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feat: add 15 microbial community records from Europe PMC batch discovery - #2031
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…6) and add Stage 1-3 workflow skills
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
realmarcin
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… connectivity bounds (#2032)
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Summary
Discovers and curates 15 new evidence-backed microbial community records (
CommunityMech:000469throughCommunityMech:000483) from recent Europe PMC literature (25 candidates evaluated; 15 added, 10 rejected/evidence-limited with documented provenance), and adds the repository-localadd-community-record,curate-causal-graphs, andadd-uniprot-protein-examplesskills under.claude/skills/.New Community Records (15)
CommunityMech:000469—Rhodopseudomonas_Escherichia_Multilayered_Cross_Feeding_Coculture(PMID:41965219)CommunityMech:000470—Wetland_Lindane_Degrading_Organochlorine_Consortium(PMID:42661274)CommunityMech:000471—Pseudomonas_Achromobacter_Stenotrophomonas_Prometryn_Degrading_Consortium(PMID:42014650)CommunityMech:000472—Delftia_Klebsiella_Light_Driven_Hydrogen_Denitrifying_Coculture(PMID:41957227)CommunityMech:000473—Clostridium_Acetobutylicum_Ljungdahlii_Isopropanol_Syntrophic_Coculture(PMID:41835933)CommunityMech:000474—Bifidobacterium_Bacillus_Alginate_Biofilm_Probiotic_Coculture(PMID:42214970)CommunityMech:000475—Cold_Seep_ANME_SRB_Carbon_Monoxide_Syntrophic_Consortium(PMID:42249302)CommunityMech:000476—Whale_Fall_Vallitalea_Trichloromonas_Chitin_EET_Consortium(PMID:42321000)CommunityMech:000477—Trichoderma_Burkholderia_Atrazine_Cross_Feeding_Consortium(PMID:42694394)CommunityMech:000478—Halobacillus_Black_Gram_Halophilic_PGPR_Consortium(PMID:42759876)CommunityMech:000479—Bacillus_Pseudomonas_Chili_Root_Rot_Antagonistic_SynCom_T7(PMID:42764446)CommunityMech:000480—Bacillus_Aspergillus_Green_Waste_Vermicomposting_SynCom(PMID:41911722)CommunityMech:000481—Endophytic_SynCom_NS_Brassica_Cadmium_Phytoextraction_Consortium(PMID:42562696)CommunityMech:000482—Cucumber_Low_Phosphorus_Cross_Kingdom_Biocontrol_SynCom(PMID:41882811)CommunityMech:000483—Black_Soil_Glucose_Activated_Herbicide_Mixture_SynCom(PMID:41915538)Adversarial Review Resolution
Rice_Paddy_Methanococcus_Hypophosphite_Syntrophic_Consortium,Watermelon_Rhizosphere_Pseudomonas_Amino_Acid_Cross_Feeding_SynCom_SSC8,Chinese_Fir_Endophytic_Phosphate_Solubilizing_SynCom_P6) and documented them incoverage.json.PMID:42661274,PMID:41911722,PMID:42562696,PMID:41882811,PMID:41915538) with verbatim species-naming snippets from cached OA full text, and added the missing 5th core taxon (Dehalococcoides mccartyi,NCBITaxon:61435) toWetland_Lindane_Degrading_Organochlorine_Consortium.scope: COMMUNITY_LEVEL(omittingsource_taxon/target_taxon) on community-wide emergent functions and replaced inferred pairwise edges inCucumber_Low_Phosphorus_Cross_Kingdom_Biocontrol_SynComwith the 2 explicitly tested pairwise co-culture interactions from Section 2.5 ofPMID:41882811.CommunityMech:000469–CommunityMech:000483), updatedhistory/records/<slug>/*.yaml, re-rendered HTML/JSON/TSV exports, and updated corpus-wide census invariants.Validation
just validate-all(477 records)just validate-strict(0 errors)just validate-referencesacross all 15 new recordsjust check-history(477 current records, 0 issues)just check-site-freshnesspytestcorpus census & schema tests