mlsanityData to 14 Oct 2026

Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placement

arXiv 2306.14704 ↗First posted 26 Jun 2023cs.CLcited by 7

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Abstract (arXiv)

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

Key facts. Cited by 7 papers in the map (data through 14 Oct 2026). Builds on 13 of its 41 references that are in the map. First posted on arXiv 26 Jun 2023.

Builds on

13 of 41 references.

References · 13

  1. 2020Self-Alignment Pretraining for Biomedical Entity Representationscited by 237
  2. 2019MedMentions: A Large Biomedical Corpus Annotated with UMLS Conceptscited by 80
  3. 2020COMETA: A Corpus for Medical Entity Linking in the Social Mediacited by 50
  4. 2023Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learningcited by 50
  5. 2020TaxoExpan: Self-supervised Taxonomy Expansion with Position-Enhanced Graph Neural Networkcited by 37
  6. 2022Contextual Semantic Embeddings for Ontology Subsumption Predictioncited by 31
  7. 2023Language Model Analysis for Ontology Subsumption Inferencecited by 25
  8. 2021Taxonomy Completion via Triplet Matching Networkcited by 21
  9. 2022TaxoEnrich: Self-Supervised Taxonomy Completion via Structure-Semantic Representationscited by 20
  10. 2021Enhancing Taxonomy Completion with Concept Generation via Fusing Relational Representationscited by 19
  11. 2023Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linkingcited by 7
  12. 2022EDIN: An End-to-end Benchmark and Pipeline for Unknown Entity Discovery and Indexingcited by 5
1 more
  1. 2023NASTyLinker: NIL-Aware Scalable Transformer-based Entity Linkercited by 5

Built on by

Cited by year (2026 to 14 Oct)

Citing papers per year: 2023: 2; 2024: 2; 2025: 2; 2026: 1.

7 papers.

  1. 2023Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunitiescited by 10
  2. 2023Exploring the Reversal Curse and Other Deductive Logical Reasoning in BERT and GPT-Based Large Language Modelscited by 5
  3. 2024TransBox: EL++-closed Ontology Embeddingcited by 5
  4. 2024A Language Model based Framework for New Concept Placement in Ontologiescited by 3
  5. 2026OntoExtend: A Framework for Requirement-driven and Scalable Ontology Extension with LLMscited by 2
  6. 2025From Guidelines to Guarantees: A Graph-Based Evaluation Harness for Domain-Specific Evaluation of LLMscited by 0
  7. 2025Hierarchical Retrieval with Out-Of-Vocabulary Queries: A Case Study on SNOMED CTcited by 0