NMDC Ontology

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.

Ontology Products

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 some or only, are transformed into simple <subject> <predicate> <object> assertions. For example, in the Environment Ontology, the axiom 'lake water' 'part of' some lake is 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 of relations between classes.

Subsets

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

Term Requests, Errors, and Specific Concerns

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.

Maintenance

See MAINTAINERS.md for instructions on maintaining and updating ontology products and subsets.

Acknowledgements

This ontology repository was initally created using the ontology starter kit. Later edits were made to the Makefile.