Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification, often fail to capture complex concepts not explicitly stated in the text. To overcome this limitation, we introduce MA-COIR, a framework that reformulates concept recognition as an indexing-recognition task. By assigning semantic search indexes (ssIDs) to concepts, MA-COIR resolves ambiguities in ontology entries and enhances recognition efficiency. Using a pretrained BART-based model fine-tuned on small datasets, our approach reduces computational requirements to facilitate adoption by domain experts. Furthermore, we incorporate large language model (LLM)-generated queries and synthetic data to improve recognition in low-resource settings. Experimental results on three scenarios (CDR, HPO, and HOIP) highlight the effectiveness of MA-COIR in recognizing both explicit and implicit concepts without the need for mention-level annotations during inference, advancing ontology-driven concept recognition in biomedical domain applications. Our code and constructed data are available at https://github.com/sl-633/macoir-master.

Automatic biomedical annotation is essential for advancing medical research, diagnosis, and treatment. However, it presents significant challenges, especially when entities are not explicitly mentioned in the text, leading to difficulties in extraction of relevant information. These challenges are intensified by unclear terminology, implicit background knowledge, and the lack of labeled training data. Annotating with a specific ontology adds another layer of complexity, as it requires aligning text with a predefined set of concepts and relationships. Manual annotation is time-consuming and expensive, highlighting the need for automated systems to handle large volumes of biomedical data efficiently. In this paper, we propose an entailment-based zero-shot text classification approach to annotate biomedical text passages using the Homeostasis Imbalance Process (HOIP) ontology. Our method reformulates the annotation task as a multi-class, multi-label classification problem and uses natural language inference to classify text into related HOIP processes. Experimental results show promising performance, especially when processes are not explicitly mentioned, highlighting the effectiveness of our approach for ontological annotation of biomedical literature.