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Complete, automatically generated index of every project page in projects/

234 of 234 projects. Derived from each project's YAML frontmatter; the curated index is the hand-organized entry point. Filters combine (AND across groups, OR within a group).

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FLAGSHIPBIOLOGY_DOMAINPIPELINEEVALUATIONML_PREDICTIONSOBSOLETION
Collection
Function prediction evaluationPropagation by homology
Maturity
SCOPINGIN_PROGRESSMATURECOMPLETEARCHIVED
Species
9ARCH9CAUD9INFA9POAL9PRIMABRPRACEPAACET2ACIAMACIBAACIBZAEDAEAERERAERMEAERPEAGKCOAMPQEANOGAAQUCTARAHYARATHARTANASPFUASPNGASPORAZOVIBACANBACCEBACFGBACSPBACSUBALMUBETPNBORPEBOVINBPBPPBPD31BPG15BPP1BPP22BPPGKBPPH2BPPHTBPPRDBPT4BPT5BPZF4BRADIBREDIBRUMABUNYWCAEBRCAEELCALMICANALCANGACANLFCAPO3CERSPCHICKCHLRECHRVOCIOINCLOCLCOLLICOTJACRIGRCUCMECUPNHCUPPJDANREDAPPUDEIRADERPTDESPSDESRODESVHDICDIDOROPDORPEDROMEDROPSDROVIEBOZMECO57ECO8NECOLIECOLXEMENIENTCLENTH1ENTM13ENTPHEUPSCFELCAFERPAFLAJ1FULFLFUSOXGADMOGEOSEGEOSLGIAICGIBF5GIBZEHALSAHALVDHETGAHHV8PHORSEHORVUHYPJEJUGREKLEPNLACLALACLMLAMBDLEIMALOTJAMACFAMAIZEMEDTRMETACMETEAMETJAMETS5METTHMETTPMONBEMOOTHMYCMDMYCS2MYCSMMYCTUMYTGAMYXXANEMVENEUCRNICATNITRPNOSB1NOVADOCTBMOCTVUORYSIORYSJOSCPEPANPAPARTEPENCHPETHYPHATCPLAF7POLH7POPTRPRIPAPROREPSE14PSEAEPSEAIPSEENPSEPKPSESDPYRO7PYRORRABITRAMVARHIMERHOCBRHOPARHOTORUMJORVFVZSACENSACS2SALRSSALSPSALTYSCHPOSENDZSEPOFSFVCPSHEONSHIFLSINDVSIRV1SOLHASOLPISORBISOYBNSPHCRSPHIUSPHPISPHSMSTAATSTAAUSTAHASTAWASTECRSTHOUSTRCOSTRP1STRPUSTRTRSULACSYNE7TACTRTAKRUTETTSTHAPSTHLARTOBACTOXGMTOXGOTRIV3TRYB2TRYBBTRYCRVARPDVARPSVIBCHWHEATXANAUXANCPXENLAXENNAXENTRhumanmouseratwormyeastzebrafish
Review
READY
Project Maturity Review Tags Species Genes Docs SlidesBrief
"X involved in Y" — Precomposed GO Terms and Their Decomposition
INVOLVED_IN_PRECOMPOSITION
SCOPING — OBSOLETIONPIPELINE humanmouseDROMEwormDICDIyeast — 1 — —
Accessible Surfaceome (SurfaceBench) Comparison
SURFACEOME
IN_PROGRESS READY EVALUATIONBIOLOGY_DOMAIN human — — — brief ↗
Ad-Hoc Bioinformatics Analysis Project
AD_HOC_BIOINFORMATICS
IN_PROGRESS — PIPELINEFLAGSHIP SCHPOhumanCANALBPZF4 4 1 slides brief ↗
Adaptive Immunity
ADAPTIVE_IMMUNITY
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP human — 1 — —
Affinage Evaluation Project
AFFINAGE_EVALUATION
MATURE — PIPELINEEVALUATION human — 39 slides brief ↗
Agent-Based Modeling of Intracellular Trafficking
ABM_TRAFFICKING
IN_PROGRESS — PIPELINEBIOLOGY_DOMAIN humanmouseDROMESCHPOworm 33 — — —
Alkyl Hydroperoxide Reductase Activity — Obsoletion & Replacement
ALKYL_HYDROPEROXIDE_REDUCTASE_OBSOLETION
SCOPING — OBSOLETION ECOLIPSEAE — 1 slides brief ↗
Allergens Project
ALLERGENS
IN_PROGRESS — BIOLOGY_DOMAIN FELCACANLFHORSEBOVINDERPTBETPNmouserathuman 22 1 slides brief ↗
AlphaFold Database Integration for Gene Annotation Review
ALPHAFOLD
SCOPING — PIPELINE — — 1 slides brief ↗
Alzheimer Disease Gene Review Project
ALZHEIMER_DISEASE
MATURE — BIOLOGY_DOMAIN human 34 1 slides brief ↗
Amino Acid Activation Terms — Obsoletion of 43 Substrate-Specific tRNA Aminoacylation BPs
AMINO_ACID_ACTIVATION_OBSOLETION
IN_PROGRESS — OBSOLETION humanPSEPKPOPTRDANREMETTPDROME — 1 slides brief ↗
Anti-CRISPR Proteins Project
ANTI_CRISPR
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP BPZF4 2 1 slides brief ↗
Antimicrobial Resistance (AMR) Project
ANTIMICROBIAL_RESISTANCE
MATURE — BIOLOGY_DOMAINFLAGSHIP ECOLXECO8NENTCLSALSPAERMEKLEPNAERERBACFGBACANBACSPSTAAUBACSUPSEAIPROREACIBZACIBASPHSMSTAATMYCSMSTAHASTAWA 30 4 slides brief ↗
Apoptosis Project
APOPTOSIS
SCOPING — BIOLOGY_DOMAIN humanmousezebrafish — 2 — —
Arabidopsis Heat Stress Gene Curation Project
ARATH_HEAT_STRESS
MATURE — BIOLOGY_DOMAINFLAGSHIP ARATH 10 1 slides brief ↗
Arabidopsis Single-Cell Response to Fungal Infection
ARATH_SINGLE_CELL_FUNGAL
IN_PROGRESS — BIOLOGY_DOMAIN ARATH 6 — — —
Arabidopsis thaliana corpus
ARATH
SCOPING — BIOLOGY_DOMAINFLAGSHIP ARATH 288 3 — —
ARBA Rule Review
ARBA_REVIEW
IN_PROGRESS — PIPELINEEVALUATION humanPSEPKyeastwormDROMEmouseSCHPO — 4 — brief ↗
Archaea
ARCHAEA
IN_PROGRESS — BIOLOGY_DOMAIN METJASULACMETACMETTPFERPA9ARCHNITRPMETS5ACIAMSACS2METTHHALSAHALVD 35 1 — —
Aromatic Amino Acid Biosynthetic Process, Prephenate Pathway — Obsoletion
PREPHENATE_PATHWAY_OBSOLETION
SCOPING — OBSOLETION ARATHPETHYMYCTU — 1 slides brief ↗
ASSAY_TO_FUNCTION
ASSAY_TO_FUNCTION
MATURE — PIPELINE — — 7 slides brief ↗
Autoimmune Genetics - Greatest Hits
AUTOIMMUNE
IN_PROGRESS — BIOLOGY_DOMAIN human 20 1 slides brief ↗
Bacillus subtilis project
BACSU
MATURE — BIOLOGY_DOMAINFLAGSHIP BACSU 35 2 slides brief ↗
Bacteriophage Genome Curation & Pathway Hole Filling
PHAGES
SCOPING — BIOLOGY_DOMAINPIPELINE BPT49CAUDBPZF4BPBPPBPPHTBPD31ENTM13ENTPHSIRV1 — — — —
Behaviour Annotation Project
BEHAVIOR
MATURE — PIPELINEFLAGSHIP mousehumanratwormyeastDANREDROMEDAPPU 15 5 slides brief ↗
Bgee expression as evidence: explaining, corroborating and contesting function
BGEEDB_EXPRESSION
IN_PROGRESS — PIPELINEEVALUATION humanmouse 25 3 — —
BIOINFORMATICS Case Studies
BIOINFORMATICS
IN_PROGRESS — PIPELINE SCHPO 3 1 slides brief ↗
Biomolecular Condensates
CONDENSATES
IN_PROGRESS — BIOLOGY_DOMAIN humanwormSCHPOmouse 13 3 slides brief ↗
BioReason-Pro Comparison Project
BIOREASON_COMPARISON
MATURE — PIPELINEFLAGSHIPEVALUATION humanmouseratwormyeastSCHPODROMEARATHECOLIBACSUPSEPK9CAUDAGKCOANOGA — 23 slides brief ↗
Biosynthetic Gene Cluster (BGC) Enzyme Complexes Project
BGC
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP PSEAESTRCOSACEN 6 1 slides brief ↗
Boolean models: modules as executable logic
BOOLEAN_MODELS
SCOPING — PIPELINE human — 3 — brief ↗
C. elegans Ciliopathy/IFT Pathway Project
CAEEL_CILIOPATHY
MATURE — BIOLOGY_DOMAINFLAGSHIP worm 20 3 slides brief ↗
C. elegans Lysosome-to-Nucleus Lipid Signaling (OEA Pathway)
CAEEL_LYSOSOME_NUCLEUS_LIPID_SIGNALING
IN_PROGRESS — BIOLOGY_DOMAIN worm 4 1 slides brief ↗
C. elegans Mitophagy & Mitochondrial Quality Control Project
CAEEL_MITOPHAGY
MATURE — BIOLOGY_DOMAINFLAGSHIP worm 17 2 slides brief ↗
C. elegans P Granule/Germ Granule Dynamics Project
CAEEL_P_GRANULES
MATURE — BIOLOGY_DOMAINFLAGSHIP worm 29 1 slides brief ↗
C. elegans Proteostasis Network Project
CAEEL_PROTEOSTASIS
MATURE — BIOLOGY_DOMAINFLAGSHIP worm 17 3 slides brief ↗
C. elegans Surveillance Immunity Project
CAEEL_SURVEILLANCE_IMMUNITY
MATURE — BIOLOGY_DOMAINFLAGSHIP worm 18 4 slides brief ↗
C. elegans Unfolded Protein Response & Stress Integration Project
CAEEL_UPR_STRESS
MATURE — BIOLOGY_DOMAINFLAGSHIP worm 18 2 slides brief ↗
CACAO community annotations review
CACAO
IN_PROGRESS — EVALUATION STRP1EBOZMyeastRVFVZBUNYWBPPRDPSEAEBPP22SHIFLECOLIBPPH2BPT4BPT5BPP1BPPGK9CAUDHHV8PSENDZSINDVSFVCPSALTYTRYCRNOSB1BACSULAMBDhumanmouseratARATHDROMEMYXXARHOCBPSE14BPG15 45 2 — —
CAEEL Surveillance Immunity Project - Comprehensive Curation Recommendations
SURVEILLANCE_IMMUNITY_CURATION_RECOMMENDATIONS
COMPLETE — BIOLOGY_DOMAINFLAGSHIP worm 18 — — —
Calcitriol Biosynthesis from Calciol — Obsoletion & Replacement
CALCITRIOL_BIOSYNTHESIS_OBSOLETION
SCOPING — OBSOLETION humanmouserat 5 1 slides brief ↗
Cargo Receptor Ligand Activity (GO:0140355) — Obsoletion & Transfer
CARGO_RECEPTOR_LIGAND_ACTIVITY_OBSOLETION
SCOPING — OBSOLETION humanmouserat 6 1 slides brief ↗
CASP-like (CASPL) family curation
CASPL_FAMILY
MATURE — BIOLOGY_DOMAIN ARATHPOPTR 22 5 slides brief ↗
Cellulosome Project
CELLULOSOME
MATURE — BIOLOGY_DOMAINFLAGSHIP ACET2CLOCL 22 1 slides brief ↗
Cephalopod Neuro Gene Reviews
CEPHALOPOD
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP OCTVUOCTBMDORPESEPOFSTHOUDOROPEUPSC 16 2 slides brief ↗
cGAS-STING Cytosolic DNA Sensing Project
CGAS_STING_PATHWAY
SCOPING — BIOLOGY_DOMAINFLAGSHIP human — 1 slides brief ↗
Chimeric mRNA Trans-Fusions in Immunity
CHIMERIC_MRNA_IMMUNITY
IN_PROGRESS — BIOLOGY_DOMAIN humanmouse 2 1 slides brief ↗
Ciliary Basal Body-Plasma Membrane Docking — Obsoletion & Replacement
CILIARY_BASAL_BODY_DOCKING_OBSOLETION
SCOPING — OBSOLETION human — 1 slides brief ↗
ClinGen Mendelian Disease Genes
CLINGEN_MENDELIAN
IN_PROGRESS — BIOLOGY_DOMAIN human 2876 3 slides brief ↗
CO2-Concentrating Mechanisms
CO2_CONCENTRATING_MECHANISMS
IN_PROGRESS — BIOLOGY_DOMAIN CHLREARATH 17 — — —
Complex Portal Annotation Correctness
COMPLEXPORTAL
SCOPING — PIPELINE humanyeastDROMEwormSCHPOmouseECOLIARATHrat 17 — — —
Comprehensive GO Annotation Review: C. elegans Surveillance Immunity Genes (Priority 2)
SURVEILLANCE_IMMUNITY_GENES_REVIEW
COMPLETE — BIOLOGY_DOMAIN worm 6 — — —
Conidiation regulatory cascade — module design proposal
CONIDIATION
MATURE — BIOLOGY_DOMAIN EMENINEUCR 30 1 slides brief ↗
Conserved-function recovery: can GO annotation find a function every genome has?
CONSERVED_FUNCTION_RECOVERY
IN_PROGRESS — EVALUATION — — — — —
Contested Function Project
CONTESTED_FUNCTION
IN_PROGRESS — PIPELINEFLAGSHIP SCHPOSACENPSEAESTRCO 4 1 slides brief ↗
Contractile Vacuole Tethering — Obsoletion & Replacement (GO:0140025)
CONTRACTILE_VACUOLE_TETHERING_OBSOLETION
SCOPING — OBSOLETION DICDI — 1 slides brief ↗
COSCIENTIST
COSCIENTIST
IN_PROGRESS — PIPELINE humanECOLIMYCTUMETJASCHPOworm — 1 slides brief ↗
CRISPR-Cas immunity and anti-CRISPR counter-defence
CRISPR_ANTI_CRISPR
SCOPING — BIOLOGY_DOMAIN BPZF4 1 — — —
Cuproptosis (Copper-Dependent Cell Death) Project
CUPROPTOSIS
SCOPING — BIOLOGY_DOMAIN human 7 1 slides brief ↗
Cytochrome P450 Project: GO molecular function across the human superfamily
CYTOCHROME_P450
IN_PROGRESS — PIPELINE human 14 — — —
Deliverome GO Collaboration
DELIVEROME
IN_PROGRESS — BIOLOGY_DOMAIN humanmouse 4 1 slides brief ↗
Dictyostelium Development Project
DICTYOSTELIUM_DEVELOPMENT
MATURE — BIOLOGY_DOMAIN DICDI — 1 slides brief ↗
dismech metabolic disorders aligned with ai-gene-review
DISMECH_METABOLIC_ALIGNMENT
IN_PROGRESS — — human 154 1 — —
eggNOG-mapper Evaluation
EGGNOG_MAPPER_EVALUATION
IN_PROGRESS — EVALUATIONPIPELINE — — 2 — brief ↗
Ent-Kaurene Oxidation to Kaurenoic Acid — Obsoletion & Replacement
KAURENE_OXIDATION_OBSOLETION
SCOPING — OBSOLETIONFLAGSHIP ARATHORYSJ — 1 slides brief ↗
Entner-Doudoroff Sub-pathway Obsoletion (GO:0009255, GO:0061679, GO:0061680, GO:0061681)
ENTNER_DOUDOROFF_OBSOLETION
IN_PROGRESS — OBSOLETION PSEPK 3 1 slides brief ↗
Enzyme Specificity Project
ENZYME_SPECIFICITY
COMPLETE — PIPELINEFLAGSHIP CANALhumanSACEN 14 1 slides brief ↗
ER-phagy (Selective ER Autophagy) Project
ER_PHAGY
SCOPING — BIOLOGY_DOMAINFLAGSHIP human 12 1 slides brief ↗
Ergothioneine Biosynthesis Variant-Pathway Terms — Obsoletion
ERGOTHIONEINE_BIOSYNTHESIS_OBSOLETION
SCOPING — OBSOLETION MYCS2 — 1 slides brief ↗
ER–Plasma Membrane Tethering — Obsoletion & Replacement (GO:0061817)
ER_PM_TETHERING_OBSOLETION
SCOPING — OBSOLETIONFLAGSHIP humanyeastARATH 1 1 slides brief ↗
EVIDENCE_SOURCE_SUFFICIENCY
EVIDENCE_SOURCE_SUFFICIENCY
IN_PROGRESS — PIPELINEFLAGSHIP — — 3 slides brief ↗
Executable models: running the module knowledge base
EXECUTABLE_MODELS
IN_PROGRESS — PIPELINE human — 2 — brief ↗
Extracellular Cytochrome Nanowires
EXTRACELLULAR_CYTOCHROME_NANOWIRES
IN_PROGRESS — BIOLOGY_DOMAINPIPELINE GEOSLSHEON 3 — — —
Extracellular Matrix (ECM) Project
ECM
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP human 10 1 slides brief ↗
Ferroptosis Project
FERROPTOSIS
MATURE — BIOLOGY_DOMAINFLAGSHIP human 22 1 slides brief ↗
FlyBase gene groups as review sets
FLYBASE_GENE_GROUPS
IN_PROGRESS — BIOLOGY_DOMAIN DROME 8 — — —
Function Knowledge Gaps
FUNCTION_KNOWLEDGE_GAPS
MATURE — PIPELINEFLAGSHIP — — 4 slides brief ↗
Function Prediction Evaluation
FUNCTION_PREDICTION_EVALUATION
IN_PROGRESS — EVALUATIONPIPELINEFLAGSHIP — — 2 slides brief ↗
Function Requirement (NOT) Rules
FUNCTION_REQUIREMENT_RULES
IN_PROGRESS — PIPELINE ECOLIMETEAPSEPKhuman 17 — — —
Fungal growth and knockout phenotype resources
FUNGAL_PHENOTYPES
SCOPING — BIOLOGY_DOMAIN SCHPOyeast — 1 — —
Fungal PAINT Family Reviews
FUNGAL_PAINT_FAMILIES
IN_PROGRESS — — yeastSCHPOCANALNEUCRASPFUEMENI — — — —
G protein-coupled receptors (GPCRs): families, modules and functions
GPCR
SCOPING — BIOLOGY_DOMAINFLAGSHIP human 8 — — —
Gene model errors: fused UniProt entries
GENE_MODEL_ERRORS
SCOPING — PIPELINE RHOTO9POALASPORWHEAT 18 — — —
Genome-wide validation: system-level plausibility of annotation sets
GENOME_WIDE_VALIDATION
IN_PROGRESS — PIPELINEEVALUATION ECOLI — 3 slides brief ↗
Geranylgeranyl Reductase Activity — Obsoletion & Replacement
GERANYLGERANYL_REDUCTASE_OBSOLETION
SCOPING — OBSOLETION humanARATHTOBAC — 1 slides brief ↗
Glycobiology Project
GLYCOBIOLOGY
IN_PROGRESS — BIOLOGY_DOMAINPIPELINE human 11 6 slides brief ↗
GO Annotation Curation Review: C. elegans Surveillance Immunity Genes
SURVEILLANCE_IMMUNITY_CURATION_FINDINGS
COMPLETE — BIOLOGY_DOMAIN worm 6 — — —
GO Annotation Review Summary: C. elegans Priority 3 Surveillance Immunity Genes
SURVEILLANCE_IMMUNITY_GENE_REVIEW_SUMMARY
COMPLETE — BIOLOGY_DOMAIN worm 6 — — —
GO-CAM compartments
GOCAM_COMPARTMENTS
SCOPING — PIPELINE humanmouseSCHPO — — — —
Human BBSome Project
HUMAN_BBSOME
MATURE — BIOLOGY_DOMAIN human 14 1 slides brief ↗
Human Genes Annotation Re-Review
HUMAN_GENES_RE_REVIEW
MATURE — EVALUATION human — 2 slides brief ↗
Human Protein Atlas: Primary Cilium Life Cycle Module
HUMAN_PROTEIN_ATLAS
IN_PROGRESS — BIOLOGY_DOMAIN human 60 4 — —
Human Proteostasis Network
PROTEOSTASIS
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP human — 753 slides brief ↗
Hypochlorous Acid Metabolic Process Terms — Obsoletion
HYPOCHLOROUS_ACID_OBSOLETION
IN_PROGRESS — OBSOLETION mouse 1 1 slides brief ↗
IBA Annotation Quality Project
IBA_REVIEW
MATURE — PIPELINEFLAGSHIP humanCANALMYCTUVIBCHSCHPOECOLImouseratwormyeastANOGAPOPTRDANREDICDINEUCRPSEAESHEON 103 10 slides brief ↗
brief ↗
ICAM-3 Receptor Activity — Obsoletion & Replacement
ICAM3_RECEPTOR_ACTIVITY_OBSOLETION
SCOPING — OBSOLETION human — 1 slides brief ↗
Inferred from Expression Pattern (IEP) Evidence Code Review
IEP
MATURE — PIPELINEEVALUATION ratARATHhumanwormDICDIECOLIORYSJMEDTRmouseyeastDROME 64 3 slides brief ↗
Inferred from Sequence Orthology (ISO) Evidence Code Review
ISO
IN_PROGRESS — PIPELINEEVALUATION humanmouserat — 1 slides brief ↗
Innate Immune System Pathways Across Animals
INNATE_IMMUNITY
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP humanmouseCHICKDANREXENTRDROMEANOGAwormNEMVETACTR — 1 — —
Integrated Stress Response (ISR) Project
INTEGRATED_STRESS_RESPONSE
SCOPING — BIOLOGY_DOMAINFLAGSHIP human — 1 slides brief ↗
InterPro Mapping Review Project
INTERPRO
IN_PROGRESS — PIPELINE — — 3 slides brief ↗
IRD Evidence: How PAINT Uses Inferred from Rapid Divergence
IRD_EVIDENCE
IN_PROGRESS — EVALUATIONPIPELINE humanmouseratyeastSCHPODROMENEUCRARATH 15 5 — —
Iron-Sulfur Cluster Biogenesis Project
IRON_SULFUR_CLUSTER_BIOGENESIS
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP human 15 1 slides brief ↗
ISOFORMS: Genes with Clear Functional Differences Between Isoforms
ISOFORMS
MATURE — PIPELINEFLAGSHIP humanmouseratDROME 23 1 slides brief ↗
KW-1110 (Inhibition of host TRAFs by virus) — KW2GO remapping
KW_1110_TRAF_KW2GO
COMPLETE — PIPELINEOBSOLETION — — 1 slides brief ↗
LBNL Hackathon: Dark Protein Atlas genes
LBNL_HACKATHON
SCOPING — EVALUATION LACLMLACLASALTYECOLISYNE7RHIME 5 — — —
Ligands in signaling pathways
LIGANDS_IN_SIGNALING
IN_PROGRESS — PIPELINE humanDANREDROMESCHPO 32 1 — brief ↗
Lipoate Biosynthetic Process — Obsoletion & Merge into Protein Lipoylation
LIPOATE_BIOSYNTHESIS_OBSOLETION
IN_PROGRESS — OBSOLETION BACSUPSEPKPOPTRMETEAhumanmouseyeast — 1 slides brief ↗
MAPK Cascades: Module and Gene Review Coverage
MAPK_CASCADES
SCOPING — BIOLOGY_DOMAIN humanmouseratyeastSCHPOwormDROME — — — —
Mechanobiology Gene Review Project
MECHANOBIOLOGY
SCOPING — BIOLOGY_DOMAINFLAGSHIP human — 1 slides brief ↗
Metabolic Model Analysis Project
METABOLIC_MODEL_ANALYSIS
MATURE — PIPELINEFLAGSHIPEVALUATION METEAECOLIhuman 8 1 slides brief ↗
Metabolomics Interpretation with GO and GO-CAM
METABOLOMICS
IN_PROGRESS — PIPELINE — — 19 slides brief ↗
Methylorubrum extorquens MLL Cluster Curation Project
METEA_MLL_CLUSTER
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP METEA 10 1 slides brief ↗
Mevalonate Pathway Term Cleanup — Obsoletion & Replacement
MEVALONATE_PATHWAY_OBSOLETION
IN_PROGRESS — OBSOLETION humanratyeast 9 1 slides brief ↗
Microproteins (sORF-encoded peptides)
MICROPROTEINS
SCOPING — BIOLOGY_DOMAIN human 43 1 — —
MicroRNA Degradation / TDMD Project
MIRNA_DEGRADATION
MATURE — BIOLOGY_DOMAINFLAGSHIP human 9 2 slides brief ↗
Miscitation Audit
MISCITATION_AUDIT
IN_PROGRESS — PIPELINEEVALUATION — — 3 slides brief ↗
Miscitation Review Project
MISCITATIONS
IN_PROGRESS — PIPELINEEVALUATION humanARATH 21 3 slides brief ↗
Mitochondrial Fatty Acid β-Oxidation (cross-species)
FATTY_ACID_BETA_OXIDATION
IN_PROGRESS — BIOLOGY_DOMAIN humanDROMEmouse 27 2 slides brief ↗
Mitochondrial Import Pathways Project
MITOCHONDRIAL_IMPORT_PATHWAYS
MATURE — BIOLOGY_DOMAIN human 23 2 slides brief ↗
Mitochondrion Targeting Sequence Binding — Obsoletion & Replacement
MITOCHONDRION_TARGETING_SEQUENCE_BINDING_OBSOLETION
SCOPING — OBSOLETIONFLAGSHIP humanyeastworm 10 1 slides brief ↗
Mitochondrion–ER Membrane Tethering — Obsoletion & Replacement (GO:1990456)
MITO_ER_TETHERING_OBSOLETION
SCOPING — OBSOLETIONFLAGSHIP humanmouse 5 1 slides brief ↗
MitoMatch: The AlphaFold-Multimer Interactome of the Human Mitochondrial Proteome
MITO_INTERACTOME
IN_PROGRESS — BIOLOGY_DOMAINPIPELINE humanyeast 26 1 slides brief ↗
MitoTOL: Mitochondrial Proteomes Across the Tree of Life
MITOTOL
IN_PROGRESS — BIOLOGY_DOMAIN humanyeast 26 — — —
MOD gene descriptions as review input
MOD_DESCRIPTIONS
IN_PROGRESS — PIPELINEEVALUATION wormyeastDROME — 1 — —
Module literature, taxonomy and member review audit
MODULE_TAXON_AUDIT
IN_PROGRESS — BIOLOGY_DOMAIN — — — — —
Molecular Adaptor Activity Annotation Review
MOLECULAR_ADAPTOR_ACTIVITY
SCOPING — PIPELINEBIOLOGY_DOMAIN human — 3 — —
Mouse Genes Annotation Re-Review
MOUSE_GENES_RE_REVIEW
COMPLETE — EVALUATION mouse — — — —
Naked Mole Rat (HETGA) Annotation Review
NAKED_MOLE_RAT
IN_PROGRESS — BIOLOGY_DOMAIN HETGA 8 1 slides brief ↗
NCBI RefSeq vs UniProt/GOA: prokaryotic GO pipeline comparison
REFSEQ_GO
IN_PROGRESS — PIPELINE PSEPKPSEAE — — — brief ↗
brief ↗
NCBIFAM / CDD → GO Contribution & Gap Project
NCBIFam
IN_PROGRESS — PIPELINE — — 23 slides brief ↗
Neural and Glial Cell Fate Determination Project
NEURON_DEVELOPMENT
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP human 13 1 slides brief ↗
Neural Crest Formation (GO:0014029) — Obsoletion Proposal
NEURAL_CREST_FORMATION_OBSOLETION
SCOPING — OBSOLETION XENLAhuman 18 5 — —
Neuroblast Proliferation / Division — Vertebrate vs Protostome Disambiguation
NEUROBLAST_PROLIFERATION_DISAMBIGUATION
SCOPING — BIOLOGY_DOMAINFLAGSHIP mousehumanrat — 1 slides brief ↗
Nicotine Biosynthesis Project
NICOTINE_BIOSYNTHESIS
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP NICAT 22 2 slides brief ↗
Nitratidesulfovibrio vulgaris Pathways Project
NITV2_PATHWAYS
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP DESVH 23 1 slides brief ↗
Nitrogen Cycle Metabolic Process — do_not_annotate / Regulation Term Obsoletion
NITROGEN_CYCLE_OBSOLETION
SCOPING — OBSOLETION mousehumanAZOVI 2 1 slides brief ↗
Nitrogen Cycle Module
NITROGEN_CYCLE
SCOPING — BIOLOGY_DOMAIN — — 1 slides brief ↗
NLRP3 Inflammasome Assembly Project
NLRP3_INFLAMMASOME
SCOPING — BIOLOGY_DOMAINFLAGSHIP human — 1 slides brief ↗
No Data (ND): what an ND annotation is telling us
NO_DATA
SCOPING — PIPELINE yeastSCHPODROMECANALwormDANREARATHhumanmouse — 1 — —
Non-Physiological Reactions in EC, Rhea and GO
NONPHYSIOLOGICAL_REACTIONS
SCOPING — PIPELINEOBSOLETION yeastBACCEBACSUPSESDCUPPJSPHCRSPHIUBREDIXANAU 9 — — —
NOT Annotation Usage Audit
NOT_ANNOTATION_USAGE
IN_PROGRESS — EVALUATIONPIPELINE humanratARATHSCHPO 9 1 — —
Nuclear Localization Sequence Binding — Obsoletion & Replacement
NLS_BINDING_OBSOLETION
SCOPING — OBSOLETION humanyeastratDROMEwormARATH — 1 slides brief ↗
Omics and High-Throughput Evidence in GO Annotation
OMICS_EVIDENCE
IN_PROGRESS — PIPELINEEVALUATION humanyeastSCHPOARATH 30 1 — —
Organelle Lifecycle Modules
ORGANELLE_LIFECYCLES
SCOPING — BIOLOGY_DOMAIN — — 1 — —
Organelles
ORGANELLES
SCOPING — BIOLOGY_DOMAIN — — 2 — —
Origins of Animal Multicellularity
ORIGINS_OF_MULTICELLULARITY
IN_PROGRESS — BIOLOGY_DOMAIN SALRSMONBECAPO3OSCPEAMPQEhuman 35 2 — —
Origins of the Neural Crest
NEURAL_CREST_ORIGINS
IN_PROGRESS — BIOLOGY_DOMAIN XENLAhumanCIOIN 23 — — —
Orphan Curated: Swiss-Prot entries outside reference proteomes
ORPHAN_CURATED
IN_PROGRESS — PIPELINE ARATHBACANBREDICHLREDERPTDICDIECOLIFULFLMEDTRMOOTHNICATOCTVUORYSJPENCHPOPTRPSEPKSTAHASTAWASTECRSTRTRTHLARTOXGOXANAU 39 3 — —
Ortholog Conjecture Project
ORTHOLOG_CONJECTURE
SCOPING — EVALUATION — — 1 slides brief ↗
Over-Annotation Patterns Project
OVER_ANNOTATION_PATTERNS
MATURE — PIPELINEFLAGSHIPEVALUATION humanSCHPOCANALPSEAESTRCOSACENHORSE 11 1 slides brief ↗
Oxidative Phosphorylation (OXPHOS) Project
OXPHOS
MATURE — BIOLOGY_DOMAIN human 36 1 slides brief ↗
P. putida Gene Annotation Review Project
P_PUTIDA
IN_PROGRESS — BIOLOGY_DOMAIN PSEPK — 263 slides brief ↗
PAINT Human No-IBA Gene Review Project
PAINT
IN_PROGRESS — PIPELINEFLAGSHIP human — — slides brief ↗
brief ↗
Pancrustacea Metamorphosis Gene Families
PANCRUSTACEA_METAMORPHOSIS
MATURE — BIOLOGY_DOMAIN DROME 8 1 slides brief ↗
PANTHER family assignment discrepancies
PANTHER_FAMILY_ASSIGNMENT_DISCREPANCIES
SCOPING — EVALUATIONPIPELINE humanworm 2 — — —
PANTHER IBA family review
PANTHER_IBA_REVIEW
MATURE — EVALUATIONPIPELINE SCHPO — 3 slides brief ↗
Parasite Immune Modulators
PARASITE_IMMUNE_MODULATORS
IN_PROGRESS — BIOLOGY_DOMAIN DESRO — 1 slides brief ↗
Parasites
PARASITES
IN_PROGRESS — BIOLOGY_DOMAIN STECRBRUMA 6 1 slides brief ↗
Pathway satisfiability: context-resolved module logic
PATHWAY_SATISFIABILITY
IN_PROGRESS — PIPELINE — — 7 slides brief ↗
PDB: Deposited Structures as Functional-Insight Evidence
PDB
MATURE — PIPELINEEVALUATION METACBACSUPSEAIMETEAhuman — 6 slides brief ↗
Pennycress (Thlaspi arvense) Oilseed Domestication Genes
THLAR_OILSEED
IN_PROGRESS — BIOLOGY_DOMAIN THLARARATH 9 5 — —
Peroxisome Biogenesis Project
PEROXISOME
MATURE — BIOLOGY_DOMAIN human 16 1 slides brief ↗
Peroxisome Targeting Signal Binding — Obsoletion & Replacement
PEROXISOME_TARGETING_SIGNAL_OBSOLETION
COMPLETE — OBSOLETION human 3 1 slides brief ↗
Pfam → GO Mapping: A Precision Gap-Filling Experiment
PFAM
MATURE — PIPELINEEVALUATION — — 4 slides brief ↗
Phagocytosis Modules
PHAGOCYTOSIS
IN_PROGRESS — BIOLOGY_DOMAIN humanmousewormDROMEDICDI 34 — — —
Phosphorylation Annotation Refactor Project
PHOSPHORYLATION_REFACTOR
MATURE — PIPELINEFLAGSHIP humanmouse — 4 slides brief ↗
Photosynthesis Project
PHOTOSYNTHESIS
IN_PROGRESS — BIOLOGY_DOMAIN CHLREARATH — 1 slides brief ↗
PINK1-Parkin Mitophagy Project
MITOPHAGY
SCOPING — BIOLOGY_DOMAINFLAGSHIP human 8 1 slides brief ↗
Plant Bioenergy Modules
PLANT_BIOENERGY
IN_PROGRESS — BIOLOGY_DOMAIN ARATHPOPTRSORBI — 1 slides brief ↗
Plant-Encoded Sense & Response Biosensors
BIOSENSORS
SCOPING — BIOLOGY_DOMAIN ARATH 12 1 slides brief ↗
Plant-Fungal Interactions
PLANT_FUNGAL_INTERACTIONS
IN_PROGRESS — BIOLOGY_DOMAIN ARATHORYSJHORVUMEDTRLOTJAPYRO7FULFLMYCMDGIBZESOLPISOLHAPYRORFUSOX 55 — — —
Prokaryotic Immunity Term Prediction
PROKARYOTIC_IMMUNITY_TERM_PREDICTION
SCOPING — PIPELINE — — 1 slides brief ↗
Propagation by Homology
HOMOLOGY_PROPAGATION
IN_PROGRESS — PIPELINEEVALUATION — — 2 slides brief ↗
Protein Complex Functions Project
PROTEIN_COMPLEX_FUNCTIONS
IN_PROGRESS — PIPELINEFLAGSHIP human — 23 slides brief ↗
Protein Families
FAMILIES
IN_PROGRESS — PIPELINEEVALUATION — — 4 slides brief ↗
Protein Localization to ER Exit Site — Obsoletion
ER_EXIT_SITE_LOCALIZATION_OBSOLETION
IN_PROGRESS — OBSOLETIONFLAGSHIP humanyeast 3 1 slides brief ↗
Protists
PROTISTS
IN_PROGRESS — BIOLOGY_DOMAIN PLAF7TOXGMTOXGOTRYB2TRYBBLEIMATETTSPARTEGIAICTRIV3ENTH1PHATCTHAPSDICDICHLRESALRSMONBECAPO3 25 — — —
ProtNLM2 Evaluation
PROTNLM_EVALUATION
IN_PROGRESS — EVALUATIONML_PREDICTIONS humanHORSE9PRIMABRPRAEDAEAQUCTARAHYARATHARTANASPORBALMUBORPEBOVINCAEELCALMICANLFCHRVOCOLLICOTJACUCMEDANREDEIRADROMEDROPSDROVIGADMOGIBF5JUGREMACFAMAIZEMYTGANEUCRORYSIORYSJPANPAPARTEPHATCRABITSCHPOSOYBNSTRCOTAKRUTOBACTRIV3WHEATXANCPXENLAXENNAXENTRmouseratworm 282 162 slides ↗ brief ↗
PseudoCAP annotation review: P. aeruginosa seeds of PAINT IBAs
PSEUDOCAP
IN_PROGRESS — BIOLOGY_DOMAINPIPELINE PSEAE 107 5 — —
Pseudoenzymes Project
PSEUDOENZYMES
MATURE — PIPELINEFLAGSHIP RAMVASCHPOSACENPSEAESTRCO 9 1 slides brief ↗
Quantum Sensing Proteins and Engineering Chassis
QUANTUM_SENSING
SCOPING — BIOLOGY_DOMAIN DROMEARATHhuman — 5 slides —
Radical SAM Enzymes: GO annotation across the superfamily
RADICAL_SAM
IN_PROGRESS — PIPELINE humanECOLI 29 — — —
Rare Earth Element (REE) Extraction Pathways (Biological Systems)
REE
SCOPING — BIOLOGY_DOMAIN METEA 16 1 slides —
Re-examining the RAR misannotation study (Wei et al. 2020)
RAR_MISANNOTATION
IN_PROGRESS — EVALUATION ARATHwormDROMEmousehumanCHICK 17 1 — —
Reactome Black Box Event Gap-Filling
REACTOME_GAP_FILLING
IN_PROGRESS — PIPELINE human 1 1 slides —
Reactome-GO Alignment Project
REACTOME
SCOPING — PIPELINE human — 10 — —
Regulation of COPII Vesicle Coating — Obsoletion & Replacement
COPII_VESICLE_COATING_REGULATION_OBSOLETION
SCOPING — OBSOLETION humanyeast — 1 slides brief ↗
Regulation of Synaptic Vesicle Docking — Obsoletion & MF Refactor
SYNAPTIC_VESICLE_DOCKING_OBSOLETION
IN_PROGRESS — OBSOLETIONFLAGSHIP mouseworm 1 1 slides —
Regulation Sign Errors: Activator vs Inhibitor
REGULATION_SIGN
SCOPING — EVALUATION humanDROMEARATHworm 12 — — —
Retracted Literature Behind Annotations
RETRACTIONS
IN_PROGRESS — PIPELINEEVALUATION — — 3 slides —
Review Quality Audit
REVIEW_QUALITY_AUDIT
MATURE — PIPELINEEVALUATION — — 2 slides —
RGD Pathway Ontology: GO Mappings, GO-CAM Completeness and Module Seeds
RGD_PATHWAY_ONTOLOGY
SCOPING — PIPELINE human 7 — — —
RHEA → GO Contribution & Gap Project
RHEA
IN_PROGRESS — PIPELINE — — 7 slides —
Ribosome Quality Control (RQC) Project
RIBOSOME_QUALITY_CONTROL
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP human 13 1 slides —
Satellite Model Organisms
SATELLITE_MODEL_ORGANISMS
IN_PROGRESS — BIOLOGY_DOMAIN CAEBRPRIPA 11 1 slides —
Sea Urchin Endomesoderm GRN
STRPU_ENDOMESODERM_GRN
IN_PROGRESS — BIOLOGY_DOMAIN STRPU 27 — — —
SNIPE: Membrane-Bound Nuclease Anti-Phage Defence
SNIPE
IN_PROGRESS — BIOLOGY_DOMAIN ECOLX 1 3 slides —
Specific Annotation Edit Recommendations
SURVEILLANCE_IMMUNITY_ANNOTATION_EDITS
ARCHIVED — BIOLOGY_DOMAIN worm 6 — — —
Stilbene Cleavage Oxygenases (SCO / lignostilbene α,β-dioxygenase family)
STILBENE_CLEAVAGE_OXYGENASES
IN_PROGRESS — BIOLOGY_DOMAIN NEUCRNOVADSPHPIMYCMD 7 1 slides —
Stress Granule Assembly Project
STRESS_GRANULES
SCOPING — BIOLOGY_DOMAINFLAGSHIP human 7 1 slides —
Structural Reasoning in Annotation Review
STRUCTURAL_REASONING
IN_PROGRESS — PIPELINEBIOLOGY_DOMAIN human 5 — — —
Structure-Based Function Prediction for Gene Review
STRUCTURE_FUNCTION
IN_PROGRESS — PIPELINE — — 1 slides —
Substrate Localization to Autophagosome (GO:0061753) — Obsoletion & Transfer
SUBSTRATE_LOCALIZATION_TO_AUTOPHAGOSOME_OBSOLETION
SCOPING — OBSOLETION humanmouse 6 1 slides —
Succinate Dehydrogenase (Complex II) — gp2term Relation Review (`enables` → `contributes_to`)
SDH_GP2TERM_CONTRIBUTES_TO
IN_PROGRESS — PIPELINEFLAGSHIP human9POALPSEPK 9 1 slides —
Sulfide Oxidation Children — Obsoletion & Replacement
SULFIDE_OXIDATION_OBSOLETION
IN_PROGRESS — OBSOLETION human 3 1 slides —
Surveillance Immunity Gene Curation: Implementation Checklist
SURVEILLANCE_IMMUNITY_CURATION_CHECKLIST
ARCHIVED — BIOLOGY_DOMAIN worm 6 — — —
SwissProt Keywords (SPKW) Unique Terms Project
SPKW
MATURE — PIPELINEFLAGSHIPEVALUATION humanSCHPOANOGADROMEPSEPKARATHBPT4ECO57 — 15 slides —
Tardigrade Stress Response Protein Curation Project
TARDIGRADE_STRESS_RESPONSE
MATURE — BIOLOGY_DOMAINFLAGSHIP RAMVA 18 1 slides —
Taxon Pathway Variance
TAXON_PATHWAY_VARIANCE
IN_PROGRESS — BIOLOGY_DOMAIN wormDROMEhumanDICDICHICK 11 — — —
TCDB → GO Transporter-Activity Mapping & Gap Project
TCDB
IN_PROGRESS — PIPELINE ARATHhuman — 2 slides —
The Lipid Divide: enzymes that cross it
LIPID_DIVIDE
SCOPING — BIOLOGY_DOMAIN BACSUECOLIMETJAMETTHAERPEGEOSEFLAJ1 6 — — —
Top-Nots: Candidate NOT Annotations from Existing Reviews
TOP_NOTS
IN_PROGRESS — PIPELINEEVALUATION humanmouseyeastSCHPODROMEANOGAACET2BACSUDESVHECOLIMETEAMETTPPSEAEPSEPKSACENSALTYSTRCOCANGACLOCLARATHworm — 1 slides —
Transcription Factor Annotation Review Project
TRANSCRIPTION_FACTORS
IN_PROGRESS — BIOLOGY_DOMAINEVALUATION human 7 7 slides —
TreeGrafter Inference Evaluation
TREEGRAFTER
MATURE — EVALUATIONPIPELINE — — 11 slides brief ↗
Unfolded Protein Binding Annotation Review
UNFOLDED_PROTEIN_BINDING
MATURE — BIOLOGY_DOMAINFLAGSHIP humanmouseratyeastSCHPODROMEDANREARATHBOVINCANALCRIGRECOLINEUCRASPNGSALTYHYPJEworm — 1 slides —
UniPathway Unique Terms Project
UNIPATHWAY
MATURE — PIPELINEFLAGSHIP humanPSEPKRHOPACUPNHFERPA9ARCHDESPSPOLH7BRADI — 1 slides —
UniProt CAUTION Note Project
UNIPROT_CAUTION_NOTE
MATURE — PIPELINEFLAGSHIP human 13 8 slides —
UniProt Proteome Removal Impact Assessment
PROTEOME_REMOVAL
IN_PROGRESS — PIPELINE 9INFAPSEAIACEPARUMJOECO57ANOGANITRPCERSPPSEENCLOCL9CAUD 15 1 slides brief ↗
UniProt Subcellular Locations (SL) Unique Terms Project
SL
IN_PROGRESS — PIPELINEEVALUATION humanmouseyeastSCHPOwormDICDI — 6 slides —
Validating E. coli ML Predictions
VALIDATING_ECOLI_PREDICTIONS
COMPLETE — PIPELINEFLAGSHIPEVALUATION ECOLI 7 1 slides —
VAMPIROME
VAMPIROME
IN_PROGRESS — BIOLOGY_DOMAIN DESRO 14 3 slides —
Variovorax Metal Recovery & Rhizosphere Interactions
VARIOVORAX
IN_PROGRESS — BIOLOGY_DOMAIN VARPSVARPD 58 1 — —
Vesicle Docking BP Subtree — Obsoletion & MF Refactor (GO:0048278)
VESICLE_DOCKING_OBSOLETION
IN_PROGRESS — OBSOLETION human 2 1 slides —
Vesicle Targeting (GO:0006903) & Descendants — Obsoletion & Replacement
VESICLE_TARGETING_OBSOLETION
SCOPING — OBSOLETIONFLAGSHIP humanyeast 7 1 slides —
Vesicle Tethering BP Subtree — Obsoletion & MF Refactor (GO:0099022)
VESICLE_TETHERING_OBSOLETION
IN_PROGRESS — OBSOLETION human 10 1 slides —
Wrong-Gene Leads
WRONG_GENE_LEADS
IN_PROGRESS — PIPELINE humanECOLIARATHDICDIDROMEmouse 28 — — —
Yeast Cell Cycle & Translation Control
YEAST_CELL_CYCLE
SCOPING — BIOLOGY_DOMAINFLAGSHIP yeast 11 1 slides —
Yeast DNA Repair & Chromatin Dynamics
YEAST_DNA_REPAIR_CHROMATIN
IN_PROGRESS — BIOLOGY_DOMAINFLAGSHIP yeast 4 1 slides —
Yeast Epigenetics & Histone Inheritance
YEAST_EPIGENETICS_HISTONE_INHERITANCE
MATURE — BIOLOGY_DOMAINFLAGSHIP yeast 28 1 slides —
Yeast Metabolic Engineering & Bioproduction
YEAST_METABOLIC_ENGINEERING
SCOPING — BIOLOGY_DOMAINFLAGSHIP yeast — 1 slides —
Yeast Replicative Aging & mRNA Processing
YEAST_REPLICATIVE_AGING
COMPLETE — BIOLOGY_DOMAINFLAGSHIP yeast 20 2 slides —
YeastPathways to Modules
YEAST_PATHWAYS
IN_PROGRESS — BIOLOGY_DOMAINPIPELINE yeastSCHPO — 3 — —
Zebrafish Genome Duplication and Paralog Pairs
DANRE_DUPLICATION
SCOPING — BIOLOGY_DOMAIN DANRE 2 67 — —