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| ==Sandbox begins below== | | == LIS User Requirements for the Physician Office Laboratory (POL) == |
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| |title_full = A data quality strategy to enable FAIR, programmatic access across large,<br />diverse data collections for high performance data analysis
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| |journal = ''Informatics''
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| |authors = Evans, Ben; Druken, Kelsey; Wang, Jingbo; Yang, Rui; Richards, Clare; Wyborn, Lesley
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| |affiliations = Australian National University
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| |contact = Email: Jingbo dot Wang at anu dot edu dot au
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| |editors = Ge, Mouzhi; Dohnal, Vlastislav
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| |pub_year = 2017
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| |vol_iss = '''4'''(4)
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| |pages = 45
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| |doi = [http://10.3390/informatics4040045 10.3390/informatics4040045]
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| |issn = 2227-9709
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| |license = [http://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International]
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| |website = [http://www.mdpi.com/2227-9709/4/4/45/htm http://www.mdpi.com/2227-9709/4/4/45/htm]
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| |download = [http://www.mdpi.com/2227-9709/4/4/45/pdf http://www.mdpi.com/2227-9709/4/4/45/pdf] (PDF)
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| ==Abstract==
| | ;Chapter 1 Introduction |
| To ensure seamless, programmatic access to data for high-performance computing (HPC) and [[Data analysis|analysis]] across multiple research domains, it is vital to have a methodology for standardization of both data and services. At the Australian National Computational Infrastructure (NCI) we have developed a data quality strategy (DQS) that currently provides processes for: (1) consistency of data structures needed for a high-performance data (HPD) platform; (2) [[quality control]] (QC) through compliance with recognized community standards; (3) benchmarking cases of operational performance tests; and (4) [[quality assurance]] (QA) of data through demonstrated functionality and performance across common platforms, tools, and services. By implementing the NCI DQS, we have seen progressive improvement in the quality and usefulness of the datasets across different subject domains, and demonstrated the ease by which modern programmatic methods can be used to access the data, either ''in situ'' or via web services, and for uses ranging from traditional analysis methods through to emerging machine learning techniques. To help increase data re-usability by broader communities, particularly in high-performance environments, the DQS is also used to identify the need for any extensions to the relevant international standards for interoperability and/or programmatic access.
| | :[[Clinical laboratory]] |
| | | :[[Health informatics]] |
| '''Keywords''': data quality, quality control, quality assurance, benchmarks, performance, data management policy, netCDF, high-performance computing, HPC, fair data
| | ;Chapter 2 The Physician Office Laboratory (POL) |
| | | :[[Physician office laboratory]] |
| ==Introduction==
| | :[[LII:The Practical Guide to the U.S. Physician Office Laboratory]] |
| The National Computational Infrastructure (NCI) manages one of Australia’s largest and more diverse repositories (10+ petabytes) of research data collections spanning datasets from climate, coasts, oceans, and geophysics through to astronomy, [[bioinformatics]], and the social sciences.<ref name="WangLarge14">{{cite journal |title=Large-Scale Data Collection Metadata Management at the National Computation Infrastructure |journal=Proceedings from the American Geophysical Union, Fall Meeting 2014 |author=Wang, J.; Evans, B.J.K.; Bastrakova, I. et al. |pages=IN14B-07 |year=2014}}</ref> Within these domains, data can be of different types such as gridded, ungridded (i.e., line surveys, point clouds), and raster image types, as well as having diverse coordinate reference projections and resolutions. NCI has been following the Force 11 FAIR data principles to make data findable, accessible, interoperable, and reusable.<ref name="F11FAIR">{{cite web |url=https://www.force11.org/group/fairgroup/fairprinciples |title=The FAIR Data Principles |publisher=Force11 |accessdate=23 August 2017}}</ref> These principles provide guidelines for a research data repository to enable data-intensive science, and enable researchers to answer problems such as how to trust the scientific quality of data and determine if the data is usable by their software platform and tools.
| | ;Chapter 3 Defining LIS Requirements with the LIMSpec |
| | | :[[LIS feature]] |
| To ensure broader reuse of the data and enable transdisciplinary integration across multiple domains, as well as enabling programmatic access, a dataset must be usable and of value to a broad range of users from different communities.<ref name="EvansExtend16">{{cite journal |title=Extending the Common Framework for Earth Observation Data to other Disciplinary Data and Programmatic Access |journal=Proceedings from the American Geophysical Union, Fall General Assembly 2016 |author=Evans, B.J.K.; Wyborn, L.A.; Druken, K.A. et al. |pages=IN22A-05 |year=2016}}</ref> Therefore, a set of standards and "best practices" for ensuring the quality of scientific data products is a critical component in the life cycle of data management. We undertake both QC through compliance with recognized community standards (e.g., checking the header of the files to make sure it is compliant with community convention standard) and QA of data through demonstrated functionality and performance across common platforms, tools, and services (e.g., verifying the data to be functioning with designated software and libraries).
| | :[[Clinical Laboratory Improvement Amendments]] |
| | | :[[Health Insurance Portability and Accountability Act]] |
| The Earth Science Information Partners (ESIP) Information Quality Cluster (IQC) has been established for collecting such standards and best practices and then assisting data producers in their implementation, and users in their taking advantage of them.<ref name="RamapriyanEnsuring17">{{cite journal |title=Ensuring and Improving Information Quality for Earth Science Data and Products |journal=D-Lib Magazine |author=Ramapriyan, H.; Peng, G.; Moroni, D.; Shie, C.-L. |volume=23 |issue=7/8 |year=2017 |doi=10.1045/july2017-ramapriyan}}</ref> ESIP considers four different aspects of [[information]] quality in close relation to different stages of data products in their four-stage life cycle<ref name="RamapriyanEnsuring17" />: (1) define, develop, and validate; (2) produce, access, and deliver; (3) maintain, preserve, and disseminate; and (4) enable use, provide support, and service.
| | ;Chapter 4 Example LIMSpec for the Physician Office Lab |
| | | :[[POL Registration/accession|Registration/Accession]] |
| Science teams or data producers are responsible for managing data quality during the first two stages, while data publishers are responsible for the latter two stages. As NCI is both a digital repository, which manages the storage and distribution of reference data for a range of users, as well as the provider of high-end compute and data analysis platforms, the data quality processes are focused on the latter two stages. A check on the scientific correctness is considered to be part of the first two stages and is not included in the definition of "data quality" that is described in this paper.
| | :[[POL Assays|Assays]] |
| | | :[[POL Data entry|Data Entry]] |
| ==NCI's data quality strategy (DQS)==
| | :[[POL Reporting|Reporting]] |
| NCI developed a DQS to establish a level of assurance, and hence confidence, for our user community and key stakeholders as an integral part of service provision.<ref name="AtkinTotal05">{{cite book |chapter=Chapter 8: Service Specifications, Service Level Agreements and Performance |title=Total Facilities Management |author=Atkin, B.; Brooks, A. |publisher=Wiley |isbn=9781405127905}}</ref> It is also a step on the pathway to meet the technical requirements of a trusted digital repository, such as the CoreTrustSeal certification.<ref name="CTSData">{{cite web |url=https://www.coretrustseal.org/why-certification/requirements/ |title=Data Repositories Requirements |publisher=CoreTrustSeal |accessdate=24 October 2017}}</ref> As meeting these requirements involves the systematic application of agreed policies and procedures, our DQS provides a suite of guidelines, recommendations, and processes for: (1) consistency of data structures suitable for the underlying high-performance data (HPD) platform; (2) QC through compliance with recognized community standards; (3) benchmarking performance using operational test cases; and (4) QA through demonstrated functionality and benchmarking across common platforms, tools, and services.
| | :[[POL Compliance|Compliance]] |
| | | :[[POL Interfacing|Interfacing]] |
| NCI’s DQS was developed iteratively through firstly a review of other approaches for management of data QC and data QA (e.g., Ramapriyan ''et al.''<ref name="RamapriyanEnsuring17"> and Stall<ref name="StallAGU16">{{cite web |url=https://www.scidatacon.org/2016/sessions/100/ |title=AGU's Data Management Maturity Model |work=Auditing of Trustworthy Data Repositories |author=Stall, S.; Downs, R.R.; Kempler, S.J. |publisher=SciDataCon 2016 |date=2016}}</ref>) to establish the DQS methodology and secondly applying this to selected use cases at NCI which captured existing and emerging requirements, particularly the use cases that relate to HPC.
| | :[[POL System|System]] |
| | | :[[POL General|General]] |
| ==References==
| | :[[POL Functions - General]] |
| {{Reflist|colwidth=30em}}
| | ;Chapter 5 LIS Products for the Physician Office Lab |
| | | :[[Vendor:Apex HealthWare, LLC|Apex HealthWare, LLC]] |
| ==Notes==
| | :[[Vendor:CompuGroup Medical AG|CompuGroup Medical AG]] |
| This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added.
| | :[[Vendor:J&S Medical Associates, Inc.|J&S Medical Associates, Inc.]] |
| | :[[Vendor:Orchard Software Corporation|Orchard Software Corporation]] |
| | :[[Schuyler House]] |
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| [[Category:LIMSwiki journal articles (added in 2018)]]
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| [[Category:LIMSwiki journal articles (all)]]
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| [[Category:LIMSwiki journal articles on data quality]]
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| [[Category:LIMSwiki journal articles on informatics]]
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