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Article ; Online: FAIR Header Reference genome: a TRUSTworthy standard.

Wright, Adam / Wilkinson, Mark D / Mungall, Christopher / Cain, Scott / Richards, Stephen / Sternberg, Paul / Provin, Ellen / Jacobs, Jonathan L / Geib, Scott / Raciti, Daniela / Yook, Karen / Stein, Lincoln / Molik, David C

Briefings in bioinformatics

2024 Volume 25, Issue 3

Abstract: The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard ... ...

Abstract	The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
MeSH term(s)	Humans ; Genome ; Genomics ; Information Dissemination ; Software
Language	English
Publishing date	2024-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae122
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Article: DATA RESOURCES AND ANALYSES FAIR Header Reference genome: A TRUSTworthy standard.

Wright, Adam / Wilkinson, Mark D / Mungall, Chris / Cain, Scott / Richards, Stephen / Sternberg, Paul / Provin, Ellen / Jacobs, Jonathan L / Geib, Scott / Raciti, Daniela / Yook, Karen / Stein, Lincoln / Molik, David C

bioRxiv : the preprint server for biology

2023

Abstract: The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard ... ...

Abstract	The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
Language	English
Publishing date	2023-12-20
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.29.569306
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Complementation.

Yook, Karen

WormBook : the online review of C. elegans biology

2005 , Page(s) 1–17

Abstract: Mutations in many genes can result in a similar phenotype. Finding a number of mutants with the same phenotype tells you little about how many genes you are dealing with, and how mutable those genes are until you can assign those mutations to genetic ... ...

Abstract	Mutations in many genes can result in a similar phenotype. Finding a number of mutants with the same phenotype tells you little about how many genes you are dealing with, and how mutable those genes are until you can assign those mutations to genetic loci. The genetic assay for gene assignment is called the complementation test. The simplicity and robustness of this test makes it a fundamental genetic tool for gene assignment. However, there are occasional unexpected outcomes from this test that bear explanation. This chapter reviews the complementation test and its various outcomes, highlighting relatively rare but nonetheless interesting exceptions such as intragenic complementation and non-allelic non-complementation.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Genetic Complementation Test/methods ; Humans
Language	English
Publishing date	2005-10-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ISSN	1551-8507
ISSN (online)	1551-8507
DOI	10.1895/wormbook.1.24.1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Perceptions, barriers and enablers on salt reduction in the out-of-home sectors in Malaysia (MySaltOH) from the perspective of street food vendors, caterers and consumers

Zainorain Natasha Zainal Arifen / Hasnah Haron / Suzana Shahar / Zaliha Harun / Viola Michael / Yee Xing You / Zahara Abdul Manaf / Hazreen Abdul Majid / Yook Chin Chia / Feng J He / Mhairi Karen Brown / Graham A MacGregor

Public Health Nutrition, Vol

2024 Volume 27

Abstract: Abstract Objective: To explore the perspectives, barriers and enablers on salt reduction in out-of-home sectors in Malaysia among street food vendors, caterers and consumers. Design: A qualitative study involving twenty-two focus group discussions and ... ...

Abstract	Abstract Objective: To explore the perspectives, barriers and enablers on salt reduction in out-of-home sectors in Malaysia among street food vendors, caterers and consumers. Design: A qualitative study involving twenty-two focus group discussions and six in-depth interviews was conducted, recorded and transcribed verbatim. An inductive thematic analysis approach was employed to analyse the data. Setting: Two in-depth interviews and twenty-two focus group discussions were conducted face-to-face. Four in-depth interviews were conducted online. Participants: Focus group discussions were conducted among twenty-three street food vendors, twenty-one caterers and seventy-six consumers of various eateries. In-depth interviews were conducted among two street food vendors and four caterers, individually. Results: Consumers and food operators perceived a high-salt intake within Malaysia’s out-of-home food sectors. Food operators emphasised the necessity for a comprehensive salt reduction policy in the out-of-home sector involving all stakeholders. Consumers faced limited awareness and knowledge, counterproductive practices among food operators and challenges in accessing affordable low-Na food products, whereas food operators faced the lack of standardised guidelines and effective enforcement mechanisms and uncooperative consumer practices. Both groups expressed that food quality and price of salt were also the barriers, and they advocated for awareness promotion, enhanced regulation of manufactured food products and stricter enforcement targeting vendors. Consumers also suggested promoting and recognising health-conscious food premises, whereas food operators suggested on knowledge enhancement tailored to them, strategies for gaining consumers acceptance and maintaining food quality. Conclusions: These findings provide valuable insights that serve as foundational evidence for developing and implementing salt reduction policies within Malaysia’s out-of-home sectors.
Keywords	Perceptions ; Barriers ; Enablers ; Salt reduction ; Out-of-home sectors ; Food vendors ; Caterers ; Consumers ; Public aspects of medicine ; RA1-1270 ; Nutritional diseases. Deficiency diseases ; RC620-627
Subject code	360
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Cambridge University Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Western and Chinese exercise training for blood pressure reduction among hypertensive patients: An overview of systematic reviews.

Tsoi, Kelvin / Lam, Amy / Tran, Joshua / Hao, Ziyu / Yiu, Karen / Chia, Yook-Chin / Turana, Yuda / Siddique, Saulat / Zhang, Yuqing / Cheng, Hao-Min / Wang, Ji-Guang / Kario, Kazuomi

Journal of clinical hypertension (Greenwich, Conn.)

2023

Abstract: Hypertension remains the world's leading cause of premature death. Interventions such as exercise, diet modification, and pharmacological therapy remain the mainstay of hypertension treatment. Numerous systematic reviews and meta-analyses demonstrated ... ...

Abstract	Hypertension remains the world's leading cause of premature death. Interventions such as exercise, diet modification, and pharmacological therapy remain the mainstay of hypertension treatment. Numerous systematic reviews and meta-analyses demonstrated the effectiveness of western exercises, such as aerobic exercise and resistance exercise, in reducing blood pressure in hypertensive patients. There is recently emerging evidence of blood pressure reduction with Chinese exercises, such as Tai Chi, Baduanjin, and Qigong. The current overview of systematic reviews aims to evaluate the quality and descriptively summarize the evidence for the effectiveness of western and Chinese exercises for hypertension management. Thirty-nine systematic reviews were included in this overview, with 15 of those being on Chinese exercise. Evidence suggests that exercise training, regardless of Western or Chinese exercise, generally reduced both systolic and diastolic blood pressure. High-intensity intermittent training did not further reduce blood pressure when compared to moderate-intensity continuous training. Conflicting results on the effectiveness of blood pressure reduction when comparing Chinese and Western exercise training were observed. This suggests the comparable effectiveness of Chinese exercise training, in particularly Tai Chi, to general or aerobic exercise training in terms of blood pressure reduction. The Chinese exercise modality and intensity may be more suitable for the middle-aged and elderly population.
Language	English
Publishing date	2023-03-22
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2077222-1
ISSN	1751-7176 ; 1524-6175
ISSN (online)	1751-7176
ISSN	1524-6175
DOI	10.1111/jch.14610
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Article ; Online: WormBase 2024: status and transitioning to Alliance infrastructure.

Sternberg, Paul W / Van Auken, Kimberly / Wang, Qinghua / Wright, Adam / Yook, Karen / Zarowiecki, Magdalena / Arnaboldi, Valerio / Becerra, Andrés / Brown, Stephanie / Cain, Scott / Chan, Juancarlos / Chen, Wen J / Cho, Jaehyoung / Davis, Paul / Diamantakis, Stavros / Dyer, Sarah / Grigoriadis, Dionysis / Grove, Christian A / Harris, Todd /

Howe, Kevin / Kishore, Ranjana / Lee, Raymond / Longden, Ian / Luypaert, Manuel / Müller, Hans-Michael / Nuin, Paulo / Quinton-Tulloch, Mark / Raciti, Daniela / Schedl, Tim / Schindelman, Gary / Stein, Lincoln

Genetics

2024 Volume 227, Issue 1

Abstract: WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. ... ...

Abstract	WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.
MeSH term(s)	Caenorhabditis elegans/genetics ; Animals ; Databases, Genetic ; Genome, Helminth ; Genomics/methods
Language	English
Publishing date	2024-04-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyae050
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Article ; Online: Perceptions, barriers and enablers on salt reduction in the out-of-home sectors in Malaysia (MySaltOH) from the perspective of street food vendors, caterers and consumers.

Zainal Arifen, Zainorain Natasha / Haron, Hasnah / Shahar, Suzana / Harun, Zaliha / Michael, Viola / You, Yee Xing / Manaf, Zahara Abdul / Majid, Hazreen Abdul / Chia, Yook Chin / He, Feng J / Brown, Mhairi Karen / MacGregor, Graham A

Public health nutrition

2023 Volume 27, Issue 1, Page(s) e12

Abstract: Objective: To explore the perspectives, barriers and enablers on salt reduction in out-of-home sectors in Malaysia among street food vendors, caterers and consumers.: Design: A qualitative study involving twenty-two focus group discussions and six in- ...

Abstract	Objective: To explore the perspectives, barriers and enablers on salt reduction in out-of-home sectors in Malaysia among street food vendors, caterers and consumers. Design: A qualitative study involving twenty-two focus group discussions and six in-depth interviews was conducted, recorded and transcribed verbatim. An inductive thematic analysis approach was employed to analyse the data. Setting: Two in-depth interviews and twenty-two focus group discussions were conducted face-to-face. Four in-depth interviews were conducted online. Participants: Focus group discussions were conducted among twenty-three street food vendors, twenty-one caterers and seventy-six consumers of various eateries. In-depth interviews were conducted among two street food vendors and four caterers, individually. Results: Consumers and food operators perceived a high-salt intake within Malaysia's out-of-home food sectors. Food operators emphasised the necessity for a comprehensive salt reduction policy in the out-of-home sector involving all stakeholders. Consumers faced limited awareness and knowledge, counterproductive practices among food operators and challenges in accessing affordable low-Na food products, whereas food operators faced the lack of standardised guidelines and effective enforcement mechanisms and uncooperative consumer practices. Both groups expressed that food quality and price of salt were also the barriers, and they advocated for awareness promotion, enhanced regulation of manufactured food products and stricter enforcement targeting vendors. Consumers also suggested promoting and recognising health-conscious food premises, whereas food operators suggested on knowledge enhancement tailored to them, strategies for gaining consumers acceptance and maintaining food quality. Conclusions: These findings provide valuable insights that serve as foundational evidence for developing and implementing salt reduction policies within Malaysia's out-of-home sectors.
MeSH term(s)	Humans ; Sodium Chloride, Dietary ; Malaysia ; Food ; Food Services ; Qualitative Research
Chemical Substances	Sodium Chloride, Dietary
Language	English
Publishing date	2023-12-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1436024-x
ISSN	1475-2727 ; 1368-9800
ISSN (online)	1475-2727
ISSN	1368-9800
DOI	10.1017/S136898002300277X
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Article ; Online: Micropublication: incentivizing community curation and placing unpublished data into the public domain.

Raciti, Daniela / Yook, Karen / Harris, Todd W / Schedl, Tim / Sternberg, Paul W

Database : the journal of biological databases and curation

2018 Volume 2018

Abstract: Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental ... ...

Abstract	Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery. Database url: www.micropublication.org.
MeSH term(s)	Biomedical Research ; Data Curation/methods ; Databases, Factual ; Humans ; Periodicals as Topic
Language	English
Publishing date	2018-04-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/bay013
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Article ; Online: Developing a policy to reduce the salt content of food consumed outside the home in Malaysia

Suzana Shahar / Yee Xing You / Viola Michael / Hasnah Haron / Feng J He / Graham A MacGregor / Yook Chin Chia / Hazreen Abdul Majid / Mhairi Karen Brown / Zahara Abdul Manaf / Noor Shahida Sukiman

BMJ Open, Vol 11, Iss

protocol of a qualitative study

2021 Volume 7

Abstract: Introduction Current salt intake in Malaysia is high. The existing national salt reduction policy has faced slow progress and does not yet include measures to address the out of home sector. Dishes consumed in the out of home sector are a known leading ... ...

Abstract	Introduction Current salt intake in Malaysia is high. The existing national salt reduction policy has faced slow progress and does not yet include measures to address the out of home sector. Dishes consumed in the out of home sector are a known leading contributor to daily salt intake. This study aims to develop a salt reduction strategy, tailored to the out of home sector in Malaysia.Methods and analysis This study is a qualitative analysis of stakeholder views towards salt reduction. Participants will be recruited from five zones of Malaysia (Western, Northern, Eastern and Southern regions and East Malaysia), including policy-makers, non-governmental organisations, food industries, school canteen operators, street food vendors and consumers, to participate in focus group discussions or in-depth interviews. Interviews will be transcribed and analysed using thematic analysis. Barriers will be identified and used to develop a tailored salt reduction strategy.Ethics and dissemination Ethical approval has been obtained from the Universiti Kebangsaan Malaysia Medical Research Ethics Committee (UKM PPI/1118/JEP-2020–524), the Malaysian National Medical Research Ethics Committee (NMRR-20-1387-55481 (IIR)) and Queen Mary University of London Research Ethics Committee (QMERC2020/37) . Results will be presented orally and in report form and made available to the relevant ministries for example, Ministry of Health, Ministry of Education and Ministry of Trade to encourage adoption of strategy as policy. The findings of this study will be disseminated through conference presentations, peer-reviewed publications and webinars.
Keywords	Medicine ; R
Subject code	170
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Barriers, Enablers, and Perceptions on Dietary Salt Reduction in the Out-of-Home Sectors

Viola Michael / Yee Xing You / Suzana Shahar / Zahara Abdul Manaf / Hasnah Haron / Siti Nurbaya Shahrir / Hazreen Abdul Majid / Yook Chin Chia / Mhairi Karen Brown / Feng J. He / Graham A. MacGregor

International Journal of Environmental Research and Public Health, Vol 18, Iss 8099, p

A Scoping Review

2021 Volume 8099

Abstract: In this review, we have investigated the perceptions, barriers, and enabling factors that were responsible for a dietary salt reduction in the out-of-home sectors. For this purpose, we examined different knowledge databases such as Google Scholar, ... ...

Abstract	In this review, we have investigated the perceptions, barriers, and enabling factors that were responsible for a dietary salt reduction in the out-of-home sectors. For this purpose, we examined different knowledge databases such as Google Scholar, Ebscohost, MEDLINE (PubMed), Ovid, and Cochrane Library for research articles from September to December 2020. The inclusion criteria for the research articles were that they had to be published in English and had to be a qualitative or quantitative study that was conducted after 2010. These studies also had to report the various enablers, barriers, and perceptions regarding salt reduction in the out-of-home sectors. After implementing the inclusion criteria, we successfully screened a total of 440 studies, out of which 65 articles fulfilled all the criteria. The perceived barriers that hindered salt reduction among the out-of-home sectors included lack of menu and food variabilities, loss of sales due to salt reduction, lack of technical skills for implementing the salt reduction processes for cooking or reformulation, and an absence of environmental and systemic support for reducing the salt concentration. Furthermore, the enablers for salt reduction included the intervention programs, easy accessibility to salt substitutes, salt intake measurement, educational availability, and a gradual reduction in the salt levels. With regards to the behavior or perceptions, the effect of organizational and individual characteristics on their salt intake were reported. The majority of the people were not aware of their salt intake or the effect of salt on their health. These people also believed that low salt food was recognized as tasteless. In conclusion, the enablers, barriers, and perceptions regarding salt reduction in the out-of-home sectors were multifaceted. Therefore, for the implementation of the strategies, policies, and initiatives for addressing the barriers, the policymakers need to encourage a multisectoral collaboration for reducing the salt intake in the ...
Keywords	barriers ; enablers ; perception ; salt reduction ; out-of-home ; Medicine ; R
Subject code	360
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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