v8.0.0

Curated release notes

Overhaul of the definition and usage of CURIe prefixes.

• Most notably, the default_curi_maps assertions have been
  removed from all schema source file, like src/schema/nmdc.yaml. All prefixes that will be used in the schema
  (slot_uris, mappings, id_prefixes, etc.) must be defined in either nmdc.yaml or another source field that it
  imports. There is now a single, auto-generated file that contains all prefix definitions across the merged schema:
  project/jsonld/nmdc.context.jsonld. Note that it uses two patterns for expanding prefixes. Both are accessed from the
  @context outer key.
  • direct: "EFO": "http://www.ebi.ac.uk/efo/"
  • via an @id inner key: "ENVO": { "@id": "http://purl.obolibrary.org/obo/ENVO_"}.
    Other keys in these dictionaries can usually be ignored.
• The GOLD prefix is no longer allowed in the schema or any schema compliant data. Only gold is allowed now.
• A discussion of prefixes, CURIes, identifiers and mappings has been added: src/docs/prefixes_curies_ids_mappings_etc.md
• https://bioregistry.io is now consistently preferred over http://identifiers.org as a CURIe resolving service.
  The version is this release is a draft, and community members are welcome to ask questions or make suggestions.

New data migration code:

• Extractions must replace usages of the sample_mass slot with input_mass
• replacement of GOLD prefixes with gold prefixes in three classes
• updates to src/data files: /valid shows the post migration state.

Other

• SPARQL queries have been added or updated in assets/sparql
  • see also nmdc_schema/class_sparql.py
• example python QC code, using LinkML SchemaView, has been added
  • nmdc_schema/list_id_prefixes_and_patterns.py
  • nmdc_schema/list_slot_usages.py
  • nmdc_schema/list_structured_patterns.py
• many definitional attributes of slots have been moved out of per-class slot_usage blocks.
  Especially in src/schema/workflow_execution_activity.yaml. Likewise, all class should not assert their slots with a
  slots list, not implicitly via the slot_usage blocks. required: true, customized ranges and customized descriptions
  can still be found in slot_usage blocks. Not that some of these are non-monotonic and need further attention.
  An example would be when the global definition of a slot uses an enumeration range but a slot_usage uses a string range.

Auto-generated (but equally important) release notes

• Remove invalid water content examples by @aclum in #1084
• Issue1031 input sample mass by @brynnz22 in #1109
• Issue 24 omics processing move by @brynnz22 in #1118
• Issue1097 study consortia by @brynnz22 in #1098
• update nucleicAcidQuantMethod mapping by @brynnz22 in #1036
• Prefixes standardization (no default curi maps) and making some slot_usage attributes global by @turbomam in #1116

Full Changelog: v7.8.0...v8.0.0