invalid asserted examples

[turbomam]

poetry run linkml-validate --target-class ExhaustiveTestClassCollection --schema generated_schema/GSC_MIxS_6.yaml extracted_data/mixs_v6.xlsx.extracted_examples.yaml

• ✗ 'coverage and kmer' is not one of ['codon usage', 'combination', 'coverage', 'homology search', 'kmer'] in $.exhaustive_test_set[0].bin_param
• ✗ 'other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)' is not one of ['marker gene', 'other', 'reference based'] in $.exhaustive_test_set[0].compl_appr
• ✗ 'water well (ENVO:01000002)' is not one of ['brackish', 'canal', 'collected rainwater', 'ditch', 'estuary', 'freshwater', 'lake', 'manmade', 'melt pond', 'municipal', 'natural', 'pond', 'reservior', 'river', 'saline', 'storage tank', 'stream', 'well'] in $.exhaustive_test_set[0].farm_water_source[0]
• ✗ 'rinsed with water|scrubbed with brush' is not one of ['drum and drain', 'manual spinner', 'rinsed with sanitizer solution', 'rinsed with water', 'scrubbed with brush', 'scrubbed with hand', 'soaking'] in $.exhaustive_test_set[0].food_clean_proc[0]
• ✗ 'non-binary' is not one of ['female', 'hermaphrodite', 'male', 'neuter'] in $.exhaustive_test_set[0].host_sex
• ✗ 'slatted aluminum awning' is not one of ['bahama shutters', 'exterior roll blind', 'gambrel awning', 'hood awning', 'porchroller awning', 'sarasota shutters', 'slatted aluminum', 'solid aluminum awning', 'sun screen', 'tree', 'trellis', 'venetian awning'] in $.exhaustive_test_set[0].shading_device_type
• ✗ 'other: rpoB gene' is not one of ['16S rRNA gene', 'multi-marker approach', 'other'] in $.exhaustive_test_set[0].tax_ident
• ✗ 'filtration + FeCl Precipitation + ultracentrifugation + DNAse' is not one of ['CsCl density gradient', 'DNAse', 'FeCl Precipitation', 'PEG Precipitation', 'RNAse', 'centrifugation', 'filtration', 'none', 'other', 'targeted sequence capture', 'ultracentrifugation', 'ultrafiltration'] in $.exhaustive_test_set[0].virus_enrich_appr

[turbomam]

• set the examples to empty strings in config/mixs_tables_stage_modifications.tsv
• asserted new examples with comments, as lists if necessary, in config/linkml_stage_mixs_modifications.yaml

[turbomam]

It's seems like there's some confusion among MIxS contributors about what an enumeration is.

The "other: ..." patterns could be written as a patterns like 16S rRNA gene|multi-marker approach|other.*

[turbomam]

It seems like there's also some confusion about how to provide a list of examples. If all of them used "|" as the delimiter, I would have written a parser for that. But there were also "+" and "and" delimited examples

[turbomam]

Enumerated values shouldn't be confused with the {term} [{term_id}] pattern

[turbomam]

The examples ahve been re-written and a slide on this topic has been included in this project's GSC 2023 slide deck.