AI Gene Review Projects

Curated gene annotation review projects organized by topic and organism

See the complete auto-generated list of all projects →

C. elegans Projects

Ciliopathy Pathway diagram
Mitophagy Pathway diagram
Proteostasis Pathway diagram
P Granules
Surveillance Immunity Pathway diagram
UPR Stress Pathway diagram

Yeast Projects

Cell Cycle
DNA Repair & Chromatin
Epigenetics & Histone Inheritance
Fungal PAINT Family Reviews
Metabolic Engineering
Replicative Aging

Human / Mammalian Projects

Adaptive Immunity

Antigen presentation, V(D)J recombination, T and B cell receptor signaling, co-stimulation and antibody diversification

Allergens
Alzheimer Disease
Accessible Surfaceome (SurfaceBench) Comparison

All 147 SurfaceBench proteins reviewed; how well public GO annotations call extracellular accessibility (in progress)

G Protein-Coupled Receptors (GPCRs)

GPCR family reviews, transducer pathway modules, and receptor gene reviews; paired with dismech GPCR drug-mechanism and disease modules

Microproteins (sORF-encoded peptides) Census & GO coverage
Chimeric mRNA Trans-Fusions in Immunity
ClinGen Mendelian Disease Genes
Cytochrome P450 GO Molecular Function
Radical SAM Enzymes
Glycobiology Resources dossier Pathway modules
PAINT (No-IBA Genes)
Ferroptosis
Isoform-Specific Functions
PINK1-Parkin Mitophagy
Mitochondrial Interactome (MitoMatch)
Mitochondrial Proteomes Across the Tree of Life (MitoTOL)
Human Proteostasis Network
Reactome-GO Alignment
Neuron Development
Neuroblast Proliferation (vertebrate vs protostome disambiguation)
cGAS-STING Pathway
Innate Immune System Pathways Across Animals
Phagocytosis Modules
Extracellular Matrix
Evidence-Source Sufficiency
Mechanobiology
Deliverome GO Collaboration Endosomal routing module Endosomal routing ABM, in the browser
ER-Phagy
Integrated Stress Response
MicroRNA Degradation / TDMD
NLRP3 Inflammasome
Ribosome Quality Control
Stress Granules
Sea Urchin Endomesoderm GRN
Transcription Factors (dbTF annotation review)
Stilbene Cleavage Oxygenases (SCO / LSD family)
Unfolded Protein Binding (GO:0051082 obsoletion)
"X involved in Y" precomposed terms (decomposition to extensions / GO-CAMs / modules)
ER-PM Tethering (GO:0061817 obsoletion)
Mitochondrion-ER Tethering (GO:1990456 obsoletion)
Mitochondrion Targeting Sequence Binding (GO:0030943 obsoletion)
Synaptic Vesicle Docking (GO:0099148 obsoletion)
Vesicle Targeting (GO:0006903 obsoletion)
Protein Localization to ER Exit Site (GO:0070973 obsoletion)
Calcitriol Biosynthesis from Calciol (GO:0036378 obsoletion)
Substrate Localization to Autophagosome (GO:0061753 obsoletion)
Cargo Receptor Ligand Activity (GO:0140355 obsoletion)
Succinate Dehydrogenase gp2term (GO:0008177 enables→contributes_to)
KW-1110 TRAF-inhibition KW2GO remapping (GO:0039527 → GO:0140476)

Bacterial Projects

Antimicrobial Resistance (CARD/ARO)
CRISPR-Cas immunity and anti-CRISPR counter-defence
B. subtilis
PseudoCAP annotations seeding PAINT IBAs (P. aeruginosa)
Cellulosome
Plant Bioenergy Modules
Biosynthetic Gene Cluster Complexes
Nitrogen Cycle
Extracellular Cytochrome Nanowires
P. putida Genome-wide Curation Module plan
Variovorax Metal Recovery & Rhizosphere Interactions Module plan
Bacteriophage Genome Curation & Pathway Hole Filling
Lipoate Biosynthesis (GO:0009107 obsoletion)

Archaeal Projects

Archaea
The Lipid Divide: enzymes that cross it

Plant Projects

A. thaliana Corpus
A. thaliana Heat Stress
A. thaliana Single-Cell Fungal Infection
Nicotine Biosynthesis
Ent-Kaurene Oxidation (GO:0010241 obsoletion)
Neural Crest Formation (GO:0014029 obsoletion)
Pennycress Oilseed Domestication Genes
CO2-Concentrating Mechanisms (Pyrenoid)
Plant-Fungal Interactions

Other Organism Projects

Cephalopod Neuro Genes
Origins of the Neural Crest
Origins of Animal Multicellularity
Protists
Tardigrade Stress Response
Pancrustacea Metamorphosis Gene Families
Satellite Model Organisms
Parasites
Fungal Conidiation Cascade (Aspergillus / Neurospora)
Fungal Growth & Knockout Phenotype Resources
Naked Mole Rat (HETGA) Annotation Review
Zebrafish Genome Duplication & Paralog Pairs Background research
Quantum Sensing Proteins (cryptochrome magnetoreception)

Cross-Cutting & Methodology

Organelle Lifecycle Modules
Protein Families
Structural Reasoning in Annotation Review
MAPK Cascades (module and gene review coverage)
Amino Acid Activation (43 tRNA aminoacylation BP obsoletions)
Biomolecular Condensates (scaffold vs client curation) GO and annotation audit
Human Protein Atlas: Primary Cilium Life Cycle Module HPA subcellular evidence re-evaluation
UniProt Subcellular Locations (SL) Unique Terms Membrane · Cytoskeleton · Secreted · Mitochondria Methodology
COSCIENTIST (AI co-scientist compute-driven hypotheses)
Pathway Satisfiability (context-resolved module logic)
Bgee Expression as Evidence (explain, corroborate, contest function; paralogs; developmental timing) Methods & reproduction
Boolean Models (modules as executable logic; external BMs as calibration) MAPK demo results Sources & tooling landscape Schema gaps
Executable Models (modules you can run: Boolean & ABM now, kinetic/FBA next) All executable models ERK cascade, in the browser Endosomal routing ABM, in the browser
Agent-Based Modeling of Intracellular Trafficking (Deliverome & endosomal routing) Endosomal escape ABM LDLR endocytosis ABM
Genome-wide Validation (system-level plausibility of annotation sets)
Taxon Pathway Variance (lineage pathway variants and proposed GO taxon constraints)
Ad-Hoc Bioinformatics
Anti-CRISPR Systems
Contested Function (Pseudo-enzymes)
UniProt CAUTION Notes
Orphan Curated: Swiss-Prot outside reference proteomes
NOT Annotation Usage Audit
IRD Evidence (Inferred from Rapid Divergence)
Enzyme Specificity
Mitochondrial Fatty Acid β-Oxidation
Function Knowledge Gaps
No Data (ND): what an ND annotation is telling us ND inventory

Partitions ND annotations into stale, inferable, existence, true-gap, ontology-blocked, negative and bookkeeping cases, and couples true gaps to knowledge_gaps

IBA Annotation Review
ARBA Rule Review
PANTHER IBA Family Review (S. pombe)
RAR Misannotation Re-examination (Wei et al. 2020)
PANTHER Family Assignment Discrepancies
IEP Evidence Code Review
Omics and High-Throughput Evidence (HDA/HTP/RCA)
InterPro Mapping Review
Iron-Sulfur Cluster Biogenesis
Metabolic Model Analysis
Metabolomics Interpretation with GO / GO-CAM Tools landscape
METEA MLL Cluster
Miscitation Review Register
NITV2 Pathways
Non-Physiological Reactions in EC, Rhea and GO
Organelles

When is a root organelle term (e.g. mitochondrion) informative, versus its membrane or lumen?

GO-CAM Compartments

Do GO-CAM activity locations resolve to a distinct compartment, and do causal edges join adjacent compartments?

Over-Annotation Patterns
Regulation Sign Errors: Activator vs Inhibitor
Behaviour Annotations (Over-Annotation)
Review Quality Audit (Boilerplate)
Miscitation Audit Citation defect register Anomaly detectors
Retracted Literature Behind Annotations Retraction register
Pseudoenzymes
Function Requirement (NOT) Rules
Wrong-Gene Leads
Phosphorylation Refactor
Protein Complex Functions
Complex Portal Annotation Correctness
RHEA → GO Contribution & Gaps
TCDB → GO Transporter-Activity Mapping & Gaps
Pfam → GO Precision Gaps Results
NCBIFAM / CDD → GO Contribution & Gaps
NCBI RefSeq vs UniProt/GOA: Prokaryotic GO Pipelines
Swiss-Prot Keywords
UniPathway Unique Terms
RGD Pathway Ontology → GO, GO-CAM & Modules
Surveillance Immunity Curation
Function Prediction Evaluation

ProtNLM, BioReason, DeepECTransformer, Affinage, and annotation-transfer reviews

Propagation by Homology

ISO, ISS/ISA, IBA, and electronic orthology transfers, with a donor → target browser

BioReason-Pro Comparison
ProtNLM2 Evaluation
Validating E. coli ML Predictions
Cuproptosis (Copper-Dependent Cell Death)
TreeGrafter Inference Evaluation
eggNOG-mapper Evaluation

Orthology-based GO transfer by eggNOG-mapper 2.1, scored against 520 reviewed proteins

Conserved-function recovery
FlyBase Gene Groups as Review Sets
Human Genes Annotation Re-Review
Mouse Genes Annotation Re-Review
YeastPathways to Modules
dismech metabolic disorders aligned with ai-gene-review
Ligands in signaling pathways
Gene Model Errors: Fused UniProt Entries
MOD gene descriptions as review input
LBNL Hackathon: Dark Protein Atlas genes
CACAO community annotations review