Clinical Laboratory Informatics

• Clinical laboratory informatics

  • Subdiscipline of clinical informatics which encompasses all of the subject matter of informatics in the general discipline of clinical informatics
  • Specialized field within healthcare informatics that focuses on the management and analysis of laboratory data
  • Use of information technology to improve efficiency, accuracy, quality of laboratory testing and reporting
• Fundamentals of clinical informatics

  • They should be viewed from the more holistic perspective of supporting the underlying collective needs of health care in general and the clinical laboratory specifically to generate, analyze, disseminate, and curate primary data
  • Pathology Informatics involves collecting, examining, reporting, and storing large complex sets of data derived from tests performed in clinical laboratories, anatomic pathology laboratories, or research laboratories to improve patient care and enhance our understanding of disease-related processes
• Homer Warner and Octo Barnett systematically explored the utility of applying computational and analytical methodologies on healthcare data sets and workflow models


  1950
• Database


  • A program (or assembly of programs, recognizing modern distributed software architecture) that allows for the aggregation, storage, curation, retrieval, transformation, and dissemination of primary data, as well as derivatized and extracted forms of this data
  • Serves the purpose of adding a critical layer of provenance to every accumulated data element that is housed within it such that both its source and level of confidence concerning its veracity can be examined and confirmed upon demand
• Database design, implementation, and maintenance


  • DATABASE FUNDAMENTALS
• CRUD


  Create, Read, Update, and Delete - the four basic functions that allow for essentially all required information steward ship operations
• ACID properties of databases

  • Atomicity is perhaps the most important in that it ensures that any intended transaction is either fully executed or not executed at all
  • Atomicity, Consistency, Isolation, Durability
• Database structures

  Tables - fundamentally, most contemporary databases are rendered as relational databases, implying that tabular information is stored in separate and distinct tables, which have both rows and columns
• Database operations


  Select statement - the most encountered operation in the SQL language to accomplish a typical query
• Master keys


  A table that contains master keys for its various rows of tabular data necessarily implies that each row contains elements of unique identity data, with each row distinguished from all other rows in that table by a key variable, which is defined to be unique
• Subordinate keys


  A table that contains subordinate keys necessarily implies that generation of a more complete view of any single table row entry is predicated on using the subordinate key to identify the row in the linked table where the master key of that row matches the subordinate key
• Transformational operations

  Insertion, update, and deletion operations - routine operations carried out on databases that result in modification to table/row contents
• Database insertions


  The intent is to add one or more rows of data to existing tables while at the same time ensuring that the overall database schema's referential integrity is not compromised
• Database updates


  One or more data elements in one or more rows of a given table are replaced by new information
• Database deletions


  One or more data elements from one or more rows in a given table are requested for deletion, with the contents of the deleted records maintained in an external set of auditing tables
• Positive patient and specimen identification and barcoding


  Solutions and technologies that can assist with both positive patient identification and positive specimen identification along every step associated with the preanalytical, analytical, and postanalytical journeys that specimens and primary data take in the hopeful generation of an accurate result
• Laboratory information systems (LIS)


  Stewardship of the LIS is one of the core activities of central interest to pathology informatics
• LIS system selection


  An area that is not without some measure of contemporary controversy given the constricting universe of typically deployed solutions in the setting of a very small number of leading EHR solution providers that are also offering an integrated LIS as an integral module to the overall EHR solution
• Specialized lab information system modules

  • Histocompatibility
  • Flow Cytometry
  • Molecular Diagnostics
  • Cytogenetics
• Histocompatibility


  The modern histocompatibility laboratory exhibits complex workflow that differs in its level of internal documentation and process steps, with a number of stand-alone HLA lab solutions commonly deployed in tandem with a core LIS solution
• Flow cytometry


  The flow cytometry laboratory section is another area of complex and intense workflow, in which specialized data capture and analysis capabilities are required
• Molecular diagnostics


  The molecular diagnostics laboratory is one of the "heavy hitters" in terms of requiring significant pathology informatics expertise and operational support, with complex intrinsic workflow involving many steps, very large data sets, and utilizing extraordinarily sophisticated algorithms for data analysis
• Cytogenetics


  The cytogenetics laboratory, by virtue of the image-intensive subject matter that it generates and then analyzes, requires specialized software for image management and analysis as well as for assistance in assembly of the specialized descriptive language used to communicate genetic alterations in a systematized and consistent manner. Preanalytically, the cytogenetics laboratory shoulders a significant burden for maintaining an active cell culture process
• Artificial intelligence


  Generally discouraged from use in the data sciences fields, with machine learning being the far-preferred term
• Clinician interpreting two common laboratory panels in tandem

  1. Complete blood count

  2. Comprehensive chemistry
• BYOD (bring your own device)


  A central IT strategy for cost savings by which employees are encouraged to purchase their own IT devices (PCs, laptops, and smartphones) and bring them to work for routine work-related activities
• Client-Server Model


  In computing and business applications, the client-server model remains one of the dominant contemporary approaches for deploying solutions
• Data Security Strategy


  Recognizing that health institutions are under increasing scrutiny to implement and maintain best practices for ensuring data security of all classes of protected health information, the implementation of a data security strategy has become an essential element of most IT organizations' overall data stewardship strategy
• DHCP (Dynamic Host Configuration Protocol)


  As a response to the configurational burden of adding new devices to any given network, could utilize an interactive protocol to receive a centrally assigned IP number along with a stipulated lease time, whereupon another or different IP number would be assigned. This protocol is fully autonomous
• DHCP Reservation


  An extension of the DHCP, whereby any device attaching to a network, upon presenting its six-byte MAC Address, will be assigned the same IP number by the DHCP server if it is the case that the MAC ID in question is already registered in that DHCP server's assignment table as having a permanently reserved IP number
• Domain Name System (DNS)


  The DNS layer was developed to allow for a simplified way of assigning human-readable and easily remembered/recognized textual names to each of the IP numbers that constitute unique devices/nodes on the internet
• Firewall


  An integral hardware component of any private network that serves as a physical and topological demarcation between internal intranet traffic and all external internet traffic
• List-Mode Data (Flow Cytometry)


  Flow cytometry data is high-dimensional data by virtue of the multichannel nature of the quantitative indices captured for each individual cell interrogated in a flow cell by the light of a columnated laser beam
• Internet / Intranet


  In any institution's network topology, there is an almost always present demarcation between the internal network (the intranet), where secure business information (and protected health information [PHI], in the case of health care-related institutions, including clinical laboratories) can be exchanged internally, and the remainder of the world (the Internet)
• IP Address


  This is one of the two device address classes (the other being the Media Access Control Address) that any device on a network will possess and with which it will identify itself when interrogated
• Media Access Control Address (MAC Address)


  The MAC address is a unique, six-byte identifier assigned by the device manufacturer to the network interface controller (NIC) of any network-capable device, allowing for physical identification of a specific device by network devices such as routers and switches
• MODEM (MOdulator / DEModulator)


  In telecommunications, the modem is a fundamental hardware device that allows for a serial digital data stream to be converted to the audio format of common carrier telephony networks (telephone lines)
• Network


  This is a general term that refers to the collective assembly of data channel interconnections within an enterprise (which can be extended as a concept to the whole of the Internet), by which devices (e.g. nodes) on the network communicate with all other devices on that same network
• Relational Database


  In the general field of database technology, relational databases are application environments that provide database functionality in the form of normalized information, where atomically distinct data elements are typically not reduplicated within a plurality of tablets
• Router


  In data network architecture, the router is a fundamental building block of both intranets and the Internet proper