#30 backfill batch 2: 4 metals + 3 gut/rhizosphere communities#83
Merged
Conversation
Continues the SPRUCE/wetland dogfood pattern from PRs #79/#80/#81. Each entry uses CHEBI terms with snippets taken verbatim from cached PMID/DOI abstracts; no cross-repo IDs (MIM IDs haven't been minted). AMD/biomining/REE (4 of 16 remaining): | Community | Ingredients | Source | |---|---|---| | Cyprus_Copper_Sulphide_Bioleaching_Consortium | chalcopyrite (Cu(II) surrogate), chalcocite (Cu(I) sulfide), iron(2+) | PMID:41381092 | | Ferroplasma_Leptospirillum_Syntrophy | iron(2+), pyrite | PMID:16104851 | | Iberian_Pit_Lake_Stratified_Community | sulfate, iron(2+) | PMID:23840525 | | Ewaste_Bioleaching_Consortium | glycine (10 g/L cyanide substrate), hydrogen cyanide (gold lixiviant) | PMID:26704063 | Gut/rhizosphere (3 of ~13 remaining): | Community | Ingredients | Source | |---|---|---| | Bacteroides_Eubacterium_Gnotobiotic_Gut_Model | acetate, butyrate, host-derived mucin glycans | PMID:19321416 | | Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community | root exudates, labile root carbon | PMID:37280433 | | ORNL_PMI_Populus_PD10_SynCom | glucose (minimal-medium axis) | PMID:33995895 | #30 related_ingredients adoption: 12/265 -> 19/265. Test plan: just test (136 passed), all 7 modified files validate clean against the schema. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
There was a problem hiding this comment.
Pull request overview
This PR continues the Issue #30 “dogfood” adoption by adding related_ingredients entries (with CHEBI terms and evidence snippets) to 7 existing community YAML records spanning AMD/biomining and gut/rhizosphere cohorts.
Changes:
- Added
related_ingredientsblocks to 7 community YAMLs, linking key environmental/metabolic ingredients via CHEBI terms. - Anchored each added ingredient with evidence items referencing cached PMID abstracts.
Reviewed changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml | Adds glucose as a related ingredient for the minimal-medium axis in the passaging design. |
| kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml | Adds sulfate and Fe(II) as related ingredients for pit-lake stratified geochemistry/redox cycling. |
| kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml | Adds Fe(II) and pyrite as related ingredients relevant to acidophile syntrophy/bioleaching. |
| kb/communities/Ewaste_Bioleaching_Consortium.yaml | Adds glycine and cyanide as related ingredients for two-step e-waste bioleaching. |
| kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml | Adds chalcopyrite, chalcocite, and Fe(II) as related ingredients for copper-sulfide bioleaching. |
| kb/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.yaml | Adds root-exudate/organic-matter related ingredients for rhizosphere niche definition. |
| kb/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.yaml | Adds SCFAs and mucin-glycan substrate related ingredients for the gnotobiotic gut model. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Five findings, all valid:
1. Cyprus chalcopyrite was mapped to CHEBI:30074 / "copper(2+)", which
is wrong on both axes. Updated to CHEBI:50885 / "chalcopyrite" —
the mapping the repo already uses (Copper_Biomining_Heap_Leach
metabolites).
2. Ewaste cyanide entry's `chebi_term.label` said "hydrogen cyanide"
but CHEBI:17514's canonical label is "cyanide". Aligned label.
3. Ewaste cyanide entry's snippet ("This gold complexing agent was
used…") did not literally mention cyanide. Replaced with the more
direct adjacent abstract sentence ("cyanide-producing heterotrophic
Pseudomonas fluorescens and Pseudomonas putida were used") and
moved the gold-complexing context into the explanation field.
4. Iberian Pit Lake relevance text described an Fe(II)/Fe(III) cycle
across the chemocline but only iron(2+) was listed. Added a
separate iron(3+) related_ingredient with its own snippet
anchoring the bottom-layer iron-reducing guild
(Acidiphilium / Ferroplasma / Acidithiobacillus ferrooxidans in
reducing mode); split the original Fe(II) relevance text to
reference only the oxidising guild.
5. Ewaste "gold-mobilisation" -> "gold-mobilization" for spelling
consistency with the rest of the repo (American spelling).
136 tests still pass; all 3 modified YAMLs validate clean.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Continues the SPRUCE/wetland dogfood pattern from PRs #79/#80/#81. Each entry uses CHEBI terms with snippets taken verbatim from cached PMID/DOI abstracts; no cross-repo IDs (MIM hasn't minted any yet).
AMD/biomining/REE (4 of 16 remaining)
Gut/rhizosphere (3 of ~13 remaining)
Status of #30
related_ingredientsadoptionTest plan
just test— 136 passed, 9 skippedlinkml-validate— all 7 modified YAMLs clean🤖 Generated with Claude Code