Most graphs only remember hits. This one keeps curated negatives right alongside the positives, so a "no" carries as much weight as a "yes." None of it is sampled or inferred.
Negatives are curated, experimentally-confirmed non-interactions and inactive screening outcomes. An inactive result records inactivity under the reported assay conditions; it does not establish non-binding in general. Positive evidence spans clinical genetics, drug–target pharmacology, precision-medicine associations, and disease ontology.
Genes dominate: 123M+ across vertebrates, plants, fungi, invertebrates, protists, and ~20k bacterial genomes. But that's just the start. Transcripts, exons, chemicals, diseases, pathways, and 20 more entity types all live in the same graph, ready to traverse together. Bars are log-scaled to keep every type visible.
The central dogma is now materialized end to end (gene → transcript → exon → coding → protein) for 20k+ organisms, with genomic-neighbor edges giving every gene its operon/synteny context. Function annotation alone now spans 13k+ species.
Genome assemblies across the tree of life were parsed into the graph, with genes created wherever a clade isn't already covered. Function annotations carry evidence-tagged relationships (enables, involved_in, located_in) across 13k+ species.
Every protein connects to proxy nodes for what it shares: its family, the ligands it binds, its modifications, its functional keywords, its domains. Two proteins in the same family, or binding the same cofactor, meet at that shared node: two edges, one traversal, no custom query required.
The molecular, clinical, and regulatory core below sits alongside the tree-of-life, shared-attribute, and RNA layers above; 80 predicates in all, each one a relationship the co-scientist can reason across. Bars are scaled within each layer.
Every edge carries source, evidence_type (experimental · computational · predicted · text_mined · curated), a native score, a negated flag, and evidence_count. Per-edge provenance and affinity measurements are stored separately, so both can be queried without denormalizing the core graph. Where sources disagree, the conflicting edges are all retained with their own evidence; positive evidence takes precedence only where a query has to resolve to a single sign.
Canonicalized and feature-complete: 39k+ duplicate nodes were merged into a single structured canonical form and their edges repointed, so no two nodes represent the same thing. Proteins carry amino-acid sequences for 98% of entries, and every structured chemical carries a machine-readable structure.
A live edge pulled from the graph for every predicate below, with entity types, evidence, and sign: actual rows, not mockups.
| Predicate | Example edge (subject → object) | Evidence | Sign |
|---|---|---|---|
| binds | Mequitazinechemical→HRH1protein | Experimental | + |
| physically_interacts_with | PARP1protein→MAPK7protein | Curated | − |
| interacts_with | HNRNPA2B1protein→SUMO2protein | Computational | + |
| expressed_in | FCGRTgene→material anatomical entityanatomy | Curated | + |
| participates_in | PARP1protein→D4-GDI Signaling Pathwaypathway | Curated | + |
| located_in | ARHGEF7gene→cell cortexcell_component | Curated | + |
| enables | GALNT7gene→carbohydrate bindingmol_function | Curated | + |
| drug_drug_interaction | Protriptylinechemical→Cisatracuriumchemical | Curated | + |
| affects | Resiniferatoxinchemical→TRPV1gene | Curated | + |
| has_side_effect | Isofluranechemical→Jaundicephenotype | Curated | + |
| investigates_condition | Jump Start Plus COVID-19 Supporttrial→mental health wellnessdisease | Curated | + |
| in_clinical_trial_for | CS1chemical→pulmonary arterial hypertensiondisease | Curated | + |
| tests_intervention | SBRT or TACE for Advanced HCCtrial→DEBchemical | Curated | + |
| has_reactant | Chloro N-alkylationreaction→Methyl alcoholchemical | Curated | + |
| has_product | Sulfanyl to sulfinylreaction→CHEMBL4793427chemical | Curated | + |
| derives_from | CHEMBL1885180chemical→CHEMBL1305819chemical | Curated | + |
| has_phenotype | diffuse palmoplantar keratodermadisease→Palmoplantar keratodermaphenotype | Curated | + |
| gene_associated_with_condition | HSBP1L1gene→Thiel-Behnke corneal dystrophydisease | Computational (60) | + |
| variant_associated_with_disease | NM_000355.4(TCN2):c.581-17variant→transcobalamin II deficiencydisease | Curated | + |
| is_sequence_variant_of | NM_000355.4(TCN2):c.581-17variant→TCN2gene | Curated | + |
| exact_match | Hurler syndromedisease→mucopolysaccharidosis type 1disease | Curated | + |
| regulates | POU2F1gene (TF)→TMEM9Bgene | Experimental (both-confirmed) | + |
| encodes | GAD1gene→GAD1protein | Curated | + |
| chem_associated_with_disease | mefloquinechemical→hearing loss, suddendisease | Curated | + |
| treats | Rutinchemical→bacterial infectionsdisease | Curated | + |
| contraindicated_for | Pheniraminechemical→benign prostatic hyperplasiadisease | Curated | + |
| subclass_of | collagen metabolic processbio_process→collagen biosynthetic processbio_process | Curated | + |
The graph is live behind every run the co-scientist makes. Come see what it can trace for you.