MONDO:0023124 Deprecation Discussion: A Deep Dive

Introduction to MONDO and the Deprecation Discussion

The Mondo Disease Ontology (MONDO) is a collaborative project aimed at creating a unified, standardized classification system for human diseases. This is a crucial endeavor in the realm of biomedical research, as it enables researchers, clinicians, and patients to communicate effectively about diseases and their related conditions. By providing a common language, MONDO facilitates data sharing, analysis, and ultimately, a better understanding of human health. In this context, discussions surrounding the deprecation of specific MONDO terms are vital for maintaining the accuracy and relevance of the ontology. This article delves into the discussion surrounding the deprecation of MONDO:0023124, which represents a complex condition involving familial pulmonary arterial hypertension, leucopenia, and atrial septal defect. The decision to deprecate a term within MONDO is not taken lightly; it involves careful consideration of the available evidence, the term's utility, and its alignment with current scientific understanding. This particular case highlights the challenges and complexities inherent in classifying rare and multifaceted diseases.

The deprecation of a term within MONDO signifies that the term is no longer considered an accurate or useful representation of a disease or condition. This might occur for various reasons, such as the identification of more precise classifications, the discovery that the condition is not a distinct entity, or the lack of sufficient evidence to support its existence. The process of deprecation is essential for ensuring the integrity and reliability of the ontology. When a term is flagged for deprecation, it triggers a discussion among experts and stakeholders, including curators, researchers, and clinicians. This collaborative process allows for a thorough evaluation of the term's validity and relevance. The discussion often involves examining the term's definition, its relationships to other terms within MONDO, and the available scientific literature. In the case of MONDO:0023124, the discussion centered on the lack of robust evidence supporting the term's existence as a distinct clinical entity, prompting the recommendation for its deprecation.

The discussion category for this topic falls under monarch-initiative and mondo, indicating its relevance to both the Monarch Initiative, a project focused on integrating and analyzing biomedical data, and the MONDO project itself. The additional information provided, including the MONDO term ID and label, the reason for deprecation, and the suggested terms to consider, offers a structured framework for the discussion. This structured approach ensures that all relevant aspects of the term are considered, and that the decision-making process is transparent and well-documented. The inclusion of a nano-attribution section, which encourages contributors to provide their ORCID (Open Researcher and Contributor ID), further promotes transparency and accountability within the MONDO project. The following sections will explore the specific details of the MONDO:0023124 deprecation discussion, examining the reasons behind the decision and its implications for the broader landscape of disease classification.

Detailed Analysis of MONDO:0023124

The specific MONDO term, MONDO:0023124, is labeled as "familial pulmonary arterial hypertension leucopenia and atrial septal defect." This label describes a complex condition characterized by the co-occurrence of three distinct medical entities: familial pulmonary arterial hypertension (PAH), leucopenia, and atrial septal defect (ASD). Each of these components is a significant medical condition in its own right, and their simultaneous presence raises questions about potential underlying mechanisms and genetic relationships. Familial PAH is a rare and severe form of pulmonary hypertension, a condition in which the blood pressure in the arteries leading to the lungs is abnormally high. Leucopenia refers to a decrease in the number of white blood cells, which are crucial for immune function. Atrial septal defect is a congenital heart defect in which there is an abnormal opening between the heart's two upper chambers (atria).

The reason for deprecation of MONDO:0023124 is primarily attributed to the lack of sufficient evidence to support its existence as a distinct clinical entity. The provided justification highlights that the only reference resembling an external cross-reference (x-ref) is a non-existent link to the Genetic and Rare Diseases Information Center (GARD) at the National Institutes of Health (NIH). Specifically, the link cited, https://rarediseases.info.nih.gov/diseases/10455/familial-pulmonary-arterial-hypertension-leucopenia-and-atrial-septal-defect, is invalid. This absence of a reliable external reference underscores the uncertainty surrounding the classification of this specific combination of conditions as a distinct syndrome or disease entity. The deprecation rationale suggests that the co-occurrence of familial PAH, leucopenia, and ASD may not represent a unique disease but rather a coincidental presentation of individual conditions or a manifestation of a broader, yet-to-be-defined genetic or clinical syndrome.

Given the lack of robust evidence, there is no suggested term to consider as a replacement for MONDO:0023124. This implies that the individual components of the condition—familial PAH, leucopenia, and ASD—should be classified and addressed separately within the MONDO ontology and in clinical practice. This approach aligns with the principle of classifying diseases based on well-established diagnostic criteria and underlying pathophysiology. The decision not to suggest a replacement term reflects the importance of maintaining the accuracy and reliability of the ontology by avoiding the perpetuation of poorly defined or unsubstantiated disease classifications. The deprecation of MONDO:0023124 serves as a reminder of the dynamic nature of disease classification and the ongoing need for rigorous evaluation and refinement of ontologies in light of new scientific evidence.

Implications of Deprecation and Future Directions

The implications of deprecating MONDO:0023124 extend beyond the immediate removal of a term from the ontology. It highlights the critical role of evidence-based decision-making in disease classification and the importance of regularly reviewing and updating ontologies to reflect the current state of scientific knowledge. The deprecation process underscores the collaborative nature of the MONDO project, where experts from various fields contribute to the evaluation and refinement of disease terms. This collaborative approach ensures that the ontology remains a reliable resource for researchers, clinicians, and patients.

The deprecation of a term like MONDO:0023124 also prompts reflection on the challenges of classifying rare and complex conditions. Rare diseases, by their nature, often present with limited data and varying clinical manifestations, making it difficult to establish clear diagnostic criteria and classification schemes. The co-occurrence of multiple conditions, as seen in the case of familial PAH, leucopenia, and ASD, further complicates the classification process. In such cases, it is essential to carefully evaluate the evidence supporting the existence of a distinct syndrome or disease entity, and to avoid creating classifications based solely on phenotypic similarities without a clear understanding of the underlying mechanisms.

Future directions for disease classification in this context include the integration of genomic data and advanced analytical techniques. Advances in genomics have enabled the identification of genetic variants associated with various diseases, providing a powerful tool for understanding the underlying causes of rare and complex conditions. By incorporating genomic information into disease classifications, it may be possible to identify more precise subtypes of diseases and to develop more targeted diagnostic and therapeutic strategies. Furthermore, the application of machine learning and other computational methods can aid in the analysis of large datasets, potentially revealing novel patterns and relationships between diseases and their associated factors. The deprecation of MONDO:0023124 serves as a reminder of the ongoing need for vigilance and critical evaluation in disease classification. As scientific knowledge evolves, ontologies must adapt to reflect the latest findings and to ensure that they continue to serve as accurate and reliable resources for the biomedical community. Continuous efforts to refine disease classifications, guided by evidence and collaboration, are essential for advancing our understanding of human health and disease.

Conclusion

The discussion surrounding the deprecation of MONDO:0023124 exemplifies the rigorous and collaborative process involved in maintaining the integrity of disease ontologies. The decision to deprecate this term, representing familial pulmonary arterial hypertension, leucopenia, and atrial septal defect, was driven by a lack of robust evidence supporting its existence as a distinct clinical entity. This case underscores the importance of evidence-based decision-making in disease classification and the need for continuous evaluation and refinement of ontologies in light of evolving scientific knowledge. The process highlights the challenges inherent in classifying rare and complex conditions, particularly those involving the co-occurrence of multiple distinct medical entities.

The implications of deprecating MONDO:0023124 extend beyond the immediate removal of a term from the ontology. It prompts reflection on the criteria used for disease classification and the need for a nuanced approach that considers both phenotypic similarities and underlying mechanisms. The absence of a suggested replacement term emphasizes the importance of avoiding the perpetuation of poorly defined or unsubstantiated disease classifications. Instead, the individual components of the condition—familial PAH, leucopenia, and ASD—should be classified and addressed separately, aligning with the principle of classifying diseases based on well-established diagnostic criteria and pathophysiology. The discussion also highlights the collaborative nature of the MONDO project, where experts from various fields contribute to the evaluation and refinement of disease terms, ensuring that the ontology remains a reliable resource for researchers, clinicians, and patients.

Looking ahead, the integration of genomic data and advanced analytical techniques holds promise for enhancing disease classification. Genomic information can provide valuable insights into the underlying causes of rare and complex conditions, enabling the identification of more precise subtypes of diseases and the development of targeted diagnostic and therapeutic strategies. The application of machine learning and other computational methods can aid in the analysis of large datasets, potentially revealing novel patterns and relationships between diseases and their associated factors. The deprecation of MONDO:0023124 serves as a reminder of the ongoing need for vigilance and critical evaluation in disease classification. As scientific knowledge continues to advance, ontologies must adapt to reflect the latest findings and to ensure that they continue to serve as accurate and reliable resources for the biomedical community. For further information on medical ontologies and disease classification, visit a trusted resource such as the National Center for Biomedical Ontology.