Biomni Lab x GeneCards: Grounded biomedical agentic queries powered by comprehensive integrated biomedical knowledge base
Biomni Lab now integrates GeneCards, a leading human gene knowledge base used by millions of researchers worldwide. This brings unified access to genomic, proteomic, clinical, and functional data from 200+ sources into a single agentic workflow. Genes become join points for connecting pathways, diseases, and interactions in one query. Analyses that once required multiple databases are now streamlined, traceable, and source-aware. The result is faster, more grounded biomedical discovery.
We’re excited to announce our collaboration with GeneCards, bringing one of the most widely used integrated biomedical human gene knowledge bases directly into Biomni Lab.
Used by over 5 million researchers across tens of thousands of institutions in academia, pharma and clinical institutions, GeneCards is one of the most comprehensive integrated human gene databases in the world, pulling from 200+ source databases to give genes structured, unified records spanning genomic, transcriptomic, proteomic, clinical, and functional data. It is the database scientists commonly open first when they encounter an unfamiliar gene, and is further used for target discovery and validation, genomic sequencing interpretation, patent validation and more.
Bringing it into Biomni Lab means agents can now treat gene identity as a join key across the biological literature. Disease associations, tissue expression, protein complexes, pathway memberships, regulatory elements, protein interactions, and more - all accessible in a single session, with every data point traced back to its source. The connections that previously required stitching together five different databases by hand now happen in one query, in a way that stays traceable and source-aware.
Example 1
Show me the full gene association profile for EGFR using GeneCards. For interaction partners, organize results by confidence tier based on how many source databases support each interaction, and include the association type for each gene. Also include total counts per tier, pathway memberships, and disease associations with GeneCards scores.
https://biomni.phylo.bio/replay/share_addbaf1accd6400686f39084529f17b4
Biomni returns 4,733 EGFR interaction partners ranked by confidence across seven databases. The top results include core signaling partners (CBL, GRB2, SHC1, SRC, STAT3), downstream effectors (ERBB2, KRAS, MAPK1/3, PIK3CA), and tumor suppressors (PTEN, TP53).
Example 2
I ran bulk RNA-seq on IFNγ-stimulated THP-1 macrophages vs. unstimulated (24h, 100 ng/mL, n=3). These are the significantly upregulated genes (log₂FC > 1, FDR < 0.05): STAT1, STAT2, IRF1, IRF7, IRF8, IRF9, MX1, MX2, IFIT1, IFIT2, IFIT3, IFIT5, IFITM1, IFITM2, IFITM3, ISG15, ISG20, OAS1, OAS2, OAS3, OASL, GBP1, GBP2, GBP3, GBP4, GBP5, CXCL9, CXCL10, CXCL11, IDO1, NOS2, CD274, CIITA, HLA-A, HLA-B, HLA-C, HLA-DRA, HLA-DRB1, B2M, TAP1, TAP2, TAPBP, PSMB8, PSMB9, PSME1, PSME2, TRIM21, TRIM25, HERC5, USP18, RSAD2, DDX58, SOCS1, IL6, TNF, IL1B, CCL2, CCL5, ICAM1, VCAM1, JAK2, TBK1. Using GeneCards, enrich this gene set with disease associations, expression data, and protein complexes.
https://biomni.phylo.bio/replay/share_aab0f3676195470bbe7b1e832a1edb11
Biomni maps the 61-gene set to disease associations and protein complexes using GeneCards. The top disease hub is Aicardi-Goutières Syndrome (36/61 genes), with elite associations for B2M, IRF1, and USP18. Disease links span immunodeficiencies, autoimmune disease, cancer, infectious disease, and neurodegeneration. Biomni reconstructs 11 protein complexes across 7 functional modules, including ISGF3, MHC-I peptide loading, MHC-II antigen presentation, and the immunoproteasome.
We’re excited to see what you build with GeneCards in Biomni Lab. Try it today at biomni.phylo.bio.