Manual network curation

[realmarcin]

No description provided.

[Copilot]

Pull request overview

This PR performs manual curation of community interaction networks by adding/adjusting source_taxon / target_taxon annotations (and a few new interaction entries) across multiple community YAMLs, and updates the corresponding pre-rendered HTML pages so network visualizations and interaction cards reflect the curated directionality.

Changes:

• Add source_taxon and/or target_taxon to many ecological_interactions entries to make interaction direction explicit.
• Add several new, more granular interaction entries (with supporting evidence) in select communities.
• Update generated docs HTML pages to display source/target taxa and wire edges in the embedded network JS.

Reviewed changes

Copilot reviewed 82 out of 82 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
kb/communities/Wheat_Consortium_C6.yaml	Adds target_taxon: Triticum aestivum to plant-relevant interactions.
kb/communities/Wheat_Consortium_C1.yaml	Adds target_taxon: Triticum aestivum to plant-relevant interactions.
kb/communities/Tinto_River_Iron_Cycling_Community.yaml	Adds explicit source/target for an existing interaction and introduces new interaction entries with evidence.
kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml	Adds explicit source_taxon / target_taxon for an interaction to support directed network edges.
kb/communities/Soybean_N_Fixation_sfSynCom.yaml	Adds a new interaction plus target_taxon for AHL signaling and adds plant target for nodulation interaction.
kb/communities/Sorghum_SRC1_Subset.yaml	Replaces generic “community” taxon placeholders with specific taxa and adds target_taxon: Sorghum bicolor; adds multiple new interaction entries.
kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml	Adds explicit source/target taxa and introduces an additional cross-feeding interaction entry.
kb/communities/SF356_Cellulose_Degrader.yaml	Adds explicit target taxon for an interaction and adds two new interaction entries with evidence.
kb/communities/Rifle_Uranium_Reducing_Community.yaml	Adds explicit source/target taxa for existing interactions and introduces a new sulfate/U reduction interaction entry.
kb/communities/Richmond_Mine_AMD_Biofilm.yaml	Adds explicit source/target taxa and introduces a new competition interaction entry with metabolites/processes/evidence.
kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml	Adds explicit source/target taxa to existing interactions.
kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml	Adds explicit source/target taxa to existing interactions.
kb/communities/Phormidium_Alkaline_Consortium.yaml	Adds explicit source/target taxa and introduces an additional interaction entry.
kb/communities/Phenol_Carboxylation_Consortium.yaml	Adds explicit source/target taxa for an interaction and introduces an additional syntrophy interaction entry.
kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml	Removes one target_taxon block and adds new curated interactions with explicit source/target taxa.
kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml	Adds multiple new curated interaction entries and adds missing source/target taxa to existing interactions.
kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml	Adds explicit source/target taxa to existing interactions and adds a new interaction entry.
kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml	Adds target_taxon to an interaction and adds multiple new cross-feeding interaction entries with evidence.
kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml	Adds a new cross-feeding interaction entry with explicit source/target taxa and evidence.
kb/communities/Mixed_Gallium_LED_Recovery_Consortium.yaml	Adds explicit source/target taxa for interactions.
kb/communities/Maize_Root_Simplified_Community.yaml	Adds explicit source/target taxa for multiple plant-benefit interactions and adds several new interaction entries.
kb/communities/MSC1_Dominant_Core.yaml	Adds explicit source/target taxa for multiple syntrophy interactions and adds several new interaction entries.
kb/communities/MAMC_M48_Lignocellulose.yaml	Adds explicit source/target taxa and adds additional interaction entries.
kb/communities/Lotus_LjSC3.yaml	Refines source taxon naming and adds multiple explicit plant and bacteria/bacteria targets plus new interaction entries.
kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml	Adds explicit source/target taxa for interactions and adds multiple new interaction entries.
kb/communities/Industrial_Bioreactor_Consortium.yaml	Adds explicit source/target taxa and introduces multiple new curated interactions.
kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml	Adds a new taxonomy entry and adds explicit targets plus a new interaction entry with evidence.
kb/communities/GOM_Oil_Degrading_Consortium.yaml	Adds explicit source/target taxa for hydrocarbon-degradation interactions.
kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml	Adds explicit source/target taxa for mutualism interactions.
kb/communities/Ewaste_Bioleaching_Consortium.yaml	Adds explicit source/target taxa and introduces a new interaction entry with evidence.
kb/communities/Dangl_SynComm_35.yaml	Replaces generic “community” taxon placeholders with specific taxa and adds multiple new interaction entries.
kb/communities/Coscinodiscus_Synthetic_Community.yaml	Adds explicit target taxa for interactions.
kb/communities/Copper_Biomining_Heap_Leach.yaml	Adds explicit source/target taxa for an interaction.
kb/communities/Chromobacterium_Gold_Biocyanidation.yaml	Adds explicit source_taxon for interactions.
kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml	Adds explicit source_taxon for an interaction.
kb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml	Adds explicit target taxon and introduces a new interaction entry with evidence.
kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml	Adds explicit source/target taxa and introduces a new interaction entry with evidence.
kb/communities/Australian_Lead_Zinc_Polymetallic.yaml	Adds multiple new curated interaction entries with explicit source/target taxa and evidence.
kb/communities/At_RSPHERE_SynCom.yaml	Adds explicit target taxa for multiple interactions and introduces additional interaction entries.
kb/communities/AMD_Nitrososphaerota_Archaeal.yaml	Adds a new curated interaction entry with explicit source/target taxa and evidence.
docs/communities/Wheat_Consortium_C6.html	Updates interaction cards + network JS to include/display target_taxon edges.
docs/communities/Wheat_Consortium_C1.html	Updates interaction cards + network JS to include/display target_taxon edges.
docs/communities/Thermophilic_Pyrite_QS_Consortium.html	Updates interaction cards + network JS to include/display source/target edges.
docs/communities/Soybean_N_Fixation_sfSynCom.html	Adds new interaction card and updates network JS/node count for added edges/nodes.
docs/communities/Salar_Atacama_Lithium_Brine_Community.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/SF356_Cellulose_Degrader.html	Adds new interaction cards and updates network JS/node count for curated edges/nodes.
docs/communities/Rifle_Uranium_Reducing_Community.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Richmond_Mine_AMD_Biofilm.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Rammelsberg_Cobalt_Nickel_Tailings.html	Updates interaction cards + network JS to include curated source/target edges.
docs/communities/Polaromonas_Vanadium_Reduction_Community.html	Updates interaction cards + network JS to include curated source/target edges.
docs/communities/Phormidium_Alkaline_Consortium.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Phenol_Carboxylation_Consortium.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Okeke_Lu_Cellulolytic_Consortium.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Naica_Deep_Subsurface_Thermophilic.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Mixed_Gallium_LED_Recovery_Consortium.html	Updates interaction cards + network JS to include curated source/target edges.
docs/communities/MAMC_M48_Lignocellulose.html	Adds new interaction cards and updates network JS/node count for curated edges/nodes.
docs/communities/Iberian_Pit_Lake_Stratified_Community.html	Adds taxonomy row + new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/GOM_Oil_Degrading_Consortium.html	Updates interaction cards + network JS to include curated source/target edges.
docs/communities/Ferroplasma_Leptospirillum_Syntrophy.html	Updates interaction cards + network JS to include curated source/target edges.
docs/communities/Ewaste_Bioleaching_Consortium.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Coscinodiscus_Synthetic_Community.html	Updates interaction cards + network JS to include curated target edges.
docs/communities/Copper_Biomining_Heap_Leach.html	Updates interaction cards + network JS to include curated source/target edges.
docs/communities/Chromobacterium_Gold_Biocyanidation.html	Updates interaction cards + network JS to include curated source edges.
docs/communities/Chromium_Sulfur_Reduction_Enrichment.html	Updates interaction cards + network JS to include curated source edges.
docs/communities/Chlamydomonas_Bacterial_H2_Consortium.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/Bayan_Obo_REE_Tailings_Consortium.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.
docs/communities/At_RSPHERE_SynCom.html	Adds new interaction cards and updates network JS/node count for curated edges/nodes.
docs/communities/AMD_Nitrososphaerota_Archaeal.html	Adds new interaction card and updates network JS/node count for curated edges/nodes.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[realmarcin]

@cmungall copilot actually had some potentially reasonable comments but they didn't get compiled into issues somehow:

Reviewing schemas and conventions

I need to review the differences among several YAML files and HTML documents and to inspect schema conventions. The tools operate on a repository we have access to. I’ll use list_dir and read_code to examine the ecological_interactions fields, like source_taxon and target_taxon. It’s crucial to ensure those fields are allowed and consistent. I'll check for the taxonomy as it may include phylum-level entries, which could violate conventions. I’ll also look at the communitymech.yaml for allowed taxon terms. Let's call the tools!

Call to read_code

search_dir

Call to search_dir

Call to search_dir

Call to list_dir
Considering taxonomy interaction

I’m thinking about whether removal might fix the issue, but without a target, the interaction feels incomplete. I need to check the schema details since both source_taxon and target_taxon are optional. If the name suggests nitrogen fixation by Bradyrhizobium, it might be wise to target the plant. I'll also verify if the preferred term matches the label and confirm whether synonyms are used consistently. It’s a bit of a tangled web, but I’ll sort it out! Evaluating taxonomy terms

I’m looking at the plant taxonomy with the preferred term Pongamia pinnata and label Millettia pinnata. But removing the target_taxon might not be the best choice since it impacts the interaction with the plant. This could have implications for HTML generation in the network. The PR title suggests adding source and target for clarity. Also, I noticed various taxon descriptors, and I need to verify their accuracy and ensure consistency, particularly with terms linked to NCBI taxon IDs. I'll check everything as best as I can!

search_dir

Call to search_dir

Call to search_dir

Call to search_dir

Call to search_dir

read_code

Call to read_code

Call to read_code

Call to read_code

Call to read_code
Evaluating interaction types

I’m thinking maybe the source of algae relates to heterotrophs, but that might be too specific. I can check the InteractionType enum for things like MUTUALISM—wait, it seems that one isn't used, but there is SYNTROPHY. I found that it’s valid, and there are new interactions utilizing it, such as "Aerobic Metabolic Support and Community Structuring." However, there's a concern with EvidenceItem.snippet having a minimum_value of 10 while being numeric, which feels a bit off. Plus, some evidence references might not match the required regex correctly. Identifying YAML issues

I see that in the diff for lines 236-238, there's a blank line followed by a stray single quote. This might mean that the description ended with an unmatched single quote, which could break the YAML formatting on line 237. The previous context shows that this quote is closing a multi-line string.

Also, I need to examine a schema inconsistency in the Phormidium_Alkaline_Consortium.yaml file, where the source_taxon preferred term doesn't match the current phylum name. It's okay, but I see a similar issue with the target_taxon label. Examining interaction inconsistencies

I think there are major issues with the interactions being labeled as "preferred_term: ... members," while their term labels are in singular form. A possible serious mistake is in the Dangl_SynComm_35.yaml file, where the source_taxon has been changed from "SynComm 35 bacterial community" to Dyella japonica. There’s also a mismatch in terminology regarding suppressor and nonsuppressor Pseudomonas species.

Another concern is with the Tinto_River_Iron_Cycling_Community.yaml file, which has source and target taxa listed at the phylum level, but I remember that taxonomy should ideally use genus or species entries. However, there might be exceptions for ecological interactions, so it gets tricky. Reviewing taxonomy conventions

I’m noticing that Bacillariophyceae might not be a new taxonomy entry, as it could already exist in the repo. The new pull request adds source and target for ecological interactions involving Bacillariophyceae and Chlorophyta, but there’s a concern about using phylum-level IDs in ecological interactions instead of taxonomy. Our convention is to use genus/species NCBITaxon IDs, not phylum-level ones.

In the Iberian Pit Lake file, they added a genus-level term without introducing any new phylum-level taxonomy. Also, in the Phenol_Carboxylation_Consortium.yaml file, the use of NCBITaxon:2 for both source and target may cause issues since many nodes could end up sharing the same generic key of "Bacteria." Analyzing preferred terms in taxonomy

I’m noticing a discrepancy where the preferred_terms differ ("Short motile rod bacterium" vs. "Long non-motile rod bacterium"), yet they share the same term id. This could mean that in the network graph, taxon nodes are keyed by preferred_term instead of term id. If I look at the HTML, it seems that taxonNodeIds are linked to preferred_term from the taxonomy section. So, I'm thinking we should check the YAML entries to confirm if "Short motile rod bacterium" is included.