diff --git a/data/testResults/README.md b/data/testResults/README.md index 6ed6d67d..733a7fc6 100644 --- a/data/testResults/README.md +++ b/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 diff --git a/data/testResults/memote_score.md b/data/testResults/memote_score.md index cd43081b..b3bd26cc 100644 --- a/data/testResults/memote_score.md +++ b/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% | diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md index fdac8f39..c9442074 100644 --- a/data/testResults/model_qc_summary.md +++ b/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 |
Per-test scores @@ -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
-**Full suite: 64.2%**   · _from the last_ `/run memote`. +**Full suite: 64.2%**   0 · _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._ diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5dc46667..a8a74e83 100644 --- a/model/Human-GEM.yml +++ b/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" diff --git a/model/genes.tsv b/model/genes.tsv index 797c979d..c4d6a232 100644 --- a/model/genes.tsv +++ b/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" "" "" ""