diff --git a/data/traits/environment/alkaphilic.yaml b/data/traits/environment/alkaphilic.yaml index 974d85f5..a20e9039 100644 --- a/data/traits/environment/alkaphilic.yaml +++ b/data/traits/environment/alkaphilic.yaml @@ -98,6 +98,7 @@ causal_graphs: - reference: DOI:10.1016/j.bbamem.2005.09.010 snippet: promote proton capture and retention notes: Review supports proton capture/retention mechanisms in alkaline pH homeostasis. + predicate_id: METPO:2000208 - subject: cytoplasmic_ph_homeostasis predicate: enables object: alkaphilic_trait @@ -162,3 +163,9 @@ curation_history: changes: Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000208×1). + llm_assisted: true diff --git a/data/traits/environment/euryhaline.yaml b/data/traits/environment/euryhaline.yaml index 0c44e4e6..a6651bb6 100644 --- a/data/traits/environment/euryhaline.yaml +++ b/data/traits/environment/euryhaline.yaml @@ -98,6 +98,7 @@ causal_graphs: snippet: biosynthesis and/or uptake of compatible solutes notes: Review supports compatible-solute uptake and biosynthesis as bacterial salt-stress responses. + predicate_id: METPO:2000208 - subject: compatible_solutes predicate: mitigates object: osmotic_imbalance @@ -172,3 +173,9 @@ curation_history: changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000208×1). + llm_assisted: true diff --git a/data/traits/environment/facultatively_alkaphilic.yaml b/data/traits/environment/facultatively_alkaphilic.yaml index e6c86aea..2f931906 100644 --- a/data/traits/environment/facultatively_alkaphilic.yaml +++ b/data/traits/environment/facultatively_alkaphilic.yaml @@ -105,6 +105,7 @@ causal_graphs: - reference: DOI:10.1016/S0005-2728(00)00285-1 snippet: Na+ efflux notes: Supports sodium efflux through Na+/H+ antiporters. + predicate_id: METPO:2000209 - subject: sodium_proton_antiporter predicate: accumulates object: proton @@ -114,6 +115,7 @@ causal_graphs: - reference: DOI:10.1016/S0005-2728(00)00285-1 snippet: net H+ accumulation notes: Supports proton accumulation by antiporters in alkaliphiles. + predicate_id: METPO:2000210 - subject: cytoplasmic_ph_homeostasis predicate: enables object: facultatively_alkaphilic_trait @@ -189,3 +191,9 @@ curation_history: changes: Overwrote 2 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000209×1, METPO:2000210×1). + llm_assisted: true diff --git a/data/traits/environment/halophily_preference.yaml b/data/traits/environment/halophily_preference.yaml index 24c6fa1f..cfa50a65 100644 --- a/data/traits/environment/halophily_preference.yaml +++ b/data/traits/environment/halophily_preference.yaml @@ -110,6 +110,7 @@ causal_graphs: snippet: biosynthesis and/or uptake of compatible solutes notes: Review supports uptake and biosynthesis of compatible solutes in bacterial high-salinity responses. + predicate_id: METPO:2000208 - subject: compatible_solutes predicate: mitigates object: osmotic_stress @@ -186,3 +187,9 @@ curation_history: changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000208×1). + llm_assisted: true diff --git a/data/traits/environment/halotolerant.yaml b/data/traits/environment/halotolerant.yaml index 31f9383d..face7d69 100644 --- a/data/traits/environment/halotolerant.yaml +++ b/data/traits/environment/halotolerant.yaml @@ -90,6 +90,7 @@ causal_graphs: snippet: biosynthesis and/or uptake of compatible solutes notes: Adds explicit source support for transport-mediated compatible-solute accumulation in bacterial salt-stress responses. + predicate_id: METPO:2000208 - subject: compatible_solutes predicate: contributes to object: stress_protection @@ -161,3 +162,9 @@ curation_history: changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000208×1). + llm_assisted: true diff --git a/data/traits/environment/non_halophilic.yaml b/data/traits/environment/non_halophilic.yaml index 0550661b..75b0b794 100644 --- a/data/traits/environment/non_halophilic.yaml +++ b/data/traits/environment/non_halophilic.yaml @@ -110,6 +110,7 @@ causal_graphs: - reference: DOI:10.1128/AEM.01934-12 snippet: osmotically controlled uptake systems notes: Supports uptake systems for compatible solutes in Bacillus subtilis. + predicate_id: METPO:2000208 - subject: proline predicate: enables tolerance of object: high_osmolarity @@ -161,3 +162,9 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001657×1). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000208×1). + llm_assisted: true diff --git a/data/traits/environment/obligately_aerobic.yaml b/data/traits/environment/obligately_aerobic.yaml index c735964a..59f76518 100644 --- a/data/traits/environment/obligately_aerobic.yaml +++ b/data/traits/environment/obligately_aerobic.yaml @@ -71,6 +71,7 @@ causal_graphs: - reference: DOI:10.1016/j.celrep.2023.112444 snippet: transfer electrons from the ETC to O2 notes: Supports oxygen reduction by terminal oxidases in an obligate aerobe. + predicate_id: METPO:2000017 - subject: electron_transport_chain predicate: includes object: terminal_oxidases @@ -147,3 +148,9 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:has_part×1). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000017×1). + llm_assisted: true diff --git a/data/traits/environment/obligately_alkaphilic.yaml b/data/traits/environment/obligately_alkaphilic.yaml index d623c9ce..7eea28de 100644 --- a/data/traits/environment/obligately_alkaphilic.yaml +++ b/data/traits/environment/obligately_alkaphilic.yaml @@ -93,6 +93,7 @@ causal_graphs: - reference: DOI:10.1016/S0005-2728(00)00285-1 snippet: Na+ efflux notes: Supports sodium efflux as part of the alkaliphile Na+ cycle. + predicate_id: METPO:2000209 - subject: sodium_proton_antiporter predicate: accumulates object: proton @@ -102,6 +103,7 @@ causal_graphs: - reference: DOI:10.1016/S0005-2728(00)00285-1 snippet: achieve net H+ accumulation notes: Supports proton accumulation by antiporters in alkaliphiles. + predicate_id: METPO:2000210 - subject: proton_coupled_atp_synthase predicate: regulates object: obligately_alkaphilic_trait @@ -189,3 +191,9 @@ curation_history: changes: Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK). llm_assisted: true +- timestamp: '2026-06-16T06:30:55Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000209×1, METPO:2000210×1). + llm_assisted: true diff --git a/data/traits/environment/slightly_halophilic.yaml b/data/traits/environment/slightly_halophilic.yaml index 4a91cbf1..a1c81043 100644 --- a/data/traits/environment/slightly_halophilic.yaml +++ b/data/traits/environment/slightly_halophilic.yaml @@ -87,6 +87,7 @@ causal_graphs: snippet: organic osmotic solutes notes: Review supports accumulation of organic osmotic solutes in bacterial osmoadaptation. + predicate_id: METPO:2000210 curation_history: - timestamp: '2026-05-05T01:35:46.863572+00:00' curator: seed_from_metpo @@ -139,3 +140,9 @@ curation_history: changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK). llm_assisted: true +- timestamp: '2026-06-16T06:30:56Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000210×1). + llm_assisted: true diff --git a/data/traits/metabolism/aerobic_respiration.yaml b/data/traits/metabolism/aerobic_respiration.yaml index f9588ca4..be44ee03 100644 --- a/data/traits/metabolism/aerobic_respiration.yaml +++ b/data/traits/metabolism/aerobic_respiration.yaml @@ -91,6 +91,7 @@ causal_graphs: - reference: DOI:10.1146/annurev.biophys.27.1.329 snippet: electron transfer from cytochrome c to molecular oxygen notes: Supports oxygen as terminal electron acceptor for cytochrome c oxidase. + predicate_id: METPO:2000017 - subject: molecular_oxygen predicate: reduced to object: water @@ -180,3 +181,9 @@ curation_history: changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.' llm_assisted: true +- timestamp: '2026-06-16T06:30:56Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2000017×1). + llm_assisted: true diff --git a/mappings/predicate_grounding.tsv b/mappings/predicate_grounding.tsv index cfda7f85..79ec39e4 100644 --- a/mappings/predicate_grounding.tsv +++ b/mappings/predicate_grounding.tsv @@ -87,3 +87,7 @@ serves as electron donor and acceptor METPO:2007603 serves as electron donor and donates electrons to METPO:2007403 transfers electrons to skos:closeMatch METPO high maps to existing proposals/metpo_traitmech_v2 predicate 'transfers electrons to'; lithotrophic donor -> ETC provides electrons to METPO:2007403 transfers electrons to skos:closeMatch METPO high maps to existing proposals/metpo_traitmech_v2 predicate 'transfers electrons to'; donor -> photosynthetic ET provides electrons for METPO:2007402 feeds electrons into skos:closeMatch METPO high maps to existing proposals/metpo_traitmech_v2 predicate 'feeds electrons into'; H2 -> Wood-Ljungdahl pathway +imports METPO:2000208 imports skos:exactMatch METPO high exact label match against existing METPO ObjectProperty; transporter -> imported chemical +exports METPO:2000209 exports skos:exactMatch METPO high exact label match against existing METPO ObjectProperty; antiporter -> exported ion +accumulates METPO:2000210 accumulates skos:exactMatch METPO high exact label match against existing METPO ObjectProperty; transporter -> accumulated solute +reduces METPO:2000017 reduces skos:exactMatch METPO high exact label match against existing METPO ObjectProperty; redox sense (oxidase -> O2), paired with oxidizes (METPO:2000016) diff --git a/pages/category/ecology.html b/pages/category/ecology.html index a4211c7c..f622fb1c 100644 --- a/pages/category/ecology.html +++ b/pages/category/ecology.html @@ -244,7 +244,7 @@

ECOLOGY (26)