| --- |
| pretty_name: Amalgam |
| license: other |
| license_name: amalgam-upstream |
| license_link: LICENSE.md |
| configs: |
| - config_name: cliques |
| default: true |
| data_files: |
| - split: activity |
| path: cliques/activity.parquet |
| - split: anatomical_entity |
| path: cliques/anatomical_entity.parquet |
| - split: behavior |
| path: cliques/behavior.parquet |
| - split: biological_entity |
| path: cliques/biological_entity.parquet |
| - split: biological_process |
| path: cliques/biological_process.parquet |
| - split: cell |
| path: cliques/cell.parquet |
| - split: cell_line |
| path: cliques/cell_line.parquet |
| - split: cellular_component |
| path: cliques/cellular_component.parquet |
| - split: chemical_entity |
| path: cliques/chemical_entity.parquet |
| - split: chemical_mixture |
| path: cliques/chemical_mixture.parquet |
| - split: clinical_attribute |
| path: cliques/clinical_attribute.parquet |
| - split: clinical_finding |
| path: cliques/clinical_finding.parquet |
| - split: clinical_intervention |
| path: cliques/clinical_intervention.parquet |
| - split: cohort |
| path: cliques/cohort.parquet |
| - split: complex_molecular_mixture |
| path: cliques/complex_molecular_mixture.parquet |
| - split: device |
| path: cliques/device.parquet |
| - split: disease |
| path: cliques/disease.parquet |
| - split: drug |
| path: cliques/drug.parquet |
| - split: event |
| path: cliques/event.parquet |
| - split: food |
| path: cliques/food.parquet |
| - split: gene |
| path: cliques/gene.parquet |
| - split: gene_family |
| path: cliques/gene_family.parquet |
| - split: genomic_entity |
| path: cliques/genomic_entity.parquet |
| - split: geographic_location |
| path: cliques/geographic_location.parquet |
| - split: gross_anatomical_structure |
| path: cliques/gross_anatomical_structure.parquet |
| - split: human |
| path: cliques/human.parquet |
| - split: information_content_entity |
| path: cliques/information_content_entity.parquet |
| - split: life_stage |
| path: cliques/life_stage.parquet |
| - split: macromolecular_complex |
| path: cliques/macromolecular_complex.parquet |
| - split: molecular_activity |
| path: cliques/molecular_activity.parquet |
| - split: molecular_entity |
| path: cliques/molecular_entity.parquet |
| - split: molecular_mixture |
| path: cliques/molecular_mixture.parquet |
| - split: named_thing |
| path: cliques/named_thing.parquet |
| - split: nucleic_acid_entity |
| path: cliques/nucleic_acid_entity.parquet |
| - split: organism_taxon |
| path: cliques/organism_taxon.parquet |
| - split: pathway |
| path: cliques/pathway.parquet |
| - split: phenomenon |
| path: cliques/phenomenon.parquet |
| - split: phenotypic_feature |
| path: cliques/phenotypic_feature.parquet |
| - split: physical_entity |
| path: cliques/physical_entity.parquet |
| - split: physiological_process |
| path: cliques/physiological_process.parquet |
| - split: polypeptide |
| path: cliques/polypeptide.parquet |
| - split: population_of_individual_organisms |
| path: cliques/population_of_individual_organisms.parquet |
| - split: posttranslational_modification |
| path: cliques/posttranslational_modification.parquet |
| - split: procedure |
| path: cliques/procedure.parquet |
| - split: protein |
| path: cliques/protein.parquet |
| - split: sequence_variant |
| path: cliques/sequence_variant.parquet |
| - split: small_molecule |
| path: cliques/small_molecule.parquet |
| - split: taxonomic_rank |
| path: cliques/taxonomic_rank.parquet |
| - config_name: crossrefs |
| data_files: |
| - split: clinvar |
| path: crossrefs/clinvar.parquet |
| - split: obo_apo |
| path: crossrefs/obo_apo.parquet |
| - split: obo_fao |
| path: crossrefs/obo_fao.parquet |
| - split: obo_fbdv |
| path: crossrefs/obo_fbdv.parquet |
| - split: obo_fypo |
| path: crossrefs/obo_fypo.parquet |
| - split: obo_hsapdv |
| path: crossrefs/obo_hsapdv.parquet |
| - split: obo_maxo |
| path: crossrefs/obo_maxo.parquet |
| - split: obo_mmusdv |
| path: crossrefs/obo_mmusdv.parquet |
| - split: obo_mp |
| path: crossrefs/obo_mp.parquet |
| - split: obo_taxrank |
| path: crossrefs/obo_taxrank.parquet |
| - split: obo_to |
| path: crossrefs/obo_to.parquet |
| - split: obo_wbls |
| path: crossrefs/obo_wbls.parquet |
| - split: obo_wbphenotype |
| path: crossrefs/obo_wbphenotype.parquet |
| - split: obo_zfs |
| path: crossrefs/obo_zfs.parquet |
| - split: obo_zp |
| path: crossrefs/obo_zp.parquet |
| task_categories: |
| - other |
| tags: |
| - biology |
| - biomedical |
| - entity-linking |
| - synonyms |
| - biolink |
| size_categories: |
| - 100M<n<1B |
| --- |
| |
| # Amalgam |
|
|
| Amalgam is a biomedical metaontology: a cross-resource integration layer of entity identifiers, names, |
| and typed cross-references organized by Biolink class. It integrates source ontologies rather than replacing |
| their semantics; typed associations are not equivalence assertions. |
|
|
| Biomedical entity names for [Biolink](https://biolink.github.io/biolink-model/) classes, built from |
| [BABEL](https://github.com/NCATSTranslator/Babel) snapshot `local:/home/sgoetz/babel-snapshots/2026jul22`. Cliques that share a preferred name |
| within a class and taxon scope may merge unless identifier namespaces conflict. Every synonym is assigned to one CURIE within its |
| class and taxon scope. Strings are kept as written; normalization is left to consumers. |
|
|
| Additional sources: |
|
|
| - [GTDB](https://gtdb.ecogenomic.org/): `GTDB:` taxa (`organism_taxon`); species carry their NCBI species taxid crossref as a `GTDB:` synonym of the `NCBITaxon:` row (at most one GTDB species per taxid). |
| - [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) `variant_summary`: one `CLINVAR:` row per variation and one `DBSNP:rs...` row per referenced rsID (`sequence_variant`), never merged with each other. |
| - OBO ontologies not in BABEL (`config/obo_sources.yaml`): active own-prefix terms with names, EXACT synonyms and alt_ids. |
| |
| ## Subsets |
| |
| ### `cliques` (default) |
| |
| One row per clique, one split per Biolink class. |
| |
| | column | type | meaning | |
| |---|---|---| |
| | `CURIE` | string | clique leader identifier | |
| | `PREFERRED_NAME` | string | preferred name, as written | |
| | `CLASS` | string | Biolink class, e.g. `biolink:Gene` (split `gene`) | |
| | `SYNONYMS` | list<string> | sorted names; may be empty when every name lost arbitration | |
| | `TAXA` | list<string> | sorted `NCBITaxon:` CURIEs; empty when taxonless | |
|
|
| | split | class | rows | |
| ---|---|---:| |
| `activity` | `biolink:Activity` | 9092 | |
| `anatomical_entity` | `biolink:AnatomicalEntity` | 149423 | |
| `behavior` | `biolink:Behavior` | 4202 | |
| `biological_entity` | `biolink:BiologicalEntity` | 110 | |
| `biological_process` | `biolink:BiologicalProcess` | 43888 | |
| `cell` | `biolink:Cell` | 9096 | |
| `cell_line` | `biolink:CellLine` | 38896 | |
| `cellular_component` | `biolink:CellularComponent` | 8779 | |
| `chemical_entity` | `biolink:ChemicalEntity` | 372988 | |
| `chemical_mixture` | `biolink:ChemicalMixture` | 489 | |
| `clinical_attribute` | `biolink:ClinicalAttribute` | 112982 | |
| `clinical_finding` | `biolink:ClinicalFinding` | 11065 | |
| `clinical_intervention` | `biolink:ClinicalIntervention` | 36772 | |
| `cohort` | `biolink:Cohort` | 950 | |
| `complex_molecular_mixture` | `biolink:ComplexMolecularMixture` | 572 | |
| `device` | `biolink:Device` | 73167 | |
| `disease` | `biolink:Disease` | 365181 | |
| `drug` | `biolink:Drug` | 293866 | |
| `event` | `biolink:Event` | 288 | |
| `food` | `biolink:Food` | 9108 | |
| `gene` | `biolink:Gene` | 2408081 | |
| `gene_family` | `biolink:GeneFamily` | 28437 | |
| `genomic_entity` | `biolink:GenomicEntity` | 42421 | |
| `geographic_location` | `biolink:GeographicLocation` | 4698 | |
| `gross_anatomical_structure` | `biolink:GrossAnatomicalStructure` | 12610 | |
| `human` | `biolink:Human` | 46 | |
| `information_content_entity` | `biolink:InformationContentEntity` | 54550 | |
| `life_stage` | `biolink:LifeStage` | 1357 | |
| `macromolecular_complex` | `biolink:MacromolecularComplex` | 19843 | |
| `molecular_activity` | `biolink:MolecularActivity` | 198929 | |
| `molecular_entity` | `biolink:MolecularEntity` | 14 | |
| `molecular_mixture` | `biolink:MolecularMixture` | 11625271 | |
| `named_thing` | `biolink:NamedThing` | 32 | |
| `nucleic_acid_entity` | `biolink:NucleicAcidEntity` | 551 | |
| `organism_taxon` | `biolink:OrganismTaxon` | 3141304 | |
| `pathway` | `biolink:Pathway` | 53769 | |
| `phenomenon` | `biolink:Phenomenon` | 332529 | |
| `phenotypic_feature` | `biolink:PhenotypicFeature` | 88485 | |
| `physical_entity` | `biolink:PhysicalEntity` | 6624 | |
| `physiological_process` | `biolink:PhysiologicalProcess` | 108 | |
| `polypeptide` | `biolink:Polypeptide` | 219 | |
| `population_of_individual_organisms` | `biolink:PopulationOfIndividualOrganisms` | 13383 | |
| `posttranslational_modification` | `biolink:PosttranslationalModification` | 1971 | |
| `procedure` | `biolink:Procedure` | 449455 | |
| `protein` | `biolink:Protein` | 2344320 | |
| `sequence_variant` | `biolink:SequenceVariant` | 7336430 | |
| `small_molecule` | `biolink:SmallMolecule` | 111621082 | |
| `taxonomic_rank` | `biolink:TaxonomicRank` | 77 | |
|
|
| ### `crossrefs` |
|
|
| Typed associations, not equivalence. One split per source; source lives in the split name, not a column. |
| Edges retain pre-merge IDs and may refer to rows absent from `cliques`. A zero-row `empty` split is emitted |
| when no source contributes edges. Read that empty split with `streaming=True`; the datasets library |
| rejects zero-row splits in materialized mode. |
|
|
| column | type | meaning | |
| ---|---|---| |
| `SUBJECT` | string | source CURIE (pre-merge identifier, may be obsolete) | |
| `PREDICATE` | string | edge type, below | |
| `OBJECT` | string | target CURIE | |
|
|
| split | source | rows | |
| ---|---|---:| |
| `clinvar` | `clinvar` | 7530759 | |
| `obo_apo` | `obo:APO` | 9 | |
| `obo_fao` | `obo:FAO` | 33 | |
| `obo_fbdv` | `obo:FBdv` | 8 | |
| `obo_fypo` | `obo:FYPO` | 100 | |
| `obo_hsapdv` | `obo:HsapDv` | 225 | |
| `obo_maxo` | `obo:MAXO` | 654 | |
| `obo_mmusdv` | `obo:MmusDv` | 77 | |
| `obo_mp` | `obo:MP` | 749 | |
| `obo_taxrank` | `obo:TAXRANK` | 96 | |
| `obo_to` | `obo:TO` | 897 | |
| `obo_wbls` | `obo:WBls` | 2 | |
| `obo_wbphenotype` | `obo:WBPhenotype` | 42 | |
| `obo_zfs` | `obo:ZFS` | 90 | |
| `obo_zp` | `obo:ZP` | 52 | |
|
|
| - `dbsnp_reference`: ClinVar variation to the dbSNP rsID it references (one rsID can cover several alleles) |
| - `gene_association`: variant to the NCBIGene it lies in (location, not identity) |
| - `replaced_by`: obsolete OBO term to its successor |
| - `xref`: OBO term cross-reference (relevance only, per OBO 1.4) |
|
|
| ## Usage |
|
|
| ```python |
| from datasets import load_dataset |
| |
| genes = load_dataset("SkyeAv/amalgam", "cliques", split="gene") |
| cliques = load_dataset("SkyeAv/amalgam", "cliques") # DatasetDict, one entry per class |
| edges = load_dataset("SkyeAv/amalgam", "crossrefs", split="clinvar") |
| ``` |
|
|
| ## Construction |
|
|
| - Synonyms are unique per (class, taxon scope); the same string may recur across classes or taxa. |
| Ties go to: preferred-name match, most synonyms, most identifiers, curated sources, smallest CURIE. |
| - Conflated BABEL files are never read; drugs and chemicals, genes and proteins stay distinct. |
| - A CURIE-like preferred name uses the first sorted, admitted non-CURIE synonym when available. |
| Existing human-readable preferred names are preserved. |
| - `biolink:Publication` and `biolink:Agent` are dropped. |
| - Except `biolink:OrganismTaxon`, rows with taxa keep at least one of the 100 allowlisted taxa (`config/taxa.yaml`). Taxonless rows first |
| inherit the taxon of single-species identifiers (MGI, RGD, ZFIN, FlyBase, WormBase, SGD, HGNC, Ensembl). |
|
|
| - Junk names are removed: numbers, `uncharacterized`, `hypothetical`, `language`, and stopwords |
| (`config/filters.yaml`). Leader CURIEs and equivalent identifiers are indexed as synonyms (fullmap parity). |
|
|
| Generated 2026-10-28 by [Amalgam](https://github.com/SkyeAv/Amalgam). |
|
|
| ## License |
|
|
| No single license covers this dataset: each name keeps the terms of the resource it came from, and several |
| (UMLS, OMIM, DrugBank, KEGG, Orphanet, HMDB) restrict redistribution or commercial use. See |
| [LICENSE.md](LICENSE.md) before use. |
|
|
