CellStructureMech

Knowledge base of microbial cell structures — organelles, envelope layers, appendages, microcompartments, inclusions, cytoskeletal systems and the multi-protein complexes that build them — one evidence-backed, ontology-grounded YAML record per structure.

CellStructureMech is the structural counterpart of TraitMech (phenotypes), ProteinTraitsMech (proteins), HabitatMech (habitats), CultureMech (growth media), MediaIngredientMech (ingredients) and CommunityMech (communities), and follows the curation pattern established by dismech: one YAML per entity, ontology-grounded, evidence-backed, closed-schema validated, curated incrementally with an append-only audit trail.

Browse the corpus online → — every record, by category, with components, distribution, functions and mechanism graphs. The site also includes a text embedding map with full-vector nearest neighbours.

The gap it fills

TraitMech says an organism is flagellated; ProteinTraitsMech says what FliC is. Neither says what a flagellum is made of, which clades have one, how the stator turns the rotor, or which trait it confers. That machine-level layer — the thing between a phenotype and a protein — is what a CellStructureRecord holds:

Section	Question it answers
components	What is it built from? Families, complexes, RNAs, lipids — with stoichiometry, essentiality, and taxon-paired UniProt examples
taxonomic_distribution	Who has it, and how consistently?
functions	What does it do (GO), with evidence?
associated_traits	Which TraitMech phenotype does it confer or diagnose?
causal_graphs	How does it assemble, work, and get regulated? Every edge cited.
part_of / has_part / parent_structures	Where does it sit in the cell's part hierarchy?

Granularity: a record is a structure you could point to in a micrograph — from a whole organelle down to a discrete multi-protein complex (ribosome, flagellar motor, ATP synthase). Individual proteins are components of records, not records; phenotypes are TraitMech records. See docs/CURATION.md.

Current corpus

1022 structure records are currently committed.

Category	Records		Status	Records
OTHER	326		PROPOSED	1022
MEMBRANE_ORGANELLE	226
CYTOSKELETON	179
RIBONUCLEOPROTEIN	89
APPENDAGE	58
ENERGY_COMPLEX	45
SPORE	23
ENVELOPE	20
INCLUSION	20
SECRETION_SYSTEM	20
MICROCOMPARTMENT	6
DIVISION_MACHINERY	5
NUCLEOID	5

873 records are grounded in GO; 149 carry minted identifiers. 848 list components, 991 carry causal graphs (4704 evidence-backed edges), 8 link to TraitMech traits, and 74 carry licensed, cited imaging evidence.

Run just report for the live report. Every current record is PROPOSED — drafted from the cited literature with LLM assistance and not yet reviewed by a second curator.

Quick start

Development uses Python 3.13 via .python-version; CI selects the same minor explicitly and runs the full quality gate once. The package compatibility floor remains declared in pyproject.toml.

just install          # uv sync --extra dev
just report           # corpus stats
just validate-all     # closed-mode schema validation of every record
just test             # unit + corpus-integrity tests
just render           # regenerate the site under pages/
just text-map-check   # cached text vectors and derived map match the corpus
just qc               # everything CI runs

To add a record:

just new-record --identifier GO:0030313 --label "cell envelope" \
    --category ENVELOPE --kind ENVELOPE_LAYER --curator you          # dry run
just new-record ... --apply                                          # write

Then fill in the YAML, run just validate-all, just render, and just docs-stats, and open a PR.

Identifiers

GO cellular component is the primary grounding: a record whose structure is exactly a GO term uses that CURIE (GO:0005840 ribosome). When no GO term is an exact fit, the record mints a cellstructuremech: identifier and records the nearest broader term in parent_structures. See docs/CURATION.md.

Schema

src/cellstructuremech/schema/cellstructuremech.yaml defines CellStructureRecord; docs/SCHEMA.md walks through it. The causal-graph classes share TraitMech's vocabulary so tooling can move between the two. mech_shared.yaml (Discussions, Datasets) is vendored byte-identically across the Mech repos from culturebotai-claw, and checked against it by just vendored-check.

This is the beginning of the README. Read the rest at the original. Read the full README ↗