feat: associate voltage-gated and store-operated Ca2+ channels with MAR11311

data/testResults/README.md

@@ -21,11 +21,11 @@ own files. The pull request in each row is the one whose run last wrote those fi
 
 | Result file(s) | Produced by | Last updated by |
 | --- | --- | --- |
-| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) |
-| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) |
-| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) |
-| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) |
-| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) |
+| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1033** (model QC checks) |
+| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1033** (model QC checks) |
+| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1033** (model QC checks) |
+| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1033** (MACAW and balance) |
+| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1033** (MEMOTE) |
 | `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) |
 
 ## 2. What each check means

data/testResults/memote_score.md

@@ -14,7 +14,7 @@ Skipped (slow) tests: test_stoichiometric_consistency, test_unconserved_metaboli
 | consistency | 42.4% |
 | annotation_met | 73.0% |
 | annotation_rxn | 72.7% |
-| annotation_gene | 46.7% |
+| annotation_gene | 46.6% |
 | annotation_sbo | 81.7% |
 
 ### Detailed scores
@@ -35,7 +35,7 @@ Skipped (slow) tests: test_stoichiometric_consistency, test_unconserved_metaboli
 | Annotation - Reactions | Reaction Annotation Conformity Per Database | 33.3% |
 | Annotation - Reactions | Uniform Reaction Identifier Namespace | 0.0% |
 | Annotation - Genes | Presence of Gene Annotation | 0.0% |
-| Annotation - Genes | Gene Annotations Per Database | 80.0% |
+| Annotation - Genes | Gene Annotations Per Database | 80.1% |
 | Annotation - Genes | Gene Annotation Conformity Per Database | 80.0% |
 | Annotation - SBO Terms | Metabolite General SBO Presence | 0.0% |
 | Annotation - SBO Terms | Metabolite SBO:0000247 Presence | 0.1% |

data/testResults/model_qc_summary.md

@@ -1,59 +1,59 @@
 ## Model quality report
 
-:warning: **6 pre-existing finding(s), no regressions vs `main`.** Non-blocking.
+:warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking.
 
-_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md)._
+_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md)._
 
 ### Model checks
 _Duplicate keys (model unloadable) and no growth block the merge; every other row is a non-blocking report._
 
-| Check | Result | Δ vs `main` | |
+| Check | Result | Δ vs `develop` | |
 | --- | ---: | ---: | :---: |
-| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#duplicate-omap-keys) | 0 | new | :white_check_mark: |
-| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#growth-biomass-producible) | 125 | new | :white_check_mark: |
-| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-with-no-metabolites) | 0 | new | :white_check_mark: |
-| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | new | :white_check_mark: |
-| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | new | :white_check_mark: |
-| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-formula) | 0 | new | :white_check_mark: |
-| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-charge) | 0 | new | :white_check_mark: |
-| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | new | :white_check_mark: |
-| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | new | :white_check_mark: |
-| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-metabolites) | 0 | new | :white_check_mark: |
-| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-genes) | 0 | new | :white_check_mark: |
-| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#malformed-cross-references) | 0 | new | :white_check_mark: |
-| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_annotation_issues.csv) | new | :warning: |
+| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: |
+| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: |
+| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: |
+| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: |
+| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: |
+| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: |
+| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: |
+| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: |
+| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: |
+| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: |
+| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: |
+| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: |
+| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |
 
 ### MACAW and mass/charge balance
 
-| Check | Result | Δ vs `main` | |
+| Check | Result | Δ vs `develop` | |
 | --- | ---: | ---: | :---: |
-| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -703 | :warning: |
-| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -2 | :warning: |
-| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: |
-| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: |
-| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_structure_consistency.csv) | new | :warning: |
+| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/macaw_results.csv) | 0 | :warning: |
+| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/macaw_results.csv) | 0 | :warning: |
+| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/balance_results.csv) | 0 | :warning: |
+| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/balance_results.csv) | 0 | :warning: |
+| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |
 
 ### Model file and metabolic tasks
 
 | Check | Result | |
 | --- | ---: | :---: |
-| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
-| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
-| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
-| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
-| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |
+| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
+| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
+| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
+| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
+| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |
 
-### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#memote)
+### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#memote)
 
-**Total score: 63.2%** (core subset)  
+**Total score: 63.2%** (core subset)   0
 
 | Section | Score | Δ vs base |
 | --- | ---: | ---: |
-| consistency | 42.4% |  |
-| annotation_met | 73.0% |  |
-| annotation_rxn | 72.7% |  |
-| annotation_gene | 46.7% |  |
-| annotation_sbo | 81.7% |  |
+| consistency | 42.4% | 0 |
+| annotation_met | 73.0% | 0 |
+| annotation_rxn | 72.7% | 0 |
+| annotation_gene | 46.6% | -0.1 :warning: |
+| annotation_sbo | 81.7% | 0 |
 
 <details><summary>Per-test scores</summary>
 
@@ -73,7 +73,7 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
 | Annotation - Reactions | Reaction Annotation Conformity Per Database | 33.3% |
 | Annotation - Reactions | Uniform Reaction Identifier Namespace | 0.0% |
 | Annotation - Genes | Presence of Gene Annotation | 0.0% |
-| Annotation - Genes | Gene Annotations Per Database | 80.0% |
+| Annotation - Genes | Gene Annotations Per Database | 80.1% |
 | Annotation - Genes | Gene Annotation Conformity Per Database | 80.0% |
 | Annotation - SBO Terms | Metabolite General SBO Presence | 0.0% |
 | Annotation - SBO Terms | Metabolite SBO:0000247 Presence | 0.1% |
@@ -89,11 +89,11 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
 
 </details>
 
-**Full suite: 64.2%** &nbsp;  &middot; _from the last_ `/run memote`.
+**Full suite: 64.2%** &nbsp; 0 &middot; _from the last_ `/run memote`.
 
 _The score above is the fast core subset. Comment_ `/run memote` _to run the full suite on this pull request; the score updates here when it finishes._
 
-### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#gene-essentiality-hart-2015)
+### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/ca-influx-channels/data/testResults/README.md#gene-essentiality-hart-2015)
 
 _Not run automatically (it takes hours). Comment_ `/run gene-essentiality` _to run it on this pull request; the result posts as its own comment._
 

model/Human-GEM.yml

@@ -223843,12 +223843,13 @@
       - confidence_score: 0
     - !!omap
       - id: "MAR11311"
-      - name: "Calcium (Ca+2) Transport via Diffusion (Extracellular to Cytosol)"
+      - name: "Calcium (Ca+2) Transport via Ion Channels (Extracellular to Cytosol)"
       - metabolites: !!omap
           - MAM01413c: 1
           - MAM01413e: -1
       - lower_bound: -1000
       - upper_bound: 1000
+      - gene_reaction_rule: "ENSG00000006283 or ENSG00000081248 or ENSG00000100346 or ENSG00000102001 or ENSG00000141837 or ENSG00000148408 or ENSG00000151067 or ENSG00000157388 or ENSG00000160991 or ENSG00000175938 or ENSG00000196557 or ENSG00000198216 or ENSG00000276045"
       - rxnFrom: "Recon3D"
       - references: "PMID:21749716"
       - subsystem: "Transport reactions"
@@ -260546,6 +260547,45 @@
     - !!omap
       - id: "ENSG00000196407"
       - name: "THEM5"
+    - !!omap
+      - id: "ENSG00000081248"
+      - name: "CACNA1S"
+    - !!omap
+      - id: "ENSG00000151067"
+      - name: "CACNA1C"
+    - !!omap
+      - id: "ENSG00000157388"
+      - name: "CACNA1D"
+    - !!omap
+      - id: "ENSG00000102001"
+      - name: "CACNA1F"
+    - !!omap
+      - id: "ENSG00000141837"
+      - name: "CACNA1A"
+    - !!omap
+      - id: "ENSG00000148408"
+      - name: "CACNA1B"
+    - !!omap
+      - id: "ENSG00000198216"
+      - name: "CACNA1E"
+    - !!omap
+      - id: "ENSG00000006283"
+      - name: "CACNA1G"
+    - !!omap
+      - id: "ENSG00000196557"
+      - name: "CACNA1H"
+    - !!omap
+      - id: "ENSG00000100346"
+      - name: "CACNA1I"
+    - !!omap
+      - id: "ENSG00000276045"
+      - name: "ORAI1"
+    - !!omap
+      - id: "ENSG00000160991"
+      - name: "ORAI2"
+    - !!omap
+      - id: "ENSG00000175938"
+      - name: "ORAI3"
 - compartments: !!omap
     - e: "Extracellular"
     - x: "Peroxisome"

model/genes.tsv

@@ -2847,3 +2847,16 @@
 "ENSG00000244005"	"ENST00000374092.9;ENST00000374085.5;ENST00000397425.5;ENST00000541387.5;ENST00000306750.3;ENST00000419569.5"	"ENSP00000363205.3;ENSP00000363198.1;ENSP00000380570.1;ENSP00000440897.1;ENSP00000304740.3;ENSP00000393482.1"	"Q9Y697"	"NFS1"	"9054"	"NFS1 cysteine desulfurase"	""	""	""
 "ENSG00000267673"	"ENST00000393708.3;ENST00000492239.5;ENST00000494368.5;ENST00000706663.1"	"ENSP00000377311.5;ENSP00000488228.1;ENSP00000467188.1;ENSP00000516489.1"	"Q6P4F2"	"FDX2"	"112812"	"ferredoxin 2"	""	""	""
 "ENSG00000214113"	"ENST00000330636.9;ENST00000464010.5;ENST00000468929.5;ENST00000480566.5;ENST00000500576.4"	"ENSP00000418787.1;ENSP00000420026.1;ENSP00000418321.1;ENSP00000419928.1;ENSP00000443900.3"	"Q9HD34"	"LYRM4"	"57128"	"LYR motif containing 4"	""	""	""
+"ENSG00000081248"	""	""	""	"CACNA1S"	""	"calcium voltage-gated channel subunit alpha1 S"	""	""	""
+"ENSG00000151067"	""	""	""	"CACNA1C"	""	"calcium voltage-gated channel subunit alpha1 C"	""	""	""
+"ENSG00000157388"	""	""	""	"CACNA1D"	""	"calcium voltage-gated channel subunit alpha1 D"	""	""	""
+"ENSG00000102001"	""	""	""	"CACNA1F"	""	"calcium voltage-gated channel subunit alpha1 F"	""	""	""
+"ENSG00000141837"	""	""	""	"CACNA1A"	""	"calcium voltage-gated channel subunit alpha1 A"	""	""	""
+"ENSG00000148408"	""	""	""	"CACNA1B"	""	"calcium voltage-gated channel subunit alpha1 B"	""	""	""
+"ENSG00000198216"	""	""	""	"CACNA1E"	""	"calcium voltage-gated channel subunit alpha1 E"	""	""	""
+"ENSG00000006283"	""	""	""	"CACNA1G"	""	"calcium voltage-gated channel subunit alpha1 G"	""	""	""
+"ENSG00000196557"	""	""	""	"CACNA1H"	""	"calcium voltage-gated channel subunit alpha1 H"	""	""	""
+"ENSG00000100346"	""	""	""	"CACNA1I"	""	"calcium voltage-gated channel subunit alpha1 I"	""	""	""
+"ENSG00000276045"	""	""	""	"ORAI1"	""	"ORAI calcium release-activated calcium modulator 1"	""	""	""
+"ENSG00000160991"	""	""	""	"ORAI2"	""	"ORAI calcium release-activated calcium modulator 2"	""	""	""
+"ENSG00000175938"	""	""	""	"ORAI3"	""	"ORAI calcium release-activated calcium modulator 3"	""	""	""