Datasets:

SkyeAv
/

amalgam

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 classes, built from 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: 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 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	sorted names; may be empty when every name lost arbitration
`TAXA`	list	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

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.

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 before use.