Schema resources for the National Microbiome Data Collaborative (NMDC)
Project description
National Microbiome Data Collaborative Schema
This repository defines a linkml schema for managing metadata from the National Microbiome Data Collaborative (NMDC). The NMDC is a multi-organizational effort to integrate microbiome data across diverse areas in medicine, agriculture, bioenergy, and the environment. This integrated platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science.
Tasks managed by the repository are:
- Generating the schema
- Converting the schema from it's native LinkML/YAML format into other artifacts
- Deploying the schema as a PyPI package
- Deploying the documentation
Background
The NMDC Introduction to metadata and ontologies primer provides some the context for this project.
See also these slides 
Dependencies
In order to make new release of the schema, you must have the following installed on your sytem:
Maintaining the Schema
See MAINTAINERS.md for instructions on maintaining and updating the schema.
NMDC metadata downloads
See https://github.com/microbiomedata/nmdc-runtime/#data-exports
Ecosystem Diagram
flowchart TD
subgraph nmdc-schema repo
ly([NMDC LinkML YAML files])
lg(generated artifacts)
ly-.make all.->lg
end
subgraph Data Validation
click ly href "https://github.com/microbiomedata/nmdc-schema/tree/main/src/schema" _top
d[(Some data)]
v[[Validation process]]
v--Has input-->d
v--Has input-->ly
end
subgraph MIxS
m([MIxS Schema])
end
subgraph SubmissionPortal
sppg[(Postgres)]
spa[Portal API]
sppg<-->spa
click spa href "https://data.dev.microbiomedata.org/docs" _top
ps[Pydantic schema]
end
subgraph MongoDB
mc[(Collections)]
ms[Implicit schema]
ma[Search API]
mc<-->ma
click ma href "https://api.dev.microbiomedata.org/docs" _top
end
mc --Ingest--> sppg
subgraph DH Template Prep
saf[sheets_and_friends repo]
sps([Submission Portal Schema])
dhjs[Data Harmoizer JS, etc.]
saf-->sps-->dhjs
end
dhjs-->SubmissionPortal
subgraph DataMapping
sa[sample-annotator repo]
end
spa-->sa-..->ma
ly-..->ps
sj[some json]
ly-..->sj-..->MongoDB-..->ps
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