Merge pull request #6 from microbiomedata/wdduncan-readme-patch-1

Update README.md

README.md

@@ -2,36 +2,33 @@
 <!-- ![Build Status](https://github.com/microbiomedata/nmdc-ontology/workflows/CI/badge.svg) -->
 # NMDC Ontology
 
-The NMDC Ontology (NMDCO) is used  by the [National Micrbiome Data Collaborative (NMDC)](https://microbiomedata.org) to provide values for [Minimum Information about any (x) Sequence (MIxS)](https://gensc.org/mixs) terms.
+The NMDC Ontology (NMDCO) is used  by the [National Micrbiome Data Collaborative (NMDC)](https://microbiomedata.org) to annotate metagemoic metadata. The ontlogy products are built by merging a number of relevant ontologies (see the [import directory](src/ontology/imports/)) into a single ontology, and then converted into the appropriate product.
 
-<!-- More information can be found at http://obofoundry.org/ontology/nmdco -->
+## Ontology Products
 
+The main ontology products generated by this repo are:
+- [nmdco.owl](nmdco.owl): An ontology build by merging the in the [import directory](src/ontology/imports/).
+- [nmdco-relation-graph.owl](nmdco-relation-graph.owl): A version of [nmdco.owl](nmdco.owl) that has been transformed into a [relation graph](https://github.com/balhoff/relation-graph). In [nmdco-relation-graph.owl](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](https://github.com/EnvironmentOntology/envo), 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](nmdco.json): A JSON version of [nmdco-relation-graph.owl](nmdco-relation-graph.owl).
+- [nmdco-classes.json](nmdco-classes.json): A JSON version of [nmdco-relation-graph.owl](nmdco-relation-graph.owl) that contains only the classes and class hierarchy . For example, it does not contain `part of` relations between classes.
 
-## Term subsets
-Sets of MIxS terms are provided 
+## Subsets
 
+For convenience, we have a extracted a number of [subsets](subsets/) from the ontology. These subsets provide terms that can be used as values for the [Minimum Information about any (x) Sequence (MIxS)](https://gensc.org/mixs) `env_broad_scale`, `env_local_scale`, or `env_medium` attributes.  
+- [astronomical-body-parts-and-manufactured-products.tsv](subsets/astronomical-body-parts-and-manufactured-products.tsv)
+- [astronomical-body-parts.tsv](subsets/astronomical-body-parts.tsv)
+- [manufactured-products.tsv](subsets/manufactured-products.tsv)
+- [non-terrestrial-biomes.tsv](subsets/non-terrestrial-biomes.tsv)
+- [soil-environmental-materials.tsv](subsets/soil-environmental-materials.tsv)
+- [terrestrial-biomes.tsv](subsets/terrestrial-biomes.tsv)
 
-## Creating term subsets
-Term subsets are created by running `make` on the `query.Makefile` targets. For example, to create the (i.e., `make -f query.Makefile`).
+## Term Requests, Errors, and Specific Concerns
+Please use this GitHub repository's [Issue tracker](https://github.com/microbiomedata/nmdc-ontology/issues) to request new terms/classes or report errors or specific concerns related to the ontology. See [CONTRIBUTING.md](CONTRIBUTING.md) for guidance.
 
-## Versions
+## Maintenance
 
-### Stable release versions
-
-The latest version of the ontology can always be found at:
-
-http://purl.obolibrary.org/obo/nmdco.owl
-
-(note this will not show up until the request has been approved by obofoundry.org)
-
-### Editors' version
-
-Editors of this ontology should use the edit version, [src/ontology/nmdco-edit.owl](src/ontology/nmdco-edit.owl)
-
-## Contact
-
-Please use this GitHub repository's [Issue tracker](https://github.com/microbiomedata/nmdc-ontology/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
+See [MAINTAINERS.md](MAINTAINERS.md) for instructions on maintaining and updating ontology products and subsets.
 
 ## Acknowledgements
 
-This ontology repository was created using the [ontology starter kit](https://github.com/INCATools/ontology-starter-kit)
+This ontology repository was initally created using the [ontology starter kit](https://github.com/INCATools/ontology-starter-kit). Later edits were made to the [Makefile](src/onotology/Makefile).