vaibhavalakshmiravideshik/emapa-uberon-4k

Uberon-EMAPA Entity Alignment 4K

Uberon-EMAPA Entity Alignment 4K is a biomedical entity alignment benchmark for heterogeneous knowledge graphs. It aligns anatomical entities between the Uber-anatomy Ontology (Uberon) and the Edinburgh Mouse Atlas Project Anatomy ontology (EMAPA) using curated cross-references embedded directly in Uberon.

The benchmark is designed for realistic entity alignment research rather than simplified label matching. The gold alignment is embedded in the full Uberon and EMAPA ontology graphs, so models must recover aligned anatomical concepts in the presence of species mismatch, temporal-vs-atemporal representation mismatch, schema asymmetry, and substantial non-gold background structure.

Dataset Summary

• KG1: Uberon (Uber-anatomy Ontology)
• KG2: EMAPA (Edinburgh Mouse Atlas Project Anatomy)
• Alignment type: curated cross-ontology anatomical alignment
• Gold source: Uberon xref: EMAPA:XXXXX annotations
• Gold links: 4,079 validated pairs
• Format: tab-separated triples and alignment pairs

Files in this repository:

• ent_links: original validated Uberon-EMAPA gold entity alignment pairs
• rel_triples_1: original Uberon relation triples
• rel_triples_2: original EMAPA relation triples
• attr_triples_1: Uberon attribute triples
• attr_triples_2: EMAPA attribute triples
• viewer/: helper files used only for Hugging Face dataset viewer compatibility

Source Ontologies

KG1 — Uberon

• Resource: Uber-anatomy Ontology
• Maintainer: Monarch Initiative / OBO Foundry
• Version used: uberon.obo, master branch as of May 2026
• Purpose: a multi-species anatomy ontology representing anatomical structures across metazoan species for cross-species integration
• License: CC BY 3.0
• Download: uberon.obo

Note: the distributed uberon.obo includes imported terms from CL, GO, ChEBI, NCBITaxon, PR, PATO, and RO. Only UBERON:-prefixed terms are used for KG1.

KG2 — EMAPA

• Resource: Edinburgh Mouse Atlas Project Anatomy ontology
• Maintainer: Edinburgh Mouse Atlas Project / OBO Foundry
• Version used: emapa.obo, release 2026-05-29
• Purpose: a developmental mouse anatomy ontology with temporal stage annotations using Theiler Stages
• License: CC BY 4.0
• Download tarball: mouse-anatomy-ontology tarball
• Extract path: developmental-mouse-anatomy-ontology-master/emapa.obo

Why This Pair Is Heterogeneous

This benchmark is cross-species and cross-purpose, not merely cross-schema:

Property	Uberon	EMAPA
Species scope	All metazoans	Mouse only
Temporal scope	Adult anatomy / largely atemporal	Developmental stages TS01–TS26
Relation vocabulary	10+ types	4 structural + temporal relations
Granularity	Broad cross-species integration	Fine-grained mouse-specific developmental staging
Unique feature	Cross-species anatomical integration	starts_at / ends_at stage grounding

The starts_at and ends_at relations in EMAPA, pointing to Theiler Stage nodes, make this benchmark unusually challenging compared with standard entity alignment datasets.

Ground Truth Construction

The gold standard is extracted directly from Uberon OBO term cross-references. Every active Uberon term carrying an xref: EMAPA:XXXXX annotation contributes a candidate alignment pair.

No separate mapping file is required. The extraction rule is:

for every active UBERON: term with exactly one xref: EMAPA:XXXXX, the pair (UBERON term, EMAPA term) is a candidate gold pair.

One-to-one filtering is applied because some Uberon terms carry multiple EMAPA xrefs, indicating one-to-many or developmentally ambiguous correspondences.

Validation and Filtering

Step	Count
Total UBERON→EMAPA xrefs in Uberon OBO	4,356
UBERON terms with exactly one EMAPA xref	4,093
UBERON terms with more than one EMAPA xref (dropped)	122
Raw 1:1 candidate pairs	4,093
Dropped — EMAPA term obsolete in emapa.obo	14
Dropped — Uberon term obsolete	0
Final valid gold pairs	4,079
Unique Uberon entities in gold	4,079
Unique EMAPA entities in gold	4,074

Note: 5 EMAPA entities appear in two gold pairs each. These are retained because the duplication occurs on the Uberon side, not by duplicating EMAPA entities themselves.

Knowledge Graph Construction

Both graphs use the full active ontology as the graph. Gold entities are embedded among non-gold background nodes.

KG1 — Uberon graph

Parsed from uberon.obo master branch May 2026, retaining only UBERON:-prefixed active terms.

• Total UBERON: terms in OBO: 16,067
• Obsolete terms removed: 1,094
• Active terms (KG1 nodes): 14,973
• Entities appearing in rel_triples_1: 14,971
• Uberon gold entities in KG1: 4,079 / 4,079
• Uberon gold missing from KG1: 0

Relation types in rel_triples_1 (top 10 by frequency):

Relation	URI / compact form	Count
rdfs:subClassOf	rdfs:subClassOf	19,617
part_of	BFO:0000050	12,286
develops_from	RO:0002202	1,844
mutually_spatially_disjoint_with	uberon#mutually_spatially_disjoint_with	793
contributes_to_morphology_of	uberon#contributes_to_morphology_of	649
connects	uberon#connects	583
composed_primarily_of	uberon#composed_primarily_of	515
has_part	BFO:0000051	418
adjacent_to	RO:0002220	353
overlaps	RO:0002131	335

Attribute types in attr_triples_1:

• rdfs:label — preferred anatomical name
• IAO:0000115 — textual definition
• skos:altLabel — synonyms
• oboInOwl:hasDbXref — cross-references to FMA, ZFA, MA, CALOHA, BTO, Wikipedia, NCIT, and others

KG2 — EMAPA graph

Parsed from emapa.obo release 2026-05-29. EMAPA: terms form the anatomical entity space, and TS: terms are retained as valid relation targets for temporal relations.

• Total EMAPA: terms in OBO: 8,130
• Obsolete terms removed: 52
• Active EMAPA: terms (KG2 nodes): 8,078
• TS: (Theiler Stage) terms: 29
• Entities appearing in rel_triples_2: 8,106 (includes 28 TS: terms)
• EMAPA gold entities in KG2: 4,074 / 4,074
• EMAPA gold missing from KG2: 0

Relation types in rel_triples_2:

Relation	URI / compact form	Count
ends_at	emapa#ends_at	8,076
starts_at	emapa#starts_at	8,076
part_of	BFO:0000050	7,468
rdfs:subClassOf	rdfs:subClassOf	4,668
develops_from	RO:0002202	11

Attribute types in attr_triples_2:

• rdfs:label — anatomical structure name
• skos:altLabel — synonyms
• oboInOwl:hasDbXref — minimal cross-references

Note: EMAPA intentionally does not provide textual definitions.

Final Dataset Statistics

File	Lines	Size
ent_links	4,079	0.38 MB
attr_triples_1	115,702	15.76 MB
attr_triples_2	9,603	1.26 MB
rel_triples_1	42,260	6.17 MB
rel_triples_2	28,299	3.80 MB
Total	200,943	27.37 MB

Graph-level summary:

KG	Entities	Attribute triples	Relation triples	Relation types
KG1 (Uberon)	14,971	115,702	42,260	10+
KG2 (EMAPA)	8,106	9,603	28,299	4

Heterogeneity Profile

This benchmark is intentionally heterogeneous and non-trivial:

1. Schema mismatch: Uberon has 10+ named relation types; EMAPA has a much smaller vocabulary plus temporal stage relations.
2. Temporal vs atemporal mismatch: Uberon represents anatomy largely atemporally, whereas EMAPA grounds structures in developmental onset and offset stages.
3. Species mismatch: Uberon is cross-species; EMAPA is mouse-specific.
4. Attribute asymmetry: Uberon has rich labels, definitions, synonyms, and xrefs; EMAPA has names and synonyms but no definitions.
5. Background ratio: only ~27% of KG1 and ~50% of KG2 participate in gold alignments.
6. Perfect gold coverage: both sides have zero gold entities missing from relation triples.

Resource Links

• Uberon home
• Uberon GitHub
• Uberon OBO Foundry page
• EMAPA home
• EMAPA GitHub
• EMAPA OBO Foundry page

File Format

All canonical benchmark files are UTF-8 plain text with tab-separated columns.

ent_links

Two columns:

1. Uberon entity URI
2. EMAPA entity URI

Example:

<http://purl.obolibrary.org/obo/UBERON_0000002>	<http://purl.obolibrary.org/obo/EMAPA_29927>

rel_triples_1 and rel_triples_2

Three columns:

1. subject entity URI
2. relation URI or compact predicate
3. object entity URI

attr_triples_1 and attr_triples_2

Three columns:

1. subject entity URI
2. attribute predicate
3. literal value

Viewer helper files

To improve dataset viewer compatibility without changing the benchmark artifact layout at the repository root, helper files are stored in viewer/:

• viewer/links/ent_links.csv
• viewer/attributes/attr_triples_1_preview.csv
• viewer/attributes/attr_triples_2_preview.csv
• viewer/relations/rel_triples_1_preview.csv
• viewer/relations/rel_triples_2_preview.csv

These files exist only so the Hugging Face Dataset Viewer can expose three browsable subsets: alignments, attributes, and relations. The actual benchmark artifacts remain the original root-level files listed above.

Recommended Uses

This dataset is intended for:

• heterogeneous biomedical entity alignment
• anatomy ontology matching
• cross-species semantic alignment research
• multimodal or structure-plus-text EA systems
• benchmarking robustness to temporal and schema mismatch

Limitations

• The benchmark covers only Uberon-EMAPA anatomical alignment and should not be generalized to all anatomy ontology matching tasks.
• Gold links come from curated xrefs in Uberon and inherit source-ontology modeling decisions.
• Some EMAPA entities are valid many-to-one targets from Uberon.
• Uberon includes only UBERON: terms in KG1; imported ontology terms are intentionally excluded.
• EMAPA lacks textual definitions, so lexical/attribute evidence is asymmetric by design.

Provenance and Licensing

• Uberon: CC BY 3.0
• EMAPA: CC BY 4.0
• This dataset release: CC BY 4.0

This dataset adopts the most restrictive upstream license among its sources and therefore requires attribution on redistribution and reuse.

Citation

If you use this dataset, please cite the benchmark and the source ontologies.

Suggested citation text:

@misc{uberon_emapa_entity_alignment_4k,
  title        = {Uberon-EMAPA Entity Alignment 4K},
  author       = {Ravideshik, Vaibhavalakshmi},
  year         = {2026},
  publisher    = {Hugging Face},
  howpublished = {\url{https://huggingface.co/datasets/vaibhavalakshmiravideshik/uberon-emapa-entity-alignment-4k}}
}

Acknowledgements

This benchmark depends on the work of the Uberon and EMAPA maintainers, the Monarch Initiative, the Edinburgh Mouse Atlas Project, and the OBO Foundry community.