aclum

remove logic to repair curies

1

remove two sections of code that repair broken CURIes and validate both the YAML dump and the RDF conversion output. spun out of https://github.com/microbiomedata/nmdc-schema/issues/1869

remove logic to repair curies

1

remove two sections of code that repair broken CURIes and validate both the YAML dump and the RDF conversion output. spun out of https://github.com/microbiomedata/nmdc-schema/issues/1869

Review id_locus pattern for `best_protein` and `all_protein` slots

9

To do when reviewing proteomics collections. Currently there is not an enforced pattern for [best_protein](https://microbiomedata.github.io/berkeley-schema-fy24/best_protein/) or [all_proteins](https://microbiomedata.github.io/berkeley-schema-fy24/all_proteins/) Note: for a subset of annotation files the gene IDs use nmdc:wfmgas instead...

Review id_locus pattern for `best_protein` and `all_protein` slots

9

To do when reviewing proteomics collections. Currently there is not an enforced pattern for [best_protein](https://microbiomedata.github.io/berkeley-schema-fy24/best_protein/) or [all_proteins](https://microbiomedata.github.io/berkeley-schema-fy24/all_proteins/) Note: for a subset of annotation files the gene IDs use nmdc:wfmgas instead...

Identify Mongo documents containing values that are empty lists (`[]`)

21

When doing the re-iding work I noticed in several places we have documents with empty lists Ie many omics_processing_set records have gold_sequencing_project_identifiers with a list size of zero. Should the...

ror is https://ror.org/041mxqs23 use case: ecofab ring 2.0 trail data.

string vs enumeration for GOLD pathway slots

4

I noticed that for GOLD pathway slots https://microbiomedata.github.io/submission-schema/gold_path_field/ the range is an enumeration in the submission portal and a string in nmdc-schema. Since most of the data will come in...

Add OBI values to `meanings`, separate out X and X Plus see https://github.com/obi-ontology/obi/pull/1804/files

These enumerations are needed to update to JGI's annotation pipeline version 5.3. To be worked on after berkeley rollout Depends on https://github.com/microbiomedata/mg_annotation/issues/36

another missing prefix, like the last one we added this isn't expected to be in the data but is a valid term for data portal search https://bioregistry.io/kegg.module:M00002