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Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Adrien Maria Vierdag WM, Volkmann N, Wählby C, Wang SS, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ARXIV 2024:arXiv:2401.13022v4. [PMID: 38351940 PMCID: PMC10862930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges, and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
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Affiliation(s)
- Nikki Bialy
- Morgridge Institute for Research, Madison, USA
| | | | | | | | | | | | | | | | | | | | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Imaging Platform, Cambridge, USA
| | - Kevin Eliceiri
- Morgridge Institute for Research, Madison, USA
- University of Wisconsin-Madison, Madison, USA
| | | | | | | | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | - Michael Halter
- National Institute of Standards and Technology, Gaithersburg, USA
| | | | | | | | - Alex Laude
- Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lundberg
- Stanford University, Palo Alto, USA
- SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, USA
| | - Leonel Malacrida
- Institut Pasteur de Montevideo, & Universidad de la República, Montevideo, Uruguay
| | - Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany
| | - Glyn Nelson
- Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Anne L Plant
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | | | | | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, USA
| | | | | | | | | | - Ziv Yaniv
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
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2
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Pan H, Ives C, Mandal M, Qin Y, Hendershot T, Popovic J, Brambilla D, Stratford J, Treadwell M, Wu X, Kroner B. CureSCi Metadata Catalog-Making sickle cell studies findable. PLoS One 2022; 17:e0256248. [PMID: 36508412 PMCID: PMC9744304 DOI: 10.1371/journal.pone.0256248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To adopt the FAIR principles (Findable, Accessible, Interoperable, Reusable) to enhance data sharing, the Cure Sickle Cell Initiative (CureSCi) MetaData Catalog (MDC) was developed to make Sickle Cell Disease (SCD) study datasets more Findable by curating study metadata and making them available through an open-access web portal. METHODS Study metadata, including study protocol, data collection forms, and data dictionaries, describe information about study patient-level data. We curated key metadata of 16 SCD studies in a three-tiered conceptual framework of category, subcategory, and data element using ontologies and controlled vocabularies to organize the study variables. We developed the CureSCi MDC by indexing study metadata to enable effective browse and search capabilities at three levels: study, Patient-Reported Outcome (PRO) Measures, and data element levels. RESULTS The CureSCi MDC offers several browse and search tools to discover studies by study level, PRO Measures, and data elements. The "Browse Studies," "Browse Studies by PRO Measures," and "Browse Studies by Data Elements" tools allow users to identify studies through pre-defined conceptual categories. "Search by Keyword" and "Search Data Element by Concept Category" can be used separately or in combination to provide more granularity to refine the search results. This resource helps investigators find information about specific data elements across studies using public browsing/search tools, before going through data request procedures to access controlled datasets. The MDC makes SCD studies more Findable through browsing/searching study information, PRO Measures, and data elements, aiding in the reuse of existing SCD data.
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Affiliation(s)
- Huaqin Pan
- RTI International, Research Triangle Park, Durham, NC, United States of America
- * E-mail:
| | - Cataia Ives
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Meisha Mandal
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Ying Qin
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Tabitha Hendershot
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Jen Popovic
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Donald Brambilla
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Jeran Stratford
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Marsha Treadwell
- Children’s Hospital & Research Center Oakland, Oakland, CA, United States of America
| | - Xin Wu
- RTI International, Research Triangle Park, Durham, NC, United States of America
| | - Barbara Kroner
- RTI International, Research Triangle Park, Durham, NC, United States of America
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3
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Quality of Life in Sickle Cell Disease. Hematol Oncol Clin North Am 2022; 36:1137-1149. [DOI: 10.1016/j.hoc.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Nnodu OE, Osei-Akoto A, Nembaware V, Kent J, Nwegbu M, Minja I, Mazandu GK, Makani J, Wonkam A. Skills Capacity Building For Health Care Services and Research Through the Sickle Pan African Research Consortium. Front Genet 2022; 13:805806. [PMID: 35783259 PMCID: PMC9240392 DOI: 10.3389/fgene.2022.805806] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
Skills development, the building of human capacity, is key to any sustainable capacity building effort, however, such undertakings require adaptable and tailored strategies. The Sickle Pan-African Research Consortium (SPARCo) is building capacity in sickle cell disease (SCD) management and research in sub-Saharan Africa, including a multi-national SCD patient registry, this is underpinned by skills development activities in data, research, and SCD management. Method: The SPARCo Skills Working Group was set up with the mandate of coordinating skills development activities across the three SPARCo sites in Ghana, Nigeria and Tanzania. To tailor activities to the requirements of the consortium, a needs assessment was conducted at the start of the project which identified skills required for SCD management and research and catalogued existing external and internal training programmes. The needs assessment highlighted differences in skill levels between the sites and different organisational structures which required tailored skills development activities at individual, site and consortium levels. Strategy: Based on the needs and the resources available, different types of training activities were implemented: these included online, blended and face to face activities. In order to create a sustainable skills development programme, existing short, medium, long-term, on-job training activities were used wherever possible. World Sickle Cell Day (19th June) was leveraged for training and health education activities. Results: SPARCo has recorded 1,726 participants in skills development activities across the three sites. Skills have been enhanced in data management, SCD and research to underpin the core deliverables of SPARCo. Conclusion and Lessons Learned: The baseline needs assessments and continual review and adjustment were critical for development of an effective skill development strategy for the consortium. This adaptability was particularly valuable during the COVID-19 pandemic. The sustainability plan leveraged existing programmes and activities and has created a pool of people with required skills for health care and research in SCD. To be effective, skills development programmes need to take into account existing capacity, training opportunities and local conditions. The model was applied to SCD and is adaptable to other skills development in healthcare and research in low and middle- income countries.
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Affiliation(s)
- Obiageli Eunice Nnodu
- University of Abuja, Abuja, Nigeria
- Centre of Excellence for Sickle Cell Disease Research and Training, University of Abuja, Abuja, Nigeria
- Department of Haematology and Blood Transfusion, College of Health Sciences, University of Abuja, Abuja, Nigeria
- *Correspondence: Obiageli Eunice Nnodu,
| | - Alex Osei-Akoto
- Department of Child Health, Komfo Anokye Teaching Hospital, Kumasi, Ghana
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Victoria Nembaware
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Jill Kent
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Maxwell Nwegbu
- Department of Chemical Pathology, College of Health Sciences, University of Abuja, Abuja, Nigeria
| | - Irene Minja
- Department of Restorative Dentistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Gaston Kuzamunu Mazandu
- African Institute for Mathematical Sciences, Faculty of Science, Stellenbosch University, Muizenberg, South Africa
- African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Julie Makani
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD, United States
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5
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Mazandu GK, Hotchkiss J, Nembaware V, Wonkam A, Mulder N. The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation. Database (Oxford) 2022; 2022:6562127. [PMID: 35363306 PMCID: PMC9216550 DOI: 10.1093/database/baac014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/15/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
The Sickle Cell Disease (SCD) Ontology (SCDO, https://scdontology.h3abionet.org/) provides a comprehensive knowledge base of SCD management, systems and standardized human and machine-readable resources that unambiguously describe terminology and concepts about SCD for researchers, patients and clinicians. The SCDO was launched in 2016 and is continuously updated in quantity, as well as in quality, to effectively support the curation of SCD research, patient databasing and clinical informatics applications. SCD knowledge from the scientific literature is used to update existing SCDO terms and create new terms where necessary. Here, we report major updates to the SCDO, from December 2019 until April 2021, for promoting interoperability and facilitating SCD data harmonization, sharing and integration across different studies and for retrospective multi-site research collaborations. SCDO developers continue to collaborate with the SCD community, clinicians and researchers to improve specific ontology areas and expand standardized descriptions to conditions influencing SCD phenotypic expressions and clinical manifestations of the sickling process, e.g. thalassemias. Database URL: https://scdontology.h3abionet.org/
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Affiliation(s)
- Gaston K Mazandu
- Department of Pathology, Division of Human Genetics, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory 7925, South Africa
| | - Jade Hotchkiss
- Department of Pathology, Division of Human Genetics, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory 7925, South Africa
| | - Victoria Nembaware
- Department of Pathology, Division of Human Genetics, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory 7925, South Africa
| | - Ambroise Wonkam
- Department of Pathology, Division of Human Genetics, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory 7925, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Computational Biology Division, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory 7925, South Africa
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Vasconcelos A, Sousa S, Bandeira N, Alves M, Papoila AL, Pereira F, Machado MC. Antenatal screenings and maternal diagnosis among pregnant women in Sao Tome & Principe-Missed opportunities to improve neonatal health: A hospital-based study. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0001444. [PMID: 36962895 PMCID: PMC10021443 DOI: 10.1371/journal.pgph.0001444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/30/2022] [Indexed: 12/30/2022]
Abstract
Newborn mortality and adverse birth outcomes (ABOs) in Sao Tome & Príncipe (STP) are overwhelmingly high, and access to quality-antenatal care (ANC) is one of the strategies to tackle it. This study aimed to fill the gaps in ANC screenings with a focus on how to improve neonatal outcomes. We conducted a retrospective hospital-based study in which ANC pregnancy cards were reviewed. Screenings were described and compared according to the total number of ANC contacts: 1-3 (inadequate), 4-7 (adequate), and ≥8 (complete). The collected data were entered into QuickTapSurvey and exported to SPSS version 25 for analysis. Statistical significance was considered at a p-value ≤0.05. A total of 511 ANC pregnancy cards were reviewed. Mothers' mean age was 26.6 (SD = 7.1), 51.7% had a first trimester early booking, 14.9% (76) had 1-3 ANC contacts, 46.4% (237) had 4-7 and 38.7% (198) ≥8. Screening absence was found in 24%-41%, lack of money was registered in 36%. Pregnant women had no screening performed for HIV in 4.5%, syphilis in 8.8%, HBV 39.3%, malaria 25.8%, hemoglobin 24.5%, blood glucose 45.4%, urine 29.7%, stool exams 27.8% and 41.1% had no ultrasound. Screening completion for blood group, HIV, malaria, urine, hemoglobin, and coproparasitological exam were found to have a statistically significant difference (p<0.001) for the complete ANC group when compared to other groups. Antenatal problems identified were: 1) bacteriuria (43.2%); 2) maternal anemia (37%); 3) intestinal parasitic infections (59.2%); 4) sickle cell solubility test positive (13%); and 5) a RhD-negative phenotype (5.8%). Missed-ANC treatments were up to 50%. This study reveals a coverage-quality gap in STP since no pregnant woman is left without ANC contact, although most still miss evidence-based screenings with an impact on neonatal outcomes. Strategies such as implementing a total free ANC screening package in STP would enhance maternal diagnosis and prompt treatments.
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Affiliation(s)
- Alexandra Vasconcelos
- Unidade de Clínica Tropical-Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | | | - Nelson Bandeira
- Hospital Dr. Ayres de Menezes, São Tomé, Sao Tome and Principe
| | - Marta Alves
- CEAUL, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ana Luísa Papoila
- CEAUL, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Filomena Pereira
- Unidade de Clínica Tropical-Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Maria Céu Machado
- Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
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7
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Kountouris P, Stephanou C, Archer N, Bonifazi F, Giannuzzi V, Kuo KHM, Maggio A, Makani J, Mañú-Pereira MDM, Michailidou K, Nkya S, Nnodu OE, Trompeter S, Tshilolo L, Wonkam A, Zilfalil BA, Inusa BPD, Kleanthous M. The International Hemoglobinopathy Research Network (INHERENT): An international initiative to study the role of genetic modifiers in hemoglobinopathies. Am J Hematol 2021; 96:E416-E420. [PMID: 34406671 PMCID: PMC10390849 DOI: 10.1002/ajh.26323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 01/09/2023]
Affiliation(s)
- Petros Kountouris
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | | | - Natasha Archer
- Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Fedele Bonifazi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, Bari, Italy
| | - Viviana Giannuzzi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, Bari, Italy
| | - Kevin H M Kuo
- Division of Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Julie Makani
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - María Del Mar Mañú-Pereira
- Translational Research in Child and Adolescent Cancer. Vall d'Hebron Institut de recerca, Barcelona, Spain
| | - Kyriaki Michailidou
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Siana Nkya
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Dar es Salaam University College of Education, Dar es Salaam, Tanzania
| | - Obiageli E Nnodu
- Department of Haematology and Blood Transfusion, University of Abuja, Abuja, Nigeria
| | - Sara Trompeter
- University College London Hospitals NHS Trust, London, UK.,NHS Blood and Transplant, London, UK
| | - Léon Tshilolo
- Centre Hospitalier Monkole and CEFA-Institut de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | | | | | - Baba P D Inusa
- Paediatric Haematology, Evelina London Children's Hospital, Guy's & St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Marina Kleanthous
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
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8
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Royal CDM, Babyak M, Shah N, Srivatsa S, Stewart KA, Tanabe P, Wonkam A, Asnani M. Sickle cell disease is a global prototype for integrative research and healthcare. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10037. [PMID: 36618444 PMCID: PMC9744540 DOI: 10.1002/ggn2.10037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023]
Abstract
Differences in health outcomes and treatment responses within and between global populations have been well documented. There is growing recognition of the need to move beyond simple inventories and descriptions of these differences and our linear explanations for them, and gain a better understanding of the multifaceted systems and networks underlying them in order to develop more precise and effective remedies. Typical targets for such integrative research have been common multifactorial diseases. We propose sickle cell disease, one of the most common monogenic diseases, as an ideal candidate for elucidating the complexity of the influences of endogenous and exogenous factors on disease pathophysiology, phenotypic diversity, and variations in responses to treatments at both the individual and population levels. We provide data-informed representations of diverse contributors to sickle cell disease complications that could guide innovative efforts to advance scientific knowledge, clinical practice, and policy formulation related to the disease; help improve outcomes for people worldwide with sickle cell disease; and inform approaches to studying and addressing other diseases.
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Affiliation(s)
- Charmaine D. M. Royal
- Department of African & African American StudiesDuke UniversityDurhamNorth CarolinaUSA,Duke Global Health InstituteDuke UniversityDurhamNorth CarolinaUSA,Center on Genomics, Race, Identity, DifferenceDuke UniversityDurhamNorth CarolinaUSA
| | - Michael Babyak
- Department of Psychiatry and Behavioral SciencesDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Nirmish Shah
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Shantanu Srivatsa
- Center on Genomics, Race, Identity, DifferenceDuke UniversityDurhamNorth CarolinaUSA
| | | | - Paula Tanabe
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA,Duke University School of NursingDurhamNorth CarolinaUSA
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa,Faculty of Medicine and Biomedical SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Monika Asnani
- Caribbean Institute for Health Research ‐ Sickle Cell UnitThe University of the West IndiesKingstonJamaica
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9
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Nembaware V, Mazandu GK, Hotchkiss J, Safari Serufuri JM, Kent J, Kengne AP, Anie K, Munung NS, Bukini D, Bitoungui VJN, Munube D, Chirwa U, Chunda-Liyoka C, Jonathan A, Flor-Park MV, Esoh KK, Jonas M, Mnika K, Oosterwyk C, Masamu U, Morrice J, Uwineza A, Nguweneza A, Banda K, Nyanor I, Adjei DN, Siebu NE, Nkanyemka M, Kuona P, Tayo BO, Campbell A, Oron AP, Nnodu OE, Painstil V, Makani J, Mulder N, Wonkam A. The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:559-567. [PMID: 33021900 PMCID: PMC7549008 DOI: 10.1089/omi.2020.0153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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, and challenges. A major component of the workshop was new approaches to harness SCDO to harmonize data elements used by different studies. This was facilitated by a web-based platform onto which participants uploaded data elements from previous or ongoing SCD-relevant research studies before the workshop, making multisite collaborative research studies based on existing SCD data possible, including multisite cohort, SCD global clinical trials, and SCD community engagement approaches. Trainees presented proposals for systematic literature reviews in key SCD research areas. This expert review emphasizes potential and prospects of SCDO-enabled data standards and harmonization to facilitate large-scale global SCD collaborative initiatives. As the fields of public and global health continue to broaden toward planetary health, the SCDO is well poised to play a prominent role to decipher SCD pathophysiology further, and co-design diagnostics and therapeutics innovation in the field.
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Affiliation(s)
- Victoria Nembaware
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K Mazandu
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jade Hotchkiss
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Jill Kent
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Andre Pascal Kengne
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Kofi Anie
- London North West University Healthcare NHS Trust and Imperial College London, London, UK.,Sickle Cell Disease Genomics Network of Africa (SickleGenAfrica), University of Ghana, Accra, Ghana
| | - Nchangwi Syntia Munung
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Daima Bukini
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Valentina Josiane Ngo Bitoungui
- Department of Microbiology, Hematology and Immunology, Faculty of Medicine and Pharmaceutical Sciences of the University of Dschang, Dschang, Cameroon
| | - Deogratias Munube
- Department of Paediatric and Child Health, Makerere University/Mulago National Referral Hospital, Kampala, Uganda
| | - Uzima Chirwa
- University Teaching Hospitals-Children's Hospital, University of Zambia, School of Medicine, Lusaka, Zambia
| | - Catherine Chunda-Liyoka
- University Teaching Hospitals-Children's Hospital, University of Zambia, School of Medicine, Lusaka, Zambia
| | - Agnes Jonathan
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Miriam V Flor-Park
- Onco-hematology Unit, Instituto da Criança, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
| | - Kevin Kum Esoh
- Department of Biochemistry, Faculty of Science, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Mario Jonas
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Khuthala Mnika
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Chandré Oosterwyk
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Upendo Masamu
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Jack Morrice
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Annette Uwineza
- University of Rwanda, School of Medicine and Pharmacy, Kigali, Rwanda
| | - Arthemon Nguweneza
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kambe Banda
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Isaac Nyanor
- Kumasi Centre for Sickle Cell Disease, Komfo Anokye Teaching Hospital, Accra, Ghana
| | - David Nana Adjei
- Sickle Cell Disease Genomics Network of Africa (SickleGenAfrica), University of Ghana, Accra, Ghana
| | - Nathan Edward Siebu
- Sickle Cell Disease Genomics Network of Africa (SickleGenAfrica), University of Ghana, Accra, Ghana
| | - Malula Nkanyemka
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Patience Kuona
- University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Bamidele O Tayo
- Department of Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, USA
| | - Andrew Campbell
- Division of Hematology, Center for Cancer and Blood Disorders, Children's National Medical Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Assaf P Oron
- Maternal, Newborn and Child Health, Institute for Disease Modeling, Bellevue, Washington, USA
| | - Obiageli E Nnodu
- Centre of Excellence for Sickle Cell Disease Research and Training, University of Abuja, Abuja, Nigeria
| | - Vivian Painstil
- Department of Child Health, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Julie Makani
- Sickle Cell Programme, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Nicola Mulder
- Computational Biology Division, Faculty of Health Sciences, Cape Town, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Nembaware V, Munung NS, Matimba A, Tiffin N. Patient-centric research in the time of COVID-19: conducting ethical COVID-19 research in Africa. BMJ Glob Health 2020; 5:bmjgh-2020-003035. [PMID: 32764129 PMCID: PMC7411326 DOI: 10.1136/bmjgh-2020-003035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Victoria Nembaware
- Human Genetics Division, University of Cape Town, Cape Town, South Africa
| | | | - Alice Matimba
- Advanced Courses and Scientific Conferences, Wellcome Genome Campus, Cambridge, UK
| | - Nicki Tiffin
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa .,Computational Biology Division, University of Cape Town, Cape Town, South Africa
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11
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A potential roadmap to overcome the current eastern DRC Ebola virus disease outbreak: From a computational perspective. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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12
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The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. Genes (Basel) 2019; 10:genes10120960. [PMID: 31766582 PMCID: PMC6947307 DOI: 10.3390/genes10120960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/31/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
Hearing impairment (HI) is a common sensory disorder that is defined as the partial or complete inability to detect sound in one or both ears. This diverse pathology is associated with a myriad of phenotypic expressions and can be non-syndromic or syndromic. HI can be caused by various genetic, environmental, and/or unknown factors. Some ontologies capture some HI forms, phenotypes, and syndromes, but there is no comprehensive knowledge portal which includes aspects specific to the HI disease state. This hampers inter-study comparability, integration, and interoperability within and across disciplines. This work describes the HI Ontology (HIO) that was developed based on the Sickle Cell Disease Ontology (SCDO) model. This is a collaboratively developed resource built around the ‘Hearing Impairment’ concept by a group of experts in different aspects of HI and ontologies. HIO is the first comprehensive, standardized, hierarchical, and logical representation of existing HI knowledge. HIO allows researchers and clinicians alike to readily access standardized HI-related knowledge in a single location and promotes collaborations and HI information sharing, including epidemiological, socio-environmental, biomedical, genetic, and phenotypic information. Furthermore, this ontology illustrates the adaptability of the SCDO framework for use in developing a disease-specific ontology.
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