This repo contains
- A rendering of the GOLD ecosystem classification as OWL
- Mappings of GOLD paths to ENVO expressions
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 |
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:
Each individual token/term used in a path is classified under AtomicElement; in Protege you can see all usages of that in paths
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
https://github.com/EnvironmentOntology/envo/labels/GOLD%2FEBI-MGNIFY