Schema: cultivation hardware setup (instrument + mode) + standardized vocab#171
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… vocab Adds an OPTIONAL, multivalued cultivation_setup to MicrobialCommunity capturing the hardware/instrumentation and operating mode used to grow/sustain a community (not all communities have one). Schema-first; datamodel regenerated. - Two enums: CultivationModeEnum (BATCH, FED_BATCH, CONTINUOUS, SEMI_CONTINUOUS, CHEMOSTAT, TURBIDOSTAT, PERFUSION, SEQUENCING_BATCH, RETENTOSTAT, OTHER) and CultivationSystemEnum (stirred-tank/photo/membrane/gas-lift/packed-bed/hollow- fiber bioreactors, microbial fuel cell, bioelectrochemical system, chemostat vessel, serum bottle, flask, microfluidic device, bioreactor-unspecified, other). - CultivationSetup class: mode + system + instrument/manufacturer detail, working volume, operating temperature, feed/dilution rate, retention time (HRT/SRT), applied potential + electrode detail (bioelectrochemical), pH/DO/temp control flags, protocol_url, notes, evidence. - New optional top-level slot cultivation_setup (multivalued, inlined_as_list). Standardized terms maintained in vocab/cultivation_terms.yaml (label, definition, synonyms, ontology mapping, status) — staged for a future METPO proposal. Only a confirmed mapping is asserted: BIOREACTOR_UNSPECIFIED -> OBI:0001046 (meaning: on the enum + status: mapped); all others are metpo-candidate. OBI prefix added. tests/test_cultivation_vocab_sync.py keeps the enums and vocab keys in exact sync, checks term well-formedness and meaning:<->vocab consistency, and smoke-tests a populated cultivation_setup. Demonstrated on the Shewanella-Geobacter exoelectrogenic biofilm community (BIOELECTROCHEMICAL_SYSTEM). Verified: gen-python, lint (black/ruff/mypy), validate-products (blocking, unaffected), validate-strict (265 files, 0 errors), 197 pytest pass. validate-schema-terms resolves OBI:0001046 (warn-only, same as existing CHEBI enum mappings; not a CI gate). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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…#173) Lifts the cultivation hardware/mode slice added in PR #171 into a new METPO proposal cohort: CultivationModeEnum (10 leaves), CultivationSystemEnum (13 minted leaves + BIOREACTOR_UNSPECIFIED mapped to existing OBI:0001046), under a new "microbial community cultivation setup" domain class, plus 3 cultivation object properties. - Classes: METPO:1008100-1008132 (above the v1 high-water mark 1008013; no overlap) - Predicates: METPO:2008100-2008102 (above 2008002) - Subset: metpo_communitymech_2026_06 - Term metadata reused from vocab/cultivation_terms.yaml Verified: ROBOT column counts (11/12), full enum coverage, parent integrity, no duplicate or v1-overlapping IDs. METPO submission is downstream/external. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
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Adds an optional, multivalued
cultivation_setuptoMicrobialCommunitycapturing the hardware/instrumentation and operating mode used to grow/sustain a community (not all communities have one). Schema-first; datamodel regenerated.What's added
CultivationModeEnum— BATCH, FED_BATCH, CONTINUOUS, SEMI_CONTINUOUS, CHEMOSTAT, TURBIDOSTAT, PERFUSION, SEQUENCING_BATCH, RETENTOSTAT, OTHER.CultivationSystemEnum— stirred-tank / photo / membrane / gas-lift / packed-bed / hollow-fiber bioreactors, microbial fuel cell, bioelectrochemical system, chemostat vessel, serum bottle, flask, microfluidic device, bioreactor-unspecified, other.CultivationSetupclass — mode + system + instrument/manufacturer detail, working volume, operating temperature, feed/dilution rate, retention time (HRT/SRT), applied potential + electrode detail (bioelectrochemical), pH/DO/temp control flags, protocol_url, notes, evidence.cultivation_setup(multivalued,inlined_as_list).Vocab file + METPO staging
vocab/cultivation_terms.yamlcarries each term's label/definition/synonyms/mapping/status — the curation + METPO-staging source (the inline enums stay canonical for LinkML). Only a confirmed mapping is asserted:BIOREACTOR_UNSPECIFIED → OBI:0001046(meaning:on the enum, statusmapped); everything else ismetpo-candidate/proposedfor a future METPO proposal. OBI prefix added.tests/test_cultivation_vocab_sync.pykeeps enum keys == vocab keys, checks term well-formedness andmeaning:↔vocab consistency, and smoke-tests a populatedcultivation_setup. Demonstrated on the Shewanella–Geobacter exoelectrogenic biofilm community.Verification
just gen-python,just lint(black/ruff/mypy)just validate-products(blocking id↔label gate) — unaffected (enum/freetext-valued, no Term grounding)just validate-strict— 265 files, 0 errorsvalidate-schema-termsresolves OBI:0001046 (warn-only label note, same as existing CHEBI enum mappings; not a CI gate)METPO proposal generation is a deliberate follow-up (per the agreed scope).
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