---
title: "Canonical vocabulary for new AI4Bio enrichment metadata."
task: ""
lineage_type: import
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/vocabulary.yml
upstream_sha: 7a064bf0
imported_at: 2026-08-08
prompt_class: unknown
upstream_changes: accepted
author: upstream
validated: false
---

# Canonical vocabulary for new AI4Bio enrichment metadata.
#
# These values are enforced only for fields explicitly added through
# data/enrichment.yml. README-derived legacy values remain backward compatible.
# Canonical terms use lowercase kebab-case.

version: 1

controlled_fields:
  entities:
    - cell
    - compound
    - disease
    - drug
    - gene
    - genome
    - molecule
    - organism
    - pathway
    - phenotype
    - protein
    - protein-complex
    - regulatory-element
    - tissue
    - transcript
    - variant

  methods:
    - autoencoder
    - contrastive-learning
    - convolutional-neural-network
    - diffusion
    - generative-model
    - geometric-deep-learning
    - graph-neural-network
    - knowledge-graph
    - language-model
    - message-passing-neural-network
    - multi-agent-system
    - optimal-transport
    - recurrent-neural-network
    - reinforcement-learning
    - retrieval-augmented-generation
    - self-supervised-learning
    - state-space-model
    - supervised-learning
    - transformer
    - unsupervised-learning
    - variational-autoencoder

  modalities:
    - cell-painting
    - chemical-structure
    - clinical
    - dna-sequence
    - electronic-health-record
    - epigenomics
    - genomics
    - histopathology
    - imaging
    - knowledge-graph
    - metabolomics
    - molecular-structure
    - multi-omics
    - protein-sequence
    - proteomics
    - rna-sequence
    - single-cell-rna-seq
    - spatial-transcriptomics
    - transcriptomics

  tasks:
    - batch-correction
    - cell-type-annotation
    - classification
    - dimensionality-reduction
    - docking
    - drug-response-prediction
    - drug-target-interaction
    - foundation-model-pretraining
    - gene-regulatory-network-inference
    - imputation
    - link-prediction
    - molecular-generation
    - perturbation-prediction
    - protein-function-prediction
    - protein-sequence-design
    - regression
    - representation-learning
    - structure-prediction
    - trajectory-inference
    - virtual-screening