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microbiomedata
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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
1 year ago
0
find-ontology-mentions probably only detects ontology abbreviations in UPPERCASE
#189
turbomam
opened
1 year ago
0
work on mapping tokens to 'taxon' in config/curated-slot-notes-by-text-mining.tsv
#188
turbomam
opened
1 year ago
0
move exhaustion checks until after remove-elements-by-deprecation-val ?
#187
turbomam
closed
1 year ago
2
linkml-run-examples missing base prefix
#186
turbomam
opened
1 year ago
6
Can't instantiate bare checklists because they're mixins ?
#185
turbomam
opened
1 year ago
0
Standardize taxon identifiers
#184
turbomam
opened
1 year ago
1
FutureWarning: Possible nested set at position 64 and not re.search(patrn, instance)
#183
turbomam
closed
1 year ago
0
nose/throat conflicts
#182
turbomam
closed
1 year ago
1
Conflicting values for soil_horizon
#181
turbomam
closed
1 year ago
5
✗ 'absolutely any text' is not of type 'array' in $.all_slots_test_set[0].host_symbiont
#180
turbomam
closed
1 year ago
1
removed per-term ontology versions and browser locations
#179
turbomam
opened
1 year ago
0
slots not present in curated-data/build-test-only/AllSlotsTestClassCollection-wrapped-example-data.yaml
#178
turbomam
closed
1 year 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
1 year ago
0
many operations are too slow for a real time system, even with only ~ 20 combinations
#176
turbomam
opened
1 year ago
0
help elements desired for data harmonizer
#175
turbomam
opened
1 year ago
0
More conflict resolution
#174
turbomam
closed
1 year ago
0
Expected to hold constant across classes
#173
turbomam
opened
1 year 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
1 year ago
2
how do we specify that we want all dynamic enums to be expanded?
#171
turbomam
opened
1 year ago
0
first-dynamic-enum
#170
turbomam
closed
1 year ago
0
readme-from-emiley
#169
turbomam
closed
1 year ago
0
In-lined subsets etc
#168
turbomam
closed
1 year ago
0
jinja-templating
#167
turbomam
closed
1 year ago
0
the schemasheets could have MIxS terminology in thier top rows
#166
turbomam
opened
1 year ago
0
Expected value of food_product_type
#165
ramonawalls
opened
1 year ago
2
Cardinality for ENVO terms should be 1 for now
#164
ramonawalls
opened
1 year ago
0
just-say-data-harmonizer
#163
turbomam
closed
1 year ago
0
Single playground underscore
#162
turbomam
closed
1 year ago
0
clearer-nav-bar
#161
turbomam
closed
1 year ago
0
relative-paths-from-dh
#160
turbomam
closed
1 year ago
0
make-schema-json-earlier
#159
turbomam
closed
1 year ago
0
Columns in the Data Harmonizer templates are not currently grouped or ordered in any way
#158
turbomam
opened
1 year ago
0
regen-dh-menu-in-gh-action
#157
turbomam
closed
1 year ago
0
update .github/workflows/deploy-docs.yaml to trigger `make data_harmonizer/menu.json`
#156
turbomam
closed
1 year ago
0
top-30-pct-combos
#155
turbomam
closed
1 year ago
0
implemented structured_patterns
#154
turbomam
closed
1 year ago
0
things to look up in NCBI BIosample
#153
turbomam
opened
1 year ago
1
migrate slots that currently have explicit `pattern`s to using `structured_pattern`s
#152
turbomam
closed
1 year ago
0
Do Expected value "room name;room number" and Value syntax "{text};{integer}" indicate both components must be present?
#151
turbomam
opened
1 year ago
0
which to trust when the examples doesn't match the informal MIxS specifications (Value syntax, etc)
#150
turbomam
opened
1 year ago
0
make sure I understand `structured_pattern`'s `interpolated` and `partial_match` options
#149
turbomam
closed
1 year ago
1
how to generate LinkML with structured_patterns materialized in code?
#148
turbomam
closed
1 year ago
1
`gen-linkml ... --materialize-patterns` emits most verbose form of LinkML YAML
#147
turbomam
opened
1 year ago
1
don't see how to utilize structured_patterns without `gen-linkml ... --materialize-patterns`
#146
turbomam
closed
1 year ago
1
#141
#145
turbomam
closed
1 year ago
0
all-combos schema JSON too large to push to GitHub
#144
turbomam
opened
1 year ago
1
generate-combo-ids
#143
turbomam
closed
1 year ago
0
way-too-much
#142
turbomam
closed
1 year ago
0
what's required to remove this "error" from SchemaMaker.create_schema
#141
turbomam
closed
1 year ago
0
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