Translation of GOLD paths to OWL and mapping to ENVO

This repo contains

1. A rendering of the GOLD ecosystem classification as OWL
2. Mappings of GOLD paths to ENVO expressions

Top level

The top level consists of the 3 gold path roots (environmental, host, engineered), plus the AtomicElement grouping for capturing "atomic" gold words/terms:

id	label
https://w3id.org/gold.path/3964	Environmental
https://w3id.org/gold.path/4086	Host-associated
https://w3id.org/gold.path/4292	Engineered
https://w3id.org/gold.path/AtomicElement	None

Gold path elements

Each gold path class is organized in a tree hierarchy using SubClassOf axioms, and are given a logical definition equivalent to the path; e..

'Environmental > Terrestrial > Geologic > Mine pit pond > Asbestos'
  SubClassOf 'Environmental > Terrestrial > Geologic > Mine pit pond'
  EquivalentTo
    (ECOSYSTEM some Terrestrial) and (ECOSYSTEM-CATEGORY some Geologic) and (ECOSYSTEM-PATH-ID some Environmental) and (ECOSYSTEM-SUBTYPE some Asbestos) and (ECOSYSTEM-TYPE some 'Mine pit pond')

We use 5 different properties for the level-based definitions:

Atomic Elements

Each individual token/term used in a path is classified under AtomicElement; in Protege you can see all usages of that in paths

DL queries

Mapping

Mapping GOLD to ENVO is an example of Complex Mapping. We don't have simple 1-1 relationships representable in SSSOM.

Instead we have mappings between GOLD paths and ENVO expressions. These can be represented in YAML or TSV, and translated to OWL expressions.

Engineered environment example:

- id: GOLDTERMS:5473
  label: Engineered > Bioreactor > Aerobic > Biofilm
  parent: GOLDTERMS:4536
  level: 4
  vocab_differentia: GOLDVOCAB:Biofilm
  mixs_extension:
    id: MIXS:MiscellaneousNaturalOrArtificialEnvironment
    label: MIXS:MiscellaneousNaturalOrArtificialEnvironment
  env_broad:
    id: ENVO:01000313
    label: anthropogenic environment
  env_local:
    id: OBI:0001046
    label: bioreactor
  other:
    id: ENVO:00002034
    label: biofilm

Host-associated example:

- id: GOLDTERMS:5148
  label: Host-associated > Amphibia > Excretory system > Kidney
  parent: GOLDTERMS:4085
  level: 4
  vocab_differentia: GOLDVOCAB:Kidney
  mixs_extension:
    id: MIXS:HostAssociated
    label: MIXS:HostAssociated
  host_taxon:
    id: NCBITaxon:8292
    label: Amphibia
  anatomical_site:
    id: UBERON:0002113
    label: kidney

Environmental:

- id: GOLDTERMS:5413
  label: Environmental > Aquatic > Floodplain > Sediment
  parent: GOLDTERMS:Environmental-Aquatic-Floodplain
  level: 4
  vocab_differentia: GOLDVOCAB:Sediment
  mixs_extension:
    id: MIXS:Sediment
    label: MIXS:Sediment
  env_broad:
    id: ENVO:01000254
    label: environmental system
  env_local:
    id: ENVO:00000255
    label: flood plain
  env_medium:
    id: ENVO:00002007
    label: sediment

• gold_definitions.yaml - base definitions
• gold_definitions_propagated.yaml - base definitions with slots propagated down
• gold_definitions.owl - OWL

TODO: Document semi-automated process

Individual terms to be added to ENVO

https://github.com/EnvironmentOntology/envo/labels/GOLD%2FEBI-MGNIFY