microbiomedata mixs-6-2-release-candidate issues

microbiomedata / mixs-6-2-release-candidate

Proposed, Harmonized MIxS 6.2

https://github.com/GenomicsStandardsConsortium/mixs6.2_release_candidate

MIT License

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more-validation-constraints

#190 turbomam closed 11 months ago
0
find-ontology-mentions probably only detects ontology abbreviations in UPPERCASE

#189 turbomam opened 11 months ago
0
work on mapping tokens to 'taxon' in config/curated-slot-notes-by-text-mining.tsv

#188 turbomam opened 11 months ago
0
move exhaustion checks until after remove-elements-by-deprecation-val ?

#187 turbomam closed 11 months ago
2
linkml-run-examples missing base prefix

#186 turbomam opened 11 months ago
3
Can't instantiate bare checklists because they're mixins ?

#185 turbomam opened 11 months ago
0
Standardize taxon identifiers

#184 turbomam opened 11 months ago
1
FutureWarning: Possible nested set at position 64 and not re.search(patrn, instance)

#183 turbomam closed 11 months ago
0
nose/throat conflicts

#182 turbomam closed 11 months ago
1
Conflicting values for soil_horizon

#181 turbomam closed 11 months ago
5
✗ 'absolutely any text' is not of type 'array' in $.all_slots_test_set[0].host_symbiont

#180 turbomam closed 11 months ago
1
removed per-term ontology versions and browser locations

#179 turbomam opened 11 months ago
0
slots not present in curated-data/build-test-only/AllSlotsTestClassCollection-wrapped-example-data.yaml

#178 turbomam closed 11 months ago
3
ERROR:root:Multiple slots with URI: https://w3id.org/mixs/0000335: ['soil_text_measure', 'texture']; consider giving each a unique slot_uri

#177 turbomam closed 11 months ago
0
many operations are too slow for a real time system, even with only ~ 20 combinations

#176 turbomam opened 11 months ago
0
help elements desired for data harmonizer

#175 turbomam opened 11 months ago
0
More conflict resolution

#174 turbomam closed 11 months ago
0
Expected to hold constant across classes

#173 turbomam opened 11 months ago
1
Do we want slots like `farm_equip` to be validated against the term label/term id syntax, or the AGRO:00000416 parent class?

#172 turbomam opened 11 months ago
2
how do we specify that we want all dynamic enums to be expanded?

#171 turbomam opened 11 months ago
0
first-dynamic-enum

#170 turbomam closed 11 months ago
0
readme-from-emiley

#169 turbomam closed 11 months ago
0
In-lined subsets etc

#168 turbomam closed 11 months ago
0
jinja-templating

#167 turbomam closed 11 months ago
0
the schemasheets could have MIxS terminology in thier top rows

#166 turbomam opened 11 months ago
0
Expected value of food_product_type

#165 ramonawalls opened 11 months ago
2
Cardinality for ENVO terms should be 1 for now

#164 ramonawalls opened 11 months ago
0
just-say-data-harmonizer

#163 turbomam closed 11 months ago
0
Single playground underscore

#162 turbomam closed 11 months ago
0
clearer-nav-bar

#161 turbomam closed 11 months ago
0
relative-paths-from-dh

#160 turbomam closed 11 months ago
0
make-schema-json-earlier

#159 turbomam closed 11 months ago
0
Columns in the Data Harmonizer templates are not currently grouped or ordered in any way

#158 turbomam opened 11 months ago
0
regen-dh-menu-in-gh-action

#157 turbomam closed 11 months ago
0
update .github/workflows/deploy-docs.yaml to trigger `make data_harmonizer/menu.json`

#156 turbomam closed 11 months ago
0
top-30-pct-combos

#155 turbomam closed 11 months ago
0
implemented structured_patterns

#154 turbomam closed 11 months ago
0
things to look up in NCBI BIosample

#153 turbomam opened 11 months ago
1
migrate slots that currently have explicit `pattern`s to using `structured_pattern`s

#152 turbomam closed 11 months ago
0
Do Expected value "room name;room number" and Value syntax "{text};{integer}" indicate both components must be present?

#151 turbomam opened 11 months ago
0
which to trust when the examples doesn't match the informal MIxS specifications (Value syntax, etc)

#150 turbomam opened 11 months ago
0
make sure I understand `structured_pattern`'s `interpolated` and `partial_match` options

#149 turbomam closed 11 months ago
1
how to generate LinkML with structured_patterns materialized in code?

#148 turbomam closed 11 months ago
1
`gen-linkml ... --materialize-patterns` emits most verbose form of LinkML YAML

#147 turbomam opened 11 months ago
1
don't see how to utilize structured_patterns without `gen-linkml ... --materialize-patterns`

#146 turbomam closed 11 months ago
1
#141

#145 turbomam closed 11 months ago
0
all-combos schema JSON too large to push to GitHub

#144 turbomam opened 11 months ago
1
generate-combo-ids

#143 turbomam closed 11 months ago
0
way-too-much

#142 turbomam closed 11 months ago
0
what's required to remove this "error" from SchemaMaker.create_schema

#141 turbomam closed 11 months ago
0