https://github.com/cmungall/agrovoc-obo
Agrovoc alignment to OBO Ontologies
https://github.com/cmungall/agrovoc-obo
mapping obofoundry ontology ontology-matching sssom
Last synced: 16 days ago
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Agrovoc alignment to OBO Ontologies
- Host: GitHub
- URL: https://github.com/cmungall/agrovoc-obo
- Owner: cmungall
- Created: 2016-04-26T16:17:16.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2016-08-02T12:51:30.000Z (over 8 years ago)
- Last Synced: 2025-02-10T09:45:05.205Z (2 months ago)
- Topics: mapping, obofoundry, ontology, ontology-matching, sssom
- Language: Prolog
- Homepage:
- Size: 2.41 MB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Agrovoc alignment to OBO Ontologies
This is an exploratory project to align Agrovoc to OBO Library ontologies, in order to
* identify gaps in ontologies such as ENVO and TO
* Provide definitions (with full provenance) for OBO classes
* Provide language translations for OBO classes
* To explore the addition of OWL semantics to Agrovoc, beyond what can be done in SKOS
* To explore the possibility of closer integration and collaboration between Agrovoc and OBO communities
For more on OBO, see http://obofoundry.org
## OWL translation of Agrovoc
The prolog program skos2obo.pl translates the skos of agrovoc to OBO/OWL
Note that for compactness we store the OWL in the compact OBO-Format,
but this should be understood to have OWL semantics.
We also provide subset files for convenience. E.g. for aligning to NCBITaxonomy we would use subset-organisms.obo
## Alignments
* [align-envo.tsv](align-envo.tsv) -- alignment to http://obofoundry.org/ontology/envo.html
* [align-ncbitaxon.tsv](align-ncbitaxon.tsv) -- alignment to http://obofoundry.org/ontology/ncbitaxon.html
* [align-pdo.tsv](align-pdo.tsv) -- alignment to http://obofoundry.org/ontology/pdo.html
* [align-po.tsv](align-po.tsv) -- alignment to http://obofoundry.org/ontology/po.html
* [align-to.tsv](align-to.tsv) -- alignment to http://obofoundry.org/ontology/to.html
* [align-uberon.tsv](align-uberon.tsv) -- alignment to http://obofoundry.org/ontology/uberon.html
## Uses
### host-pathogen relationships
See https://github.com/Planteome/plant-stress-ontology
http://globalbioticinteractions.org/
### Food
https://github.com/FoodOntology/foodon/
E.g. https://github.com/FoodOntology/foodon/issues/6
### MIREOTing Agrovoc into OBO Library ontologies
If we can get permission to publish the obo/owl via a purl we can
MIREOT in Agrovoc classes to OBO Library ontologies (would also need
CC-BY).
We would want to swap out some agrovoc PURLs with existing OBO purls -
the above mappings can help with this. For example, we would always
use an NCBITaxon purl for a taxon, or a PO purl for a plant part, a
CHEBI purl for a chemical, etc.
However, with MIREOTing we will run into issues of differing semantics:
```
[Term]
id: http://aims.fao.org/aos/agrovoc/c_928
name: biosynthesis
is_a: http://aims.fao.org/aos/agrovoc/c_27462 ! biochemical reactions
***relationship: makeUseOf http://aims.fao.org/aos/agrovoc/c_2855 ! fermentation
```
not compatible with:
```
id: GO:0006113
name: fermentation
namespace: biological_process
def: "The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP)." [GOC:curators, ISBN:0201090910, ISBN:124925502, MetaCyc:Fermentation]
```