_properties:
  name: string
  # This is the IUPAC name, which is a systematic way to name chemical compounds
  iupacName: string
  molecularFormula: string
  molecularWeight: number
  # InChI is a standard way to represent chemical substances
  # It is a text string that encodes the molecular structure
  # InChIKey is a hashed version of the InChI, used for easier searching
  # Both are used to uniquely identify chemical substances
  # In case that multiple protonation states exist, multiple InChis and 
  # InChIKeys may be provided
  inChI: string
  inChIKey: string
  smiles: string
  # Either a url or a file path to the 2D or 3D structure of the molecule
  image: string
  description: string
  alternateName:
    - string

# Additonal properties for the molecule, not covered by bioschema_properties
properties: