eLignin Ontology

Namespace: http://www.elignindatabase.com/ontology# (prefix elignin:)

This page documents the custom vocabulary terms used in eLignin's BioPAX-based JSON-LD pathway export format. Standard biochemical properties follow the BioPAX Level 3 OWL namespace (bp:). Properties specific to the eLignin database use the elignin: namespace defined here.

Compatibility note: The eLignin JSON-LD export is based on BioPAX Level 3 naming conventions but is not a standards-compliant OWL/RDF document. To convert to canonical BioPAX RDF/XML use pybiopax or a compatible RDF serialiser.

eLignin namespace terms

Term	Full URI	Applies to	Description
elignin:id	http://www.elignindatabase.com/ontology#id	Pathway / Reaction / Substrate / Enzyme / Gene	Internal eLignin database identifier (e.g. P00001, R00001, S00001).
elignin:reacId	http://www.elignindatabase.com/ontology#reacId	BiochemicalPathwayStep	Reaction eLignin ID referenced within a pathway ordering step.
elignin:stepOrder	http://www.elignindatabase.com/ontology#stepOrder	BiochemicalPathwayStep	Integer position of this step within the ordered pathway sequence.
elignin:connections	http://www.elignindatabase.com/ontology#connections	Pathway	Ordered list of <code>PathwayConnection</code> items describing upstream/downstream pathway links. Each item carries <code>elignin:id</code> (linked pathway ID), <code>elignin:direction</code> (<em>upstream</em> or <em>downstream</em>), and <code>elignin:via</code> (intermediate metabolite at the branch/handoff point).
elignin:PathwayConnection	http://www.elignindatabase.com/ontology#PathwayConnection	connections item	eLignin class representing a directed link between two pathways. Used as the <code>@type</code> of each object in the <code>elignin:connections</code> array.
elignin:direction	http://www.elignindatabase.com/ontology#direction	PathwayConnection	Direction of the metabolic flow relative to the current pathway. Allowed values: <em>upstream</em> (the linked pathway feeds into this one) or <em>downstream</em> (this pathway feeds into the linked one).
elignin:via	http://www.elignindatabase.com/ontology#via	PathwayConnection	Common name of the intermediate metabolite at which the two pathways connect (e.g. <em>protocatechuate</em>, <em>catechol</em>).
elignin:funnelingBranch	http://www.elignindatabase.com/ontology#funnelingBranch	Pathway	Named branch of aromatic catabolism that this pathway funnels into (e.g. beta-ketoadipate, catechol, protocatechuate).

BioPAX Level 3 terms (bp:)

The following BioPAX terms are used in eLignin exports and map to the http://www.biopax.org/release/biopax-level3.owl# namespace. Refer to the official BioPAX OWL for authoritative definitions.

Term	Kind	BioPAX definition (summary)
bp:Pathway	Class	A set of interactions/reactions that form a biological process.
bp:BiochemicalReaction	Class	A biochemical conversion that transforms one or more substrates into one or more products.
bp:SmallMolecule	Class	A small chemical compound (metabolite).
bp:Protein	Class	A protein entity; used here to represent enzymes.
bp:Gene	Class	A gene entity.
bp:Catalysis	Class	A control interaction in which an enzyme (controller) catalyses a reaction (controlled).
bp:BiochemicalPathwayStep	Class	An ordered step in a pathway, linking a conversion to its position.
bp:UnificationXref	Class	A cross-reference that provides a database ID for an entity (e.g. PubChem, ChEBI).
bp:PublicationXref	Class	A cross-reference to a publication (DOI, PubMed).
bp:displayName	Property	The preferred human-readable name of an entity.
bp:name	Property	Additional name(s) for an entity.
bp:comment	Property	Free-text annotation or note.
bp:eCNumber	Property	Enzyme Commission number (e.g. 1.13.11.1).
bp:chemicalFormula	Property	Molecular formula of a small molecule (plain text, e.g. C6H6O2, no HTML markup).
bp:chemicalStructure	Property	Canonical SMILES string encoding the 2D molecular structure (e.g. Oc1ccccc1O for catechol). Added by the SMILES migration; see backups/SMILES_FORMAT_ANALYSIS.md.
bp:molecularWeight	Property	Molecular weight of a small molecule (string, Da).
bp:pathwayComponent	Property	Links a Pathway to its constituent reactions/interactions.
bp:pathwayOrder	Property	Ordered list of BiochemicalPathwayStep entries.
bp:left	Property	Substrate(s) consumed on the left side of a reaction.
bp:right	Property	Product(s) produced on the right side of a reaction.
bp:controller	Property	The entity (enzyme/protein) that performs catalysis.
bp:controlled	Property	The reaction that is catalysed.
bp:stepConversion	Property	The conversion (reaction) associated with a pathway step.
bp:nextStep	Property	Links to the next BiochemicalPathwayStep in an ordered sequence.
bp:xref	Property	A cross-reference (UnificationXref or PublicationXref).
bp:db	Property	Database name in a cross-reference (e.g. 'PubChem Compound', 'ChEBI', 'UniProt', 'DOI', 'PubMed', 'Gene Ontology').
bp:id	Property	Identifier value in a cross-reference (e.g. accession number, DOI string, PubMed ID).

Full JSON-LD @context

The complete @context object embedded in every eLignin pathway export. Copy this block to validate or extend the format.

{
  "bp": "http://www.biopax.org/release/biopax-level3.owl#",
  "elignin": "http://www.elignindatabase.com/ontology#",
  "dcterms": "http://purl.org/dc/terms/",
  "xsd": "http://www.w3.org/2001/XMLSchema#",
  "Pathway": "bp:Pathway",
  "BiochemicalReaction": "bp:BiochemicalReaction",
  "SmallMolecule": "bp:SmallMolecule",
  "Protein": "bp:Protein",
  "Gene": "bp:Gene",
  "Catalysis": "bp:Catalysis",
  "BiochemicalPathwayStep": "bp:BiochemicalPathwayStep",
  "UnificationXref": "bp:UnificationXref",
  "PublicationXref": "bp:PublicationXref",
  "PathwayConnection": "elignin:PathwayConnection",
  "displayName": "bp:displayName",
  "name": "bp:name",
  "synonyms": "bp:name",
  "comment": "bp:comment",
  "eCNumber": "bp:eCNumber",
  "formula": "bp:chemicalFormula",
  "smiles": "bp:chemicalStructure",
  "molecular_weight": "bp:molecularWeight",
  "db": "bp:db",
  "id": "bp:id",
  "pathwayComponent": {
    "@id": "bp:pathwayComponent",
    "@type": "@id"
  },
  "pathwayOrder": {
    "@id": "bp:pathwayOrder",
    "@type": "@id"
  },
  "stepConversion": {
    "@id": "bp:stepConversion",
    "@type": "@id"
  },
  "nextStep": {
    "@id": "bp:nextStep",
    "@type": "@id"
  },
  "left": {
    "@id": "bp:left",
    "@type": "@id"
  },
  "right": {
    "@id": "bp:right",
    "@type": "@id"
  },
  "controller": {
    "@id": "bp:controller",
    "@type": "@id"
  },
  "controlled": {
    "@id": "bp:controlled",
    "@type": "@id"
  },
  "xref": {
    "@id": "bp:xref",
    "@type": "@id"
  },
  "generated_at": "dcterms:created",
  "title": "dcterms:title",
  "year": "dcterms:date",
  "author": {
    "@id": "dcterms:creator",
    "@container": "@list"
  },
  "elignin_id": "elignin:id",
  "reac_elignin_id": "elignin:reacId",
  "order": "elignin:stepOrder",
  "connections": "elignin:connections",
  "direction": "elignin:direction",
  "via": "elignin:via",
  "funneling_branch": "elignin:funnelingBranch",
  "pathway_type": "elignin:pathwayType",
  "connecting_substrate_elignin_id": "elignin:connectingSubstrateId"
}