The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications

Abstract

Sickle cell disease (SCD) is one of the most common blood disorders impacting planetary health. Over 300,000 newborns are diagnosed with SCD each year globally, with an increasing trend. The sickle cell disease ontology (SCDO) is the most comprehensive multidisciplinary SCD knowledge portal. The SCDO was collaboratively developed by the SCDO working group, which includes experts in SCD and data standards from across the globe. This expert review presents highlights and lessons learned from the fourth SCDO workshop that marked the beginning of applications toward planetary health impact, and with an eye to empower and cultivate multisite SCD collaborative research. The workshop was organized by the Sickle Africa Data Coordinating Center (SADaCC) and attended by 44 participants from 14 countries, with 2 participants connecting remotely. Notably, from the standpoint of democratizing and innovating scientific meeting design, an SCD patient advocate also presented at the workshop, giving a broader real-life perspective on patients' aspirations, needs,

Skills Capacity Building For Health Care Services and Research Through the Sickle Pan African Research Consortium

“…To assess how well trainees assimilated and understood the online training content, they were tested on their understanding of Linux commands, databasing, statistics and probability, Python and R programming languages, emphasizing on Python SciPy and R tidyverse libraries: the average mark was above 80%. Trainees presented their systematic review at the fourth SCD Ontology (SCDO) workshop in November 2019 ( Nembaware et al, 2020 ). Assessment of quality of training was conducted in a form of a survey using course evaluation forms to capture feedback from trainees.…”

“…Skills in data collection and data management are central to the aim of SPARCO to collect data on SCD patients ( Figure 2 ) and so training in data management was prioritized taking advantage of differing skill levels at different sites and amplifying these by virtual delivery and face to face workshops. SPARCO and SADaCC developed and provided training in data collection instruments and management focusing on REDCap, big data analytics, epidemiology and study design to help address the increasing demands for big data analytics and public health skills for pan-African audiences ( Nembaware et al, 2020 ). The curricula were tightly aligned with the SPARCO goal to implement a SCD database for a large multinational African cohort.…”

The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation

“…From the start in 2016, the training has always been a critical component to make the best use of this ontology. For example, the ontology core content was built and consolidated through different workshops, engaging with different communities, including experts and researchers from different continents ( 1 , 3 ), and most importantly, with SCD patient groups from Cape Town (South Africa), Dar-es-Salaam (Tanzania), Kumasi (Ghana) and Abuja (Nigeria). In the third workshop in 2018 ( 1 ), the structure of the ontology was refined to support basic and translational research and the derived SCDO scheme was used to design another disease-specific ontology, the Hearing Impairment Ontology ( 24 ).…”

“…the addition of new top-level (close to the root) classes or new object property associations or when curators are uncertain of technicalities, changes or questions are discussed in detail with relevant SCDO working group components before implementing changes/edits into the WebProtege project ( 12 , 13 ). Note that the SCDO working group has six components: phenotype, diagnostics, therapeutics, quality of life and care, disease modifiers and data standards ( 1 , 3 ). The WebProtege tool, which provides a distributed ontology content management system, is used to enable domain experts, ontology curators and developers to share and update information, and easily visualize the ontology classes and structure.…”

“…The Sickle Cell Disease Ontology (SCDO) is the most comprehensive standardized domain knowledge portal, which unambiguously describes sickle cell disease (SCD) concepts and terminology ( 1 , 2 ). In this ontology, existing SCD knowledge is hierarchically structured and represented in human and machine-readable formats, allowing researchers and clinicians to readily access standardized SCD‐related knowledge in a single location as well as enabling SCD information to be computationally processed and analyzed to support research ( 1 , 3 ). The SCDO knowledge base is structured around the ‘Hemoglobinopathy’ class as a central aspect and links various classes as appropriate through relevant SCDO axioms (object properties), so that their relationships can be computationally inferred using logical reasoning ( 1 ).…”