Difference between revisions of "User:Shawndouglas/sandbox/sublevel12"

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==Sandbox begins below==
==Sandbox begins below==
<div class="nonumtoc">__TOC__</div>
<div class="nonumtoc">__TOC__</div>
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[[File:Daily Operations in the Microbiology Lab Aboard USNS Comfort (49826560406).jpg|right|450px]]
'''Title''': ''What are the potential implications of the FAIR data principles to laboratory informatics applications?''
'''Title''': ''What are the key elements of a LIMS for medical microbiology?''


'''Author for citation''': Shawn E. Douglas
'''Author for citation''': Shawn E. Douglas
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'''License for content''': [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International]
'''License for content''': [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International]


'''Publication date''': April 2024
'''Publication date''': May 2024


==Introduction==
==Introduction==


This brief topical article will examine


This brief topical article will examine the informatics needs of the medical microbiology lab, including a base set of [[laboratory information management system]] (LIMS) or [[laboratory information system]] (LIS) functionality (i.e., system requirements) that is critical to fulfilling the information management and workflow requirements of this type of lab. (Going forward, for simplicity, this article will discuss these requirements largely in the scope of a LIMS; however, note that an LIS is equally viable here.) Additional unique requirements will also be briefly discussed.
==Blah blah blah==
* LIMS and FAIR: [[Journal:A roadmap for LIMS at NIST Material Measurement Laboratory]]  
* ELNs and FAIR: [[Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation]]
* Biomedical software and FAIR: https://www.nature.com/articles/s41597-023-02463-x
* Making software workflows FAIR: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538699/
* AWS and FAIR for healthcare and life sciences: https://aws.amazon.com/blogs/industries/implement-fair-scientific-data-principles-when-building-hcls-data-lakes/
* APIs and FAIR data: https://www.labguru.com/blog/fair-data-principles-and-apis
* Bioinformatics LIMS and FAIR: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8425304/
* Labbit: https://labbit.com/fair-data-lims


'''Note''': Any citation leading to a software vendor's site is not to be considered a recommendation for that vendor. The citation should however still stand as a representational example of what vendors are implementing in their systems.
* https://riojournal.com/article/96075/ Importance of metadata for FAIR data objects
* Deep talk about metadata: [[Journal:Shared metadata for data-centric materials science]]
* More metadata, for findability: "While descriptive metadata may not be available, support for generalized CRUD operations requires essential structural and administrative metadata to be captured, stored, and made available for requestors. Metadata capture must be highly automated and reliable, both in terms of technical reliability and ensured metadata quality." [[Journal:Making data and workflows findable for machines]]
* More metadat, for reusability: "make recommendations for assigning identifiers and metadata that supports sample tracking, integration, and reuse. Our goal is to provide a practical approach to sample management, geared towards ecosystem scientists who contribute and reuse sample data." [[Journal:Sample identifiers and metadata to support data management and reuse in multidisciplinary ecosystem sciences]]


==Base LIMS requirements for medical microbiology labs==
* "The principles should be considered during development of informatics systems to further promote data discovery and reuse. In Table 1, we have correlated the various BRICS functional components to the FAIR principles to illustrate the extent to which each of the components contributes towards the principles." [[Journal:Development of an informatics system for accelerating biomedical research]]
Like other labs, medical microbiology labs increasingly require an informatics solution that meets all or most of its workflow requirements. These requirements are often driven by standardized test methods, in turn driven by regulations and accreditation requirements. This requires a pre-configured and future-configurable solution that enables medical microbiology personnel to quickly select and use standardized test methods and forms, and make the changes they need to those methods and forms if those changes make sense within the overall data structure of the LIMS.


What follows is a list of fundamental LIMS functionality important to most any medical microbiology laboratory, with a majority of that functionality found in many vendor software solutions.<ref name="RhoadsClin14">{{Cite journal |last=Rhoads |first=Daniel D. |last2=Sintchenko |first2=Vitali |last3=Rauch |first3=Carol A. |last4=Pantanowitz |first4=Liron |date=2014-10 |title=Clinical Microbiology Informatics |url=https://journals.asm.org/doi/10.1128/CMR.00049-14 |journal=Clinical Microbiology Reviews |language=en |volume=27 |issue=4 |pages=1025–1047 |doi=10.1128/CMR.00049-14 |issn=0893-8512 |pmc=PMC4187636 |pmid=25278581}}</ref>
Restricted or personal information while still being FAIR
* [[Journal:FAIR Health Informatics: A health informatics framework for verifiable and explainable data analysis]]
* [[Journal:Restricted data management: The current practice and the future]]


'''Test, sample, and result management'''
* Linking databases of data that haven't seen proper "FAIR-ification" and metadata handling won't be as useful.
 
* Further discussion on data quality in the scope of FAIR: [[Journal:Towards a contextual approach to data quality]]
*Sample log-in and management, with support for unique IDs
*Sample batching
*[[Barcode]] and RFID support
*End-to-end sample and inventory tracking
*Pre-defined and configurable industry-specific test and method management for a variety of physical, mechanical, and chemical analyses
*Pre-defined and configurable industry-specific workflows
*Configurable screens and data fields
*Specification management
*Test, sampling, instrument, etc. scheduling and assignment
*Test requesting
*Data import, export, and archiving
*Robust query tools
*Analytical tools, including [[data visualization]], statistical analysis, and [[data mining]] tools
*Document and image management
*Project management
*Facility and sampling site management
*Storage management and monitoring
 
'''Quality, security, and compliance'''
 
*[[Quality assurance]] / [[quality control]] mechanisms
*Mechanisms for compliance with ISO/IEC 17025, ISO 9000, ASTM, A2LA, ANAB, and other requirements
*Result, method, protocol, batch, and material validation, review, and release
*Data validation
*Trend and control charting for statistical analysis and measurement of uncertainty
*User qualification, performance, and training management
*[[Audit trail]]s and [[chain of custody]] support
*Configurable and granular role-based security
*Configurable system access and use (i.e., authentication requirements, account usage rules, account locking, etc.)
*[[Electronic signature]] support
*Data [[encryption]] and secure communication protocols
*Archiving and [[Data retention|retention]] of data and information
*Configurable data [[backup]]s
*Status updates and alerts
*Incident and non-conformance notification, tracking, and management
 
'''Operations management and reporting'''
 
*Configurable dashboards for monitoring, by material, process, facility, etc.
*Customizable rich-text reporting, with multiple supported output formats
*Custom and industry-specific reporting, including certificates of analysis (CoAs)
*Email integration
*Bi-directional instrument interfacing and data management
*Third-party software interfacing (e.g., [[scientific data management system]] [SDMS], other databases)
*Data import, export, and archiving
*Instrument calibration and maintenance tracking
*Inventory and material management
*Supplier/vendor/customer management
*Customer portal
 
==Specialty LIMS requirements==
Some laboratory informatics software vendors are addressing medical microbiology laboratories' needs beyond the features of a basic all-purpose LIMS. A standard LIMS tailored for materials testing may already contribute to some of these wider organizational functions, as well as more advanced laboratory workflow requirements, but many may not, or may vary in what additional functionality they provide. In that regard, a materials testing LIMS vendor may also include specialized functionality that assists these labs. This includes the provision of:
 
*'''Derivative asset linking and tracking''': Unlike many other labs in the biomedical sciences, a medical microbiology lab will end up creating multiple derivative assets from a single accessioned specimen. For example, a specimen suspected of polymicrobial infection may require derivative specimens representing "aerobic bacteria, anaerobic bacteria, mycobacteria, and/or fungi, and all of these need to be linked to the original accession number."<ref name="RhoadsClin14" /> As Rhoads ''et al.'' note, "properly handling the electronic information associated with a sample, such as tracking its derivatives, modifying descriptions of its derivatives, and linking its derivatives with their accession number, is a unique and essential aspect of the microbiology LIS."<ref name="RhoadsClin14" />


==Conclusion==
==Conclusion==
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{{Reflist|colwidth=30em}}


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Latest revision as of 00:05, 30 April 2024

This is sublevel12 of my sandbox, where I play with features and test MediaWiki code. If you wish to leave a comment for me, please see my discussion page instead.

Sandbox begins below

[[File:|right|380px]] Title: What are the potential implications of the FAIR data principles to laboratory informatics applications?

Author for citation: Shawn E. Douglas

License for content: Creative Commons Attribution-ShareAlike 4.0 International

Publication date: May 2024

Introduction

This brief topical article will examine

Blah blah blah

Restricted or personal information while still being FAIR

Conclusion

References


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