cmungall/agrovoc-obo

Agrovoc alignment to OBO Ontologies

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 -- alignment to http://obofoundry.org/ontology/envo.html
• align-ncbitaxon.tsv -- alignment to http://obofoundry.org/ontology/ncbitaxon.html
• align-pdo.tsv -- alignment to http://obofoundry.org/ontology/pdo.html
• align-po.tsv -- alignment to http://obofoundry.org/ontology/po.html
• align-to.tsv -- alignment to http://obofoundry.org/ontology/to.html
• 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. FoodOntology/foodon#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]