The NMDC Ontology (NMDCO) is used by the National Microbiome Data Collaborative (NMDC) to annotate multi-omic microbiome metadata. The ontology products are built by merging a number of relevant ontologies (see the import directory) into a single ontology, and then converted into the appropriate product.
The main ontology products generated by this repo are:
- nmdco.owl: An ontology build by merging the ontologies in the import directory.
- nmdco-relation-graph.owl: A version of nmdco.owl that has been transformed into a relation graph. In nmdco-relation-graph.owl, axioms containing quantifiers, such
someoronly, are transformed into simple<subject> <predicate> <object>assertions. For example, in the Environment Ontology, the axiom'lake water' 'part of' some lakeis transformed into simply'lake water' 'part of' lake. This makes the ontology easier to query. - nmdco.json: A JSON version of nmdco-relation-graph.owl.
- nmdco-classes.json: A JSON version of nmdco-relation-graph.owl that contains only the classes and class hierarchy . For example, it does not contain
part ofrelations between classes.
For convenience, we have a extracted a number of subsets from the ontology. These subsets provide terms that can be used as values for the Minimum Information about any (x) Sequence (MIxS) env_broad_scale, env_local_scale, or env_medium attributes.
- astronomical-body-parts-and-manufactured-products.tsv
- astronomical-body-parts.tsv
- manufactured-products.tsv
- non-terrestrial-biomes.tsv
- soil-environmental-materials.tsv
- terrestrial-biomes.tsv
Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology. See CONTRIBUTING.md for guidance.
See MAINTAINERS.md for instructions on maintaining and updating ontology products and subsets.
This ontology repository was initally created using the ontology starter kit. Later edits were made to the Makefile.