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The BioPAX community standard for pathway data sharing.

ABSTRACT: Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

SUBMITTER: Demir E

PROVIDER: S-EPMC3001121 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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The BioPAX community standard for pathway data sharing.

Demir Emek E Cary Michael P MP Paley Suzanne S Fukuda Ken K Lemer Christian C Vastrik Imre I Wu Guanming G D'Eustachio Peter P Schaefer Carl C Luciano Joanne J Schacherer Frank F Martinez-Flores Irma I Hu Zhenjun Z Jimenez-Jacinto Veronica V Joshi-Tope Geeta G Kandasamy Kumaran K Lopez-Fuentes Alejandra C AC Mi Huaiyu H Pichler Elgar E Rodchenkov Igor I Splendiani Andrea A Tkachev Sasha S Zucker Jeremy J Gopinath Gopal G Rajasimha Harsha H Ramakrishnan Ranjani R Shah Imran I Syed Mustafa M Anwar Nadia N Babur Ozgün O Blinov Michael M Brauner Erik E Corwin Dan D Donaldson Sylva S Gibbons Frank F Goldberg Robert R Hornbeck Peter P Luna Augustin A Murray-Rust Peter P Neumann Eric E Ruebenacker Oliver O Samwald Matthias M van Iersel Martijn M Wimalaratne Sarala S Allen Keith K Braun Burk B Whirl-Carrillo Michelle M Cheung Kei-Hoi KH Dahlquist Kam K Finney Andrew A Gillespie Marc M Glass Elizabeth E Gong Li L Haw Robin R Honig Michael M Hubaut Olivier O Kane David D Krupa Shiva S Kutmon Martina M Leonard Julie J Marks Debbie D Merberg David D Petri Victoria V Pico Alex A Ravenscroft Dean D Ren Liya L Shah Nigam N Sunshine Margot M Tang Rebecca R Whaley Ryan R Letovksy Stan S Buetow Kenneth H KH Rzhetsky Andrey A Schachter Vincent V Sobral Bruno S BS Dogrusoz Ugur U McWeeney Shannon S Aladjem Mirit M Birney Ewan E Collado-Vides Julio J Goto Susumu S Hucka Michael M Le Novère Nicolas N Maltsev Natalia N Pandey Akhilesh A Thomas Paul P Wingender Edgar E Karp Peter D PD Sander Chris C Bader Gary D GD

Nature biotechnology 20100909 9

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community pr ...[more]

PMID: 20829833

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Project description:BackgroundThe use of government health data for secondary purposes, such as monitoring the quality of hospital services, researching the health needs of populations, and testing how well new treatments work, is increasing. This increase in the secondary uses of health data has led to increased interest in what the public thinks about data sharing, in particular, the possibilities of sharing with the private sector for research and development. Although international evidence demonstrates broad public support for the secondary use of health data, this support does not extend to sharing health data with the private sector. If governments intend to share health data with the private sector, knowing what the public thinks will be important. This paper reports a national survey to explore public attitudes in Australia toward sharing health data with private companies for research on and development of therapeutic drugs and medical devices.ObjectiveThis study aims to explore public attitudes in Australia toward sharing government health data with the private sector.MethodsA web-based survey tool was developed to assess attitudes about sharing government health data with the private sector. A market research company was employed to administer the web-based survey in June 2019.ResultsThe survey was completed by 2537 individuals residing in Australia. Between 51.8% and 57.98% of all participants were willing to share their data, with slightly fewer in favor of sharing to improve health services (51.99%) and a slightly higher proportion in favor of sharing for research and development (57.98%). There was a preference for opt-in consent (53.44%) and broad support for placing conditions on sharing health information with private companies (62% to 91.99%). Wide variability was also observed in participants' views about the extent to which the private sector could be trusted and how well they would behave if entrusted with people's health information. In their qualitative responses, the participants noted concerns about private sector corporate interests, corruption, and profit making and expressed doubt about the Australian government's capacity to manage data sharing safely. The percentages presented are adjusted against the Australian population.ConclusionsThis nationally representative survey provides preliminary evidence that Australians are uncertain about sharing their health data with the private sector. Although just over half of all the respondents supported sharing health data with the private sector, there was also strong support for strict conditions on sharing data and for opt-in consent and significant concerns about how well the private sector would manage government health data. Addressing public concern about sharing government health data with the private sector will require more and better engagement to build community understanding about how agencies can collect, share, protect, and use their personal data.

Project description:Introduction:Innovative data platforms (e.g. biobanks, repositories) continually emerge to facilitate data sharing. Extant and emerging data platforms must navigate myriad tensions for successful data sharing and re-use. Two Alberta data platforms navigated such processes and factors regarding administrative, research and nonprofit data: the Child & Youth Data Laboratory (CYDL) and Secondary Analysis to Generate Evidence (SAGE). Objectives:To clarify the social and policy factors that influenced CYDL and SAGE establishment and implementation, and the relationships, if any, between these factors and data type. Methods:This paper involves a qualitative secondary analysis of two developmental evaluations on CYDL and SAGE establishment. Six-years post-implementation, the CYDL evaluation entailed document review; website user analysis; interviews (n=30); online stakeholder survey (n=260); and an environmental scan. One-year post implementation, the SAGE evaluation included 15 interviews and document review. We used thematic analysis and comparisons with the literature to identify key factors. Results:Three (not mutually exclusive) categories of social and policy factors influenced the navigation towards CYDL and SAGE realization: trusting relationships; sustainability amidst readiness; and privacy within social context. For these platforms to be able to manage, link or share data, trust had to be fostered and maintained across multiple, dynamic and intersecting relationships between primary data producers, data subjects, secondary users and institutions. Platform sustainability required capacity building and innovation. Privacy and information sharing evolved culturally and correspondingly for these data platforms, which required constant flexibility and awareness. Conclusions:This analysis calls for more empirical research on the value of data re-use or the detriment in not re-using data. While the culture of information sharing is progressing towards greater openness and capacity for data sharing and re-use, successful data platforms must advocate, facilitate and mobilize analysis and innovation using data re-use while being cognizant of social and policy influences.

Dataset Information

The BioPAX community standard for pathway data sharing.

Publications

The BioPAX community standard for pathway data sharing.

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