Definitional Hashes

[For technical and scientific users]
Each substances has a definitional hash that provides a concise, machine-readable definition of the factors that make each substance unique. The idea is that 2 substances that share the same definitional hash are probably equivalent.

The definitional hash consists of a collection of DefinitionalElement objects (key/value/layer triplets)

• Key – what the factor is
• Value – factor’s specific result for one substance
• Layer – how central the factor is to our thinking about this substance (currently, either 1 or 2)

Each substance type has its own keys that define its definitional hash.

Chemical:

• Stereo insensitive hash - a hash of the chemical structure that ignores stereochemistry (layer 1)
• Exact hash - a hash of the chemical structure that includes stereochemistry (layer 2)
• Stereochemistry - (Absolute|Achiral|Epimeric|Mixed|Racemic|Unknown) (layer 2)
• Optical Activity -(+|-|+/-|Unspecified|None) (layer 2)
• Moieties (repeat Stereo insensitive hash, Exact hash, Stereochemistry, and Optical Activity, plus amount for each fragment).

Mixture:

• ID of each component (layer 1)
• Type (any/all...) of each component (layer 2)
• Parent substance ID (layer 2)
• Modifications (structural, agent and physical; see explanation, below) (layer 2)

Nucleic Acid:

• Sequence of bases in each subunit (layer 1)
• Linkages (including sites) (layer 2)
• Sugars (sugar identity and sites) (layer 2)
• Modifications (structural, agent and physical; see explanation, below) (layer 2)

Polymer:

• Monomer IDs (layer 1)
• Monomer amounts (layer 2)
• Structural units' exact structure hash (layer 1)
• Structural units' amounts (layer 2)
• Modifications (structural, agent and physical; see explanation, below) (layer 2)
• Properties (only when flagged as 'defining') (name/value pairs for the property itself and for associated property parameters) (layer 2)

Protein:

• Subunits (after subunits are ordered canonically, index, amino acid sequence and length for each subunit) (layer 1)
• Glycosylation sites (O, N and C; the sites and the type of glycosylation) (layer 2)
• Disulfide links (layer 2)
• Other links (layer 2)
• Modifications (structural, agent and physical; see explanation, below) (layer 2)

Specified substance group 1:

• Constituent IDs (layer 1)
• Constituent roles (layer 2)
• Constituent amounts (layer 2)
• Modifications (structural, agent and physical; see explanation, below) (layer 2)
• Properties (only when flagged as 'defining') (name/value pairs for the property itself and for associated property parameters) (layer 2)

Structurally diverse:

• Parent substance ID (layer 1)
• Family, genus, species values (layer 1)
• Author (layer 2)
• Part (layer 1)
• Part location (layer 2)
• Source material class (layer 1)
• Source material type (layer 1)
• Fraction name (layer 1)
• Fraction material type (layer 1)
• Infraspecific type (layer 2)
• Infraspecific name (layer 2)
• Modifications (structural, agent and physical; see explanation, below) (layer 2)
• Properties (only when flagged as 'defining') (name/value pairs for the property itself and for associated property parameters) (layer 2)

Concept:

• Primary name (layer 1)

Modifications (type of collection common to several substance types)

• For agent modifications, the ID of the agent substance (layer 2)
• Amount (layer 2)
• For physical modifications, the modification group (layer 2)
• For physical and structural modifications, the modification role (layer 2)
• For structural modifications, the residue modified (layer 2)

[Under construction]