https://github.com/cmungall/gold-ontology
https://github.com/cmungall/gold-ontology
environment-ontology gold-classification jgi metagenomes
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/cmungall/gold-ontology
- Owner: cmungall
- Created: 2021-06-09T02:47:28.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-01-27T23:08:10.000Z (5 months ago)
- Last Synced: 2025-02-28T05:53:01.844Z (4 months ago)
- Topics: environment-ontology, gold-classification, jgi, metagenomes
- Language: Jupyter Notebook
- Homepage: https://bioportal.bioontology.org/ontologies/GOLDTERMS?p=classes
- Size: 11.8 MB
- Stars: 3
- Watchers: 7
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
# 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 (and other ontology) *expressions*, conforming to MIxS
It can be browsed [on bioportal](https://bioportal.bioontology.org/ontologies/GOLDTERMS?p=classes)
## 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|
|---|---|
||Environmental|
||Host-associated|
||Engineered|
||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..
```owl
'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
![Uploading image.png…]()
# 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:
```yaml
- 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:
```yaml
- 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
```
In the primary OWL file, these are rendered as follows:
1. each slot (mixs_extension, env_broad, etc) is translated to an *annotation property*, the value of which is the ontology IRI
2. An rdfs:comment is added whether labels are used
Other products:
* gold_definitions - base definitions
* [gold_definitions.yaml](gold_definitions.yaml) - base definitions in YAML
* [gold_definitions.csv](gold_definitions.csv) - base definitions as a CSV
* gold_definitions_propagated - base definitions with slots propagated down
* [gold_definitions_propagated.yaml](gold_definitions_propagated.yaml) - propagated definitions in YAML
* [gold_definitions_propagated.yaml](gold_definitions_propagated.yaml) - propagated definitions as CSV
* OWL
* [gold_definitions.owl](gold_definitions.owl) - base file
* [gold_definitions_merged.owl](gold_definitions_merged.owl) - merged ontology
TODO: Document semi-automated process
## Individual terms to be added to ENVO
https://github.com/EnvironmentOntology/envo/labels/GOLD%2FEBI-MGNIFY