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

Sickle Cell Disease Ontology Working Group

doi:10.1093/database/baz118

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

Database (Oxford). 2019 Jan 1:2019:baz118. doi: 10.1093/database/baz118.

Author

Sickle Cell Disease Ontology Working Group

Collaborators

Sickle Cell Disease Ontology Working Group:
Adekunle Adekile¹, Kofi A. Anie², Cherif Ben Hamda³, Biobele Brown⁴, Daima Bukini⁵, Andrew Campbell⁶, Melek Chaouch³, Emile Chimusa⁷, Catherine Chunda-Liyoka⁸, Jemima Dennis-Antwi⁹, Vimal K. Derebail¹⁰, Miriam Flor-Park¹¹, Amy Geard^{12

13}, Kais Ghedira³, Melissa Haendel¹⁴, Neil A. Hanchard¹⁵, Jade Hotchkiss⁷, Mario Jonas⁷, Muntaser Ibrahim¹⁶, Clair Ingram⁷, Baba Inusa¹⁷, Adijat Ozohu Jimoh¹⁸, Simon Jupp¹⁹, Karen Kamga^{7

20}, Zainab Abimbola Kashim¹⁸, Jennifer Knight-Madden²¹, Guida Landouré^{22

23}, Philomene Lopez-Sall²⁴, Julie Makani⁵, Leonard Malasa⁵, Tshepiso Masekoameng⁷, Gaston Mazandu⁷, Khuthala Mnika⁷, Nicola Mulder²⁵, Nchangwi Syntia Munung²⁶, Deogratias Munube²⁷, Liberata Mwita⁵, Victoria Nembaware⁷, Obiageli Nnodu²⁸, Solomon Ofori-Acquah^{29

30}, Kwaku Ohene-Frempong³¹, Alex Osei-Akoto³², Vivian Paintsil³³, Sumir Panji²⁵, Mohamed Cherif Rahimy³⁴, Charmaine Royal³⁵, Raphael Z Sangeda³⁶, Bamidele Tayo³⁷, Ines Tiouiri³, Furahini Tluway⁵, Marsha Treadwell³⁸, Leon Tshilolo³⁹, Nicole Vasilevsky⁴⁰, Kasadhakawo Musa Waiswa⁴¹, Ambroise Wonkam⁷

Affiliations

¹ Kuwait University, Kuwait City, Kuwait.
² Haematology and Sickle Cell Centre, London North West University Healthcare NHS Trust & Imperial College London, London, United Kingdom.
³ Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia.
⁴ Department of Paediatrics, College of Medicine, University of Ibadan, Ibadan, Nigeria.
⁵ Sickle Cell Programme, Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Tanzania.
⁶ Division of Hematology, Children’s National Medical Center, George Washington School of Medicine and Health Sciences, Washington, DC, USA.
⁷ Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
⁸ University Teaching Hospitals - Children’s Hospital, University of Zambia, Lusaka, Zambia.
⁹ Sickle Cell Foundation of Ghana. East Legon-Accra, Ghana.
¹⁰ UNC Kidney Center, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill.
¹¹ Onco Hematology Unit, Instituto da Criança, Hospital das Clínicas, Universidade de São Paulo, Brazil.
¹² Gene Transfer Technology Group, UCL EGA Institute for Women’s Health, University College London, London, UK.
¹³ University of the Witwatersrand, School of Pathology, Antiviral Gene Therapy Research Unit, Health Sciences Faculty, South Africa.
¹⁴ Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA.
¹⁵ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
¹⁶ Institute of Endemic Diseases, - University of Khartoum, Sudan.
¹⁷ Department of Paediatric Haematology, Evelina Children’s Hospital, Guy’s and St Thomas NHS Trust, London.
¹⁸ Department of Genetics, Genomics and Bioinformatics - National Biotechnology Development Agency (NABDA), Abuja, Nigeria.
¹⁹ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
²⁰ FMBS, University of Yaounde.
²¹ The Sickle Cell Unit, Caribbean Institute for Health Research, the University of the West Indies.
²² Faculté de Médecine et d’Odontostomatologie, USTTB, Mali.
²³ Service de Neurologie, CHU du Point “G”, Bamako, Mali.
²⁴ Department of Pharmacy, Biochemistry Unit, Cheikh Anta Diop University, Dakar, Senegal.
²⁵ Computational Biology Division, IDM, CIDRI-Africa Wellcome Trust Centre, University of Cape Town Faculty of Health Sciences Anzio Road, Observatory, Cape Town, South Africa.
²⁶ Department of Medicine, University of Cape Town, South Africa.
²⁷ Department of Paediatrics and Child Health, Makerere University/Mulago National Referral Hospital, Kampala, Uganda.
²⁸ Department of Haematology & Blood Transfusion, College of Health Sciences, University of Abuja, Abuja, Nigeria.
²⁹ Dean, School of Biomedical and Allied Health Sciences.
³⁰ Director, SickleGenAfrica:Sickle Cell Disease Genomics Network of Africa.
³¹ President, Sickle Cell Foundation of Ghana.
³² Dept. of Child Health, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology/Komfo Anokye Teaching Hospital, Kumasi, Ghana.
³³ Komfo Anokye Teaching Hospital, Kumasi, Ghana.
³⁴ Centre de Prise en Charge Medicale Integree du Nourrisson et de la Femme Enceinte atteints de Drepanocytose, (The National Sickle Cell Disease Institute), Cotonou, Republic of Benin.
³⁵ Departments of African & African American Studies, Biology, and Community & Family Medicine, Duke University, Durham, USA.
³⁶ Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Tanzania.
³⁷ Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA.
³⁸ UCSF Benioff Children’s Hospital Oakland, Department of Hematology/Oncology 747 52nd Street Oakland, CA USA 94609.
³⁹ Centre de Formation et d’Appui sanitaire/MONKOLE, Kinshasa, DR Congo.
⁴⁰ Oregon Clinical & Translational Research Institute, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, USA.
⁴¹ Department of Medicine, Makerere University College of Health sciences, University college of Health sciences.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Anemia, Sickle Cell / pathology*
Biological Ontologies*
Humans
Knowledge Bases*
Phenotype

Abstract

Publication types

MeSH terms

Grants and funding