Source: https://docs.nygen.io/CyteOnto/reference/files/
Revision: cb82698da3fc9e2bc385eb9a70e07f9304835eba
Structured page: https://docs.nygen.io/CyteOnto/reference.files.json

Data files and formats

CyteOnto keeps the Cell Ontology and its ontology caches in data_dir, and the caches of comparison runs in user_dir. PathConfig in cyteonto/paths.py resolves the paths, except that of the label splits, which CyteOnto builds in the same way.

Data directory

data_dir defaults to the data directory inside the installed package:

<data_dir>/
├── cell_ontology/
│   ├── cell_to_cell_ontology.csv
│   ├── cell_to_cell_ontology_enriched.csv
│   └── cl.owl
└── embedding/
    ├── cell_ontology/
    │   └── embeddings_<llmKey>_<embdKey>.npz
    └── descriptions/
        └── descriptions_<llmKey>.json

from_config() requires the three files in cell_ontology/. Lookups use the enriched CSV.

Run directory

user_dir defaults to <data_dir>/user_files:

<user_dir>/
├── decompositions/
│   └── <run_id>/
│       └── decompositions_<llmKey>.json
├── descriptions/
│   └── <run_id>/
│       ├── author/
│       │   └── author_descriptions_<llmKey>.json
│       └── algorithm/
│           └── <algorithm>_descriptions_<llmKey>.json
└── embeddings/
    └── <run_id>/
        ├── author/
        │   └── author_embeddings_<llmKey>_<embdKey>.npz
        └── algorithm/
            └── <algorithm>_embeddings_<llmKey>_<embdKey>.npz

File names

<llmKey> and <embdKey> come from ModelArtifactKey.filename_segment() <https://docs.nygen.io/CyteOnto/api/configuration.html#cyteonto.ModelArtifactKey.filename_segment>: {provider}_{company}-{modelName}, where the provider is lowercased, company is the part of the model ID before the first / and modelName the part after it. A model ID without / gives both. In the result, / and : become - and spaces become _; case and dots are kept.

Provider	Model	Key

nebius	moonshotai/Kimi-K2.6	nebius_moonshotai-Kimi-K2.6

nebius	Qwen/Qwen3-Embedding-8B	nebius_Qwen-Qwen3-Embedding-8B

fireworks	accounts/fireworks/models/kimi-k2p6	fireworks_accounts-fireworks-models-kimi-k2p6

openrouter	Qwen/Qwen3-Embedding-8B	openrouter_Qwen-Qwen3-Embedding-8B

openai	text-embedding-3-small	openai_text-embedding-3-small-text-embedding-3-small

In run IDs and algorithm names, / and : become -, and spaces and . become _: liver.v1/batch 2 becomes liver_v1-batch_2.

Ontology mapping

cell_to_cell_ontology.csv has the columns ontology_id and label, with one row per name or synonym of a term. The first row of a term holds the name that CyteOnto shows for it, which is the term’s Cell Ontology name for nearly all terms. The shipped file has 6,156 rows for 2,902 terms. cell_to_cell_ontology_enriched.csv adds label_normalized, the lowercase label, and drops the rows that repeat a term’s label_normalized.

ontology_id,label,label_normalized
CL:0000000,cell,cell
CL:0000001,primary cultured cell,primary cultured cell

Descriptions

The ontology descriptions and the label descriptions of runs share one JSON format:

{
  "schemaVersion": "3.0",
  "artifactKey": {
    "provider": "nebius",
    "model": "moonshotai/Kimi-K2.6",
    "company": "moonshotai",
    "modelName": "Kimi-K2.6"
  },
  "updatedAt": "<UTC timestamp>",
  "descriptions": {
    "CL:0000815": {
      "initialLabel": "regulatory t cell;regulatory t lymphocyte;...",
      "descriptiveName": "CD4-positive regulatory T lymphocyte",
      "function": "...",
      "diseaseRelevance": "...",
      "developmentalStage": "..."
    }
  }
}

The keys of descriptions are Cell Ontology IDs in the ontology file and labels in the files of runs. Each entry has the fields of CellDescription <https://docs.nygen.io/CyteOnto/api/descriptions.html#cyteonto.CellDescription>. Files without "schemaVersion": "3.0", such as files of older versions, are not loaded. CyteOnto then generates the descriptions again: for the ontology, all 2,902 of them. Run python -m cyteonto.setup --force instead to download the current files of the precomputed model pairs.

Embeddings

The embedding files are compressed NumPy archives:

Array	Ontology files	Run files

embeddings	One float32 row per term, 2,902 × 4,096 for Qwen3-Embedding-8B	One float32 row per distinct label or part

ontology_ids	The Cell Ontology ID of each row

labels		The label of each row

metadata	A dict	A dict

metadata holds schemaVersion, a timestamp, the llm and embedding artifact keys, num_embeddings, embedding_dim and reasoning; run files add run_id, kind and identifier. The IDs, labels and metadata are object arrays, so load the files with allow_pickle=True:

import numpy as np

data = np.load(path, allow_pickle=True)
embeddings = data["embeddings"]
ids = data["ontology_ids"].tolist()
metadata = data["metadata"].item()

A run file without labels, written by an older version of CyteOnto, is stale: CyteOnto does not load it, and purge_stale() deletes it.

Decompositions

How the labels of a run were split:

{
  "schemaVersion": "3.0",
  "artifactKey": {"provider": "nebius", "model": "moonshotai/Kimi-K2.6", "company": "moonshotai", "modelName": "Kimi-K2.6"},
  "updatedAt": "<UTC timestamp>",
  "decompositions": {
    "at2 cell-plasma cell doublet": ["at2 cell", "plasma cell"],
    "t cell": ["t cell"]
  }
}

Downloads

python -m cyteonto.setup downloads the files from Nygen’s public storage at https://pub-d8bf3af01ebe421abded39c4cb33d88a.r2.dev/cyteonto_v2/, under cell_ontology/<file name>, descriptions/descriptions_<llmKey>.json and embeddings/embeddings_<llmKey>_<embdKey>.npz.