Synchronize core display names with Space

Set the display_name field in all 68 core embedding metadata.json files to the corresponding catalog name in Gene-Embeddings-Staging. This carries over the v1.1/v1_1 and PROBE-prefix display cleanups without changing stable IDs, paths, matrices, gene tables, or other metadata. The update is applied to current Dataset main, preserving every other field and all unrelated repository changes.

data/embeddings/alphagenome_tss1mb_regulatory_tracksummary_pca256/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "alphagenome_tss1mb_regulatory_tracksummary_pca256",
-  "display_name": "AlphaGenome-TSS1Mb-regulatoryTrackSummary-PCA256-v1.1",
+  "display_name": "AlphaGenome-TSS1Mb-regulatoryTrackSummary-PCA256",
   "species": "Homo sapiens",
   "n_genes": 20084,
   "n_dimensions": 256,

data/embeddings/basenji2_tss_131kb_human_central3/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "basenji2_tss_131kb_human_central3",
-  "display_name": "Basenji2-TSS-131kb-human-central3-log1p-zscore-v1.1",
+  "display_name": "Basenji2-TSS-131kb-human-central3-log1p-zscore",
   "modality": "regulatory DNA / Basenji2 TSS sequence model",
   "species": "Homo sapiens",
   "n_genes": 20097,

data/embeddings/biobert_gene_protein_summary/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "biobert_gene_protein_summary",
-  "display_name": "BioBERT-GeneProteinSummary-v1.1",
+  "display_name": "BioBERT-GeneProteinSummary",
   "modality": "literature_text_gene_summary",
   "species": "Homo sapiens",
   "n_genes": 19168,

data/embeddings/bioconceptvec_cbow/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "bioconceptvec_cbow",
-  "display_name": "BioConceptVec-CBOW-v1.1",
+  "display_name": "BioConceptVec-CBOW",
   "modality": "biomedical_literature_text",
   "species": "Homo sapiens",
   "original_identifier_type": "BioConceptVec concept key with Entrez/NCBI Gene ID, e.g. Gene_7157",

data/embeddings/bioconceptvec_fasttext/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "bioconceptvec_fasttext",
-  "display_name": "BioConceptVec-fastText-v1.1",
+  "display_name": "BioConceptVec-fastText",
   "modality": "biomedical_literature_text",
   "species": "Homo sapiens",
   "original_identifier_type": "BioConceptVec concept key with Entrez/NCBI Gene ID, e.g. Gene_7157",

data/embeddings/bioconceptvec_glove/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "bioconceptvec_glove",
-  "display_name": "BioConceptVec-GloVe-v1.1",
+  "display_name": "BioConceptVec-GloVe",
   "modality": "biomedical_literature_text",
   "species": "Homo sapiens",
   "original_identifier_type": "BioConceptVec concept key with Entrez/NCBI Gene ID, e.g. Gene_7157",

data/embeddings/bioconceptvec_skipgram/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "bioconceptvec_skipgram",
-  "display_name": "BioConceptVec-SkipGram-v1.1",
+  "display_name": "BioConceptVec-SkipGram",
   "modality": "biomedical_literature_text",
   "species": "Homo sapiens",
   "original_identifier_type": "BioConceptVec concept key with Entrez/NCBI Gene ID, e.g. Gene_7157",

data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "cmap_gse106127_cgs_mean_landmark978_zscore",
-  "display_name": "CMap-GSE106127-CGS-mean-landmark978-zscore-v1.1",
+  "display_name": "CMap-GSE106127-CGS-mean-landmark978-zscore",
   "modality": "perturbational transcriptomics / L1000 consensus genetic perturbation signatures",
   "species": "Homo sapiens",
   "n_genes": 4070,

data/embeddings/deepnf_string_v12_ppmi_svd_fusion/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "deepnf_string_v12_ppmi_svd_fusion",
-  "display_name": "deepNF-STRING-v12-PPMI-SVD-fusion-v1.1",
+  "display_name": "deepNF-STRING-v12-PPMI-SVD-fusion",
   "modality": "STRING network multimodal sparse PPMI/SVD fusion",
   "species": "Homo sapiens",
   "original_identifier_type": "STRING protein ID / Ensembl protein ID",

data/embeddings/deepsea_tss_1kb_epigenomic_probs/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "deepsea_tss_1kb_epigenomic_probs",
-  "display_name": "DeepSEA-TSS-1kb-epigenomic-probabilities-zscore-v1.1",
+  "display_name": "DeepSEA-TSS-1kb-epigenomic-probabilities-zscore",
   "modality": "regulatory DNA / promoter-TSS sequence model",
   "species": "Homo sapiens",
   "n_genes": 20097,

data/embeddings/depmap_crispr_gene_effect_pca256/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "depmap_crispr_gene_effect_pca256",
-  "display_name": "DepMap-CRISPRGeneEffect-PCA256-v1.1",
+  "display_name": "DepMap-CRISPRGeneEffect-PCA256",
   "modality": "functional genomics / CRISPR dependency",
   "species": "Homo sapiens",
   "n_genes": 18562,

data/embeddings/dnabert2_117m_cds/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "dnabert2_117m_cds",
-  "display_name": "dnabert2_117m_cds_v1_1",
+  "display_name": "dnabert2_117m_cds",
   "species": "Homo sapiens",
   "n_genes": 20085,
   "n_dimensions": 768,

data/embeddings/enformer_tss_393kb_human_central3/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "enformer_tss_393kb_human_central3",
-  "display_name": "Enformer-TSS-393kb-human-central3-log1p-zscore-v1.1",
+  "display_name": "Enformer-TSS-393kb-human-central3-log1p-zscore",
   "modality": "regulatory DNA / long-range TSS sequence model",
   "species": "Homo sapiens",
   "n_genes": 20097,

data/embeddings/esm2/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "esm2",
-  "display_name": "ESM2-v1.1",
+  "display_name": "ESM2",
   "modality": "protein_sequence",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez",

data/embeddings/frogs_archs4_256/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "frogs_archs4_256",
-  "display_name": "frogs_archs4_256_v1_1",
+  "display_name": "frogs_archs4_256",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez Gene ID",
   "n_genes": 16265,

data/embeddings/gene2vec/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "gene2vec",
-  "display_name": "Gene2Vec-v1.1",
+  "display_name": "Gene2Vec",
   "modality": "coexpression_expression",
   "species": "Homo sapiens",
   "original_identifier_type": "gene_symbol",

data/embeddings/genecompass_base_gene_token/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "genecompass_base_gene_token",
-  "display_name": "genecompass_base_gene_token_v1_1",
+  "display_name": "genecompass_base_gene_token",
   "modality": "gene expression single-cell foundation model / knowledge-informed gene-token embedding",
   "species": "Homo sapiens",
   "n_genes": 16578,

data/embeddings/geneformer_v2_316m/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "geneformer_v2_316m",
-  "display_name": "Geneformer-V2-316M-v1.1",
+  "display_name": "Geneformer-V2-316M",
   "modality": "single_cell_expression_foundation_model",
   "species": "Homo sapiens",
   "original_identifier_type": "Geneformer token dictionary Ensembl gene ID",

data/embeddings/genept_ada/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "genept_ada",
-  "display_name": "GenePT-ADA-v1.1-conservative",
+  "display_name": "GenePT-ADA-conservative",
   "modality": "biomedical_literature_text",
   "species": "Homo sapiens",
   "original_identifier_type": "gene_symbol",

data/embeddings/genept_model3_gene_protein/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "genept_model3_gene_protein",
-  "display_name": "GenePT-Model3-GeneProtein-v1.1-conservative",
+  "display_name": "GenePT-Model3-GeneProtein-conservative",
   "modality": "biomedical_literature_text_plus_protein_sequence_text",
   "species": "Homo sapiens",
   "original_identifier_type": "gene_symbol",

data/embeddings/gtex_tissue_median_log1p_zscore/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "gtex_tissue_median_log1p_zscore",
-  "display_name": "GTEx-tissue-median-log1p-zscore-v1.1",
+  "display_name": "GTEx-tissue-median-log1p-zscore",
   "modality": "bulk RNA expression / normal tissue expression",
   "species": "Homo sapiens",
   "n_genes": 19353,

data/embeddings/helix_mrna_full_transcript/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "helix_mrna_full_transcript",
-  "display_name": "helix_mrna_full_transcript_v1_1",
+  "display_name": "helix_mrna_full_transcript",
   "modality": "mRNA language model / mature transcript sequence",
   "species": "Homo sapiens",
   "n_genes": 19976,

data/embeddings/hetionet_nonppi_biomedical_context_tfidf_svd256/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "hetionet_nonppi_biomedical_context_tfidf_svd256",
-  "display_name": "Hetionet-nonPPI-biomedical-context-TFIDF-SVD256-v1.1",
+  "display_name": "Hetionet-nonPPI-biomedical-context-TFIDF-SVD256",
   "modality": "heterogeneous biomedical knowledge graph / non-PPI gene context",
   "species": "Homo sapiens",
   "n_genes": 18787,

data/embeddings/hpa_normal_ihc_tissue_level_zscore/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "hpa_normal_ihc_tissue_level_zscore",
-  "display_name": "HPA-normal-IHC-tissue-level-zscore-v1.1",
+  "display_name": "HPA-normal-IHC-tissue-level-zscore",
   "modality": "protein expression / normal tissue immunohistochemistry",
   "species": "Homo sapiens",
   "n_genes": 13420,

data/embeddings/hpa_subcellular_location_multihot_zscore/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "hpa_subcellular_location_multihot_zscore",
-  "display_name": "HPA-subcellular-location-multihot-zscore-v1.1",
+  "display_name": "HPA-subcellular-location-multihot-zscore",
   "modality": "protein subcellular localization",
   "species": "Homo sapiens",
   "n_genes": 13581,

data/embeddings/hyenadna_medium_160k_cds/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "hyenadna_medium_160k_cds",
-  "display_name": "hyenadna_medium_160k_cds_v1_1",
+  "display_name": "hyenadna_medium_160k_cds",
   "modality": "DNA language model / canonical CDS sequence",
   "species": "Homo sapiens",
   "n_genes": 20085,

data/embeddings/mahi_all_contexts_mean/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "mahi_all_contexts_mean",
-  "display_name": "mahi_all_contexts_mean_v1_1",
+  "display_name": "mahi_all_contexts_mean",
   "species": "Homo sapiens",
   "n_genes": 18918,
   "n_dimensions": 3666,

data/embeddings/mahi_global/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "mahi_global",
-  "display_name": "mahi_global_v1_1",
+  "display_name": "mahi_global",
   "species": "Homo sapiens",
   "n_genes": 18918,
   "n_dimensions": 3666,

data/embeddings/mashup_string/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "mashup_string",
-  "display_name": "Mashup-STRING-v1.1",
+  "display_name": "Mashup-STRING",
   "modality": "network_ppi",
   "species": "Homo sapiens",
   "mapping_method": "priority mapping using enriched master table: current symbols, HGNC previous symbols, HGNC alias symbols, canonical protein IDs, GRCh38 protein IDs, GRCh37 protein IDs",

data/embeddings/msa_transformer_depth1_uniprot_human/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "msa_transformer_depth1_uniprot_human",
-  "display_name": "MSATransformer-depth1-UniProt-human-v1.1",
+  "display_name": "MSATransformer-depth1-UniProt-human",
   "modality": "protein_sequence_msa_transformer_depth1",
   "species": "Homo sapiens",
   "n_genes": 19472,

data/embeddings/newt_archs4_256/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "newt_archs4_256",
-  "display_name": "NEWT-ARCHS4-256-v1.1",
+  "display_name": "NEWT-ARCHS4-256",
   "modality": "multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez Gene ID",

data/embeddings/newt_cellnet/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "newt_cellnet",
-  "display_name": "NEWT-CellNet-v1.1",
+  "display_name": "NEWT-CellNet",
   "modality": "multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez Gene ID",

data/embeddings/newt_go_256/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "newt_go_256",
-  "display_name": "NEWT-GO-256-v1.1",
+  "display_name": "NEWT-GO-256",
   "modality": "multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez Gene ID",

data/embeddings/newt_go_graph/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "newt_go_graph",
-  "display_name": "NEWT-GO-graph-v1.1",
+  "display_name": "NEWT-GO-graph",
   "modality": "multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez Gene ID",

data/embeddings/newt_msigdb_bundle/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "newt_msigdb_bundle",
-  "display_name": "NEWT-MSigDB-bundle-v1.1",
+  "display_name": "NEWT-MSigDB-bundle",
   "modality": "multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez Gene ID",

data/embeddings/node2vec_consensus_ppi/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "node2vec_consensus_ppi",
-  "display_name": "Node2Vec-consensus-PPI-v1.1",
+  "display_name": "Node2Vec-consensus-PPI",
   "modality": "PPI network embedding",
   "species": "Homo sapiens",
   "original_identifier_type": "Entrez Gene ID",

data/embeddings/nt_v2_500m_multispecies_cds/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "nt_v2_500m_multispecies_cds",
-  "display_name": "nt_v2_500m_multispecies_cds_v1_1",
+  "display_name": "nt_v2_500m_multispecies_cds",
   "modality": "DNA language model / CDS sequence",
   "species": "Homo sapiens",
   "n_genes": 20085,

data/embeddings/opa2vec_goa_human/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "opa2vec_goa_human",
-  "display_name": "OPA2Vec-GOA-human-v1.1",
+  "display_name": "OPA2Vec-GOA-human",
   "modality": "Gene Ontology / ontology-annotation semantic embedding",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/orthrus_base_4track_full_transcript/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "orthrus_base_4track_full_transcript",
-  "display_name": "orthrus_base_4track_full_transcript_v1_1",
+  "display_name": "orthrus_base_4track_full_transcript",
   "species": "Homo sapiens",
   "n_genes": 19976,
   "n_dimensions": 256,

data/embeddings/primekg_nonppi_biomedical_context_tfidf_svd256/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "primekg_nonppi_biomedical_context_tfidf_svd256",
-  "display_name": "PrimeKG-nonPPI-biomedical-context-TFIDF-SVD256-v1.1",
+  "display_name": "PrimeKG-nonPPI-biomedical-context-TFIDF-SVD256",
   "modality": "heterogeneous biomedical knowledge graph / non-PPI gene context",
   "species": "Homo sapiens",
   "n_genes": 19216,

data/embeddings/probe_aac/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_aac",
-  "display_name": "probe_aac_v1_1",
+  "display_name": "aac",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_albert/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_albert",
-  "display_name": "probe_albert_v1_1",
+  "display_name": "albert",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_apaac/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_apaac",
-  "display_name": "probe_apaac_v1_1",
+  "display_name": "apaac",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_bert_bfd/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_bert_bfd",
-  "display_name": "probe_bert_bfd_v1_1",
+  "display_name": "bert_bfd",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_bert_pfam/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_bert_pfam",
-  "display_name": "probe_bert_pfam_v1_1",
+  "display_name": "bert_pfam",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_blast/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_blast",
-  "display_name": "probe_blast_v1_1",
+  "display_name": "blast",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_cpc_prot/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_cpc_prot",
-  "display_name": "probe_cpc_prot_v1_1",
+  "display_name": "cpc_prot",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_esmb1/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_esmb1",
-  "display_name": "probe_esmb1_v1_1",
+  "display_name": "esmb1",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_gene2vec_uniprot/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_gene2vec_uniprot",
-  "display_name": "probe_gene2vec_uniprot_v1_1",
+  "display_name": "gene2vec_uniprot",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",

data/embeddings/probe_hmmer/metadata.json

@@ -1,6 +1,6 @@
 {
   "embedding_id": "probe_hmmer",
-  "display_name": "probe_hmmer_v1_1",
+  "display_name": "hmmer",
   "modality": "protein sequence / protein representation from PROBE human UniProt archive",
   "species": "Homo sapiens",
   "original_identifier_type": "UniProt accession",