The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation

Abstract

Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD.

Antenatal screenings and maternal diagnosis among pregnant women in Sao Tome & Principe—Missed opportunities to improve neonatal health: A hospital-based study

“…A sickle cell solubility test, which involves treating a thin blood film with sodium dithionate under hypoxic conditions and observing for sickling under a light microscope, is the screening technique available in STP and is performed on pregnant women with anemia or clinical suspicion [42,43]. A positive result can suggest either sickle cell anemia or the sickle cell trait [42].…”

CureSCi Metadata Catalog–Making sickle cell studies findable

“…The hierarchical structure and terminology were adopted and reused in our development when applicable and becomes the backbone of our conceptual framework [ 23 ]. The SCDO is a community-driven knowledge representation system for terminology and concepts about SCD [ 25 ]. Initial efforts to adopt SCDO structure and naming were met with some challenges.…”

The H3Africa Consortium: Publication Outputs of a Pan-African Genomics Collaboration (2013 to 2020)

“…Several projects within the Consortium are centred around the identification and functional impact of African-specific genetic variants. The network also contributed to the development of specialized ontologies for sickle cell disease Adekile et al, 2019) and hearing impairment (Hotchkiss et al, 2019). A Human Mutation Analysis (HUMA) web server and database was designed to integrate sequence data, protein structure variation and disease data into a single connected database (Brown and Tastan Bishop 2018).…”