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Commit History
17 days ago
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Rename expression categories to Bulk expression and Single-cell expression
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Remove verified synthetic live test geh_live_smoke_20261021_c7a43e
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Add geh_live_smoke_20261021_c7a43e to the catalogue
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Bootstrap automatic contribution interface
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Set Gene Embedding Hub emoji
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Update Gene Embedding Hub title
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Update references for Gene Embedding Hub rename
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Merge Ontologies into Functional and reclassify HPA tissue
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Update modality description
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Simplify embedding details and fix package links
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Hide license detail and fix package file links
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Add informative descriptions for all embeddings
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Add informative descriptions for all embeddings
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Apply final names and labels; remove all unlisted entries
Verified signatureUpdate the Space catalog display names and final taxonomy labels for the 67 authoritative embeddings listed in embedding_modalities_FINAL(1).xlsx, with GO TF-IDF SVD-256 classified as Ontologies. Set category and displayed modality to the final label, mark taxonomy as manual, remove every unlisted catalog entry including community contributions, and add CSS aliases so the final category labels retain the existing palettes.b9ded09 -
Apply final names, labels, and remove unlisted core embeddings
Verified signatureUpdate the Space catalog display names and final taxonomy labels for the embeddings listed in embedding_modalities_FINAL(1).xlsx. Set category and displayed modality to the final label, mark the taxonomy as manual, remove unlisted non-community/core catalog entries, preserve community contributions unchanged, and add CSS aliases so the new category labels retain the existing palettes.b5df75a -
Add HPO Ancestor-Propagated TF-IDF SVD-256 to catalog
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Add GO Biological Process TF-IDF SVD-256 to catalog
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Add DRKG TransE to catalog
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Add STRING WaveGC and STRING GNN to catalog
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Correct embedding modality labels
Verified signatureManually classify all current NEWT embeddings, Gene2Vec variants, and PROBE MUT2VEC as Multimodal; classify PROBE TCGA as Expression. Only category, category_source, and modality fields are changed.ad325fd
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Improve embedding methods, licenses, and descriptions
Verified signatureHide internal QC/source-dataset fields, display linked upstream license/source terms, replace method placeholders from package metadata/READMEs, and remove redundant embedding-name prefixes.856267b -
Improve embedding methods, licenses, and descriptions
Verified signatureHide internal QC/source-dataset fields, display linked upstream license/source terms, replace method placeholders from package metadata/READMEs, and remove redundant embedding-name prefixes.c9daa18
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Correct six modality categories
Verified signatureApply manually reviewed coarse categories: DNABERT2 as DNA; BioBERT, PubMedBERT, and GenePT Model3 GeneProtein as Literature; and PrimeKG/Hetionet non-PPI biomedical context as Knowledge. Only category and category_source change.59e8e9f -
Remove PROBE prefix from display names
Verified signatureRemove the visible probe_ prefix from the names of the 20 PROBE catalog entries. Stable IDs, paths, links, and Dataset content remain unchanged.efbed1b
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Remove version suffixes from embedding display names
Verified signatureRemove v1.1 and v1_1 tokens from the 68 core embedding names shown in the Space. Keep IDs, descriptions, paths, URLs, Dataset content, and all other catalog fields unchanged.b97db46 -
Remove external-reference smoke test from catalog
Verified signatureRemove only external_reference_smoke_20260727_v1 and its generated registry, manifest, catalog, summary, and target-specific path references. Leave the external source Dataset untouched.2aac4e0
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Remove theme toggle from mapping tutorial
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Fix tutorial day and night themes
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Add theme toggle to gene mapping tutorial
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Refine gene mapping tutorial
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Add gene mapping tutorial
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Clarify command-line upload instructions
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Clarify embedding submission instructions
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Clarify embedding submission instructions
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Move metadata generation note to package step
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Refine completed example wording
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Replace placeholder submission with real ESM2 example
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Clarify submission template and add example
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Simplify contribution fields and metadata
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Simplify submission package and correct template filename
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Update catalog for submissions/external_reference_smoke_20260727_v1.yaml
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Shorten DNA image and restore theme toggle position
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Reduce hero image size and fade into blue
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Create seamless hero image continuation
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Continue hero colors into page background
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Brighten hero image in day mode
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Use image as hero background
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Add DNA hero background image
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Refine submission template instructions
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Add category and modality guidance to template
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