Lab Notebook (ELN) / scientific Informatics Glossary and Acronyms
By Lab-Ally LLC
Lab Notebook jargon and abbreviations made simple.
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A list used to control access to and from a router or server. In the context of an Electronic Lab Notebook this can refer to the global or specific-data-related access roles of different users. In other words, this list controls who can see what and who is allowed to review, annotate or make changes to specific data or records.
An acronym for “attributable, legible, contemporaneous, original and accurate.” ALCOA is applicable in many contexts pertaining to good lab practices. This article discusses documentation practices for clinical research: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121265/
This is ALCOA that stresses the importance of endurability, availability, consistency and completeness of attributes.
An alternate name, usually a file directed to another file. Also called a shortcut. CERF uses the term LINKS to refer to icons that allow users to access the same file from different locations.
A programming language exclusive to Apple products that allows for tasks to be called within applications. AppleScripts may be used to create events that transmits data directly into CERF or that can perform actions on data exported from CERF.
A program or group of programs designed to carry out specific tasks.
Application Programming Interface (API)
A set of guidelines, tools and standards that allows other programmers to build or alter an application.
CERF user role with he same privileges as Digital Signer plus the ability to add annotations to Resources. (Annotators may also copy and paste as a relation).
A collection of records that are no longer active, but are being maintained in a locked state according to the purposes of the organization (e.g., a backup for long-term storage or regulations requiring record retention).
American Standard Code for Information Interchange.A common, standard 7-bit binary character system that represents each letter, number, and special character in a file.
Documented proof of any action that creates, updates, or deletes a record, together with un-editable information on who did the work, when it was performed, and what changes were made throughout the steps of a workflow. An electronic audit trail includes versioning history, tracking changes made to electronic media by author and timestamp. Audit trails are an important part of 21CFR11 may be used to track decision-making and invention thought processes and are central to proving ownership in Intellectual Property pursuits.
Authentication is the act of validating the identity of a person, organization, or system. It is most commonly applied to the process of logging on to a secure system using a username and password combination.
Specifying the access rights of users, organizations, or systems to controlled resources and processes.
The “invisible” part of systems and programs that support the part that the user sees, which is called the “front end”.
Upgraded systems that are still able to function correctly with its previous version.
The range of frequencies in a band used for transmitting signals. The bandwidth is associated with how much information can be carried over a network.
Integrating computer science and information systems with biological data to analyze and understand biological processes.
Bits Per Second. Measures the rate of data transmission.
Software applications that are accessed using web browsers. These are also sometimes called “web-based” but this term is little less well defined and is sometimes used to describe any system that communicates over the internet using HTTP, even if it does not use a browser.
Corrective And Preventative Action. These are steps to reduce problematic and undesirable occurrences. The key focus is on identifying the problem’s origin and associated risks.
Clinical Data Management System. Used here, CDMS refer to electronic data capturing systems that capture, catalog, code and archive data directly from laboratory instruments during a clinical trial in the life sciences.
After an item in CERF has been checked out for editing, it can be checked back into the system. At Check In, the previous version of the item is archived and a new version is saved. This is a key feature of version tracking.
Opens a copy of the item on your computer for editing. Only one user may check out a record at a time.
A software program that accesses services from a server.
Typically software that is accessed using a dedicated application on the user’s machine, rather than from a web browser.
A system where data is held on a central machine that can be accessed by any number of clients located elsewhere. The client may be a web browser or a dedicated client application. Good for facilitating collaboration and central management of mission critical shared data.
Software that runs from or on network servers typically outside of an organization’s internal network.
Adherence to specified government, state, agency or organizational rules or standards. For recording scientific data on a computer system in such a way that it will be admissible as evidence in certain proceedings, the most relevant rule set is known as 21CFR11.
Also called the right-click menu. The right click menu allows certain actions to be performed on CERF resources. Only appropriate actions are shown for the object or resource being clicked. One of the key elements of the CERF interface is the fact that this menu is also adjusted based on the assigned role of the user. For example, if a user does not have edit privileges for a given resource, then the edit command does not appear as an option.
A document that is access-restricted, maintained and updated. Controlled documents are formally approved and their distribution, edit history and usage are traceable. The history of views, approvals, and usage by assigned personnel is also tracked. A common example of a controlled document is a Standard Operating Procedure document (SOP). Distribution and management of SOPs and other controlled documents is often required for certain organizations to be fully compliant with applicable regulations.
Set of regulations used to ensure proper compliance and performance standards are being met. Control strategies are applicable to multiple aspects of studies, equipment, supplies, protocols, and more.
A carefully selected list of words and phrases which are used to tag units of information (document or work) so that they may be more easily retrieved by a search. Vocabularies may be flat (single level) pick lists, or may be hierarchically organized.
Software that can operate on multiple computer operating systems (i.e. Windows, MacOS, Linux).
An organized collection of data that interacts with a database management system to quickly access and analyze that data. In the case of CERF, Most data exists as files in a secure filestore, but metadata and information about the file’s history resides on an SQL database that can be the customer’s choice of MySQl, MS SQL or Oracle.
The levels of quality, accuracy, reliability, completeness and consistency of data, as well as how thoroughly the data was collected and documented.
Data Life Cycle
The complete process of collecting, processing, reviewing, analyzing, utilizing, storing and disposing of data. Regulations should be in place to ensure the integrity of the data associated risks, and consequences of potential outcomes arne handled according to organization standards.
The means by which a company or laboratory controls and regulate the information obtained through research projects. CERF ELN is an excellent tool to organize and safeguard your laboratory data.
CERF user role with the same privileges as Guest plus the ability to Cosign a Resource (may not initiate signing because this user is not permitted to be a Resource contributor). Cosigning requires that the Resource be accessible by the initial signer and cosigner and that the cosigner be a member of the initial signer’s Signature Workgroup.
A way to assert the identity of the person who created or witnessed a digital document. Used to demonstrate the authenticity of a piece of digital data; a secure equivalent of a person’s handwritten signature. “Strong” digital signatures can be used to detect forgery or tampering and to prove origin in legal situations. CERF uses a strong mathematical method based on PKI hashing that enforces non-repudiation and cannot be separated from the data it authenticates.
The act of revealing to others information about your research. Disclosure events can affect patent rights and should be diligently recorded in CERF as part of your official record.
DMS (Documentation Management System)
A computer system used to control documents during their lifecycle. The system is designed to maintain data elements about each document concerning authorship, creation, review, revision, version history, utilization, and retention. Also variously called Electronic or Enterprise Document Management System (EDMS), Electronic Content Management System (CMS or ECMS) or Research Document Management System (DMS or RDMS).
In CERF, “Domains” are a way to subdivide your user population so that not all users necessarily need to see every template and every resource type or controlled vocabulary in the system. For example, there may be no need for your legal team to see the templates used for chemical synthesis every time they make a new notebook page, although they may need to see some standardized “invention disclosure” page template that the chemists DON’T need or want to see.
Drag and Drop
Selecting a digital object by “grabbing” (click-and-hold with a computer mouse cursor) and dragging it to a different location or onto another digital object. CERF supports many drag-and-drop actions, including multiple files at once, as this is a key element of CERF’s interface.
Dynamic Record Format
Records stored in a way that allows the user to interact with their data. CERF provides a secure, easy-to-use dynamic record format.
Electronic Data Capture or eData Capture. EDC (sometimes eData Capture) refers to a computerized system (often web-based) designed for the collection of clinical data in electronic format used frequently in life sciences.
Electronic document (or Data) Management System (or Solution, or Software). Generic term for a document management system that typically would include versioning, searching and check out / check in capabilities. CERF includes all the features of a 21CFR11 compliant EDMS.
Any combination of information represented in a digital form (e.g., text, graphics, data) that is created, modified, maintained, archived, retrieved, or distributed by a computer system.
Electronic Records Management
The control of the creation, maintenance, use, and disposal of electronic records.
Electronic Lab Manager (also called ELMS, Electronic Lab Management System). Similar to an ELN but more likely to be used in a commercial lab than in discovery science as it is more concerned with project, equipment and asset management than real-time activity and thought capture.
ELN (Electronic Laboratory Notebook)
ELN (Electronic Lab Notebook) – Electronic Lab Notebooks are software programs intended to replace paper notebooks used in scientific research. ELNs modernize, simplify, and strengthen note taking, recordkeeping, and Intellectual Property protection. Also called electronic notebook, e-notebook, lab management software.
Email to CERF
A feature in CERF that allows users to send email and attachments to their CERF account. This feature is especially useful for sending items to CERF from mobile devices, or for capturing important emails into your organization’s compliant record. CERF knows which user the email should be associated with by matching the email address of the sender to that of the corresponding CERF user.
A method of data security involving encoding data that man only be deciphered with a designated key or password.
A commercial business level Content Management System (or Document Management System, EDMS) usually hosted onsite on local servers. (See also DMS)
In CERF, an entry is a distinct item added to a Notebook Page capturing information related to the overall page or experiment. Entries can be added as links (placeholders) to existing files (such as PDFs of references, Word docs, Excel spreadsheets, etc.) or entered directly as text, tables, images, audio, drawings, and more.
Electronic Resource (or Records) Management System (or Software). Yet another name for ELN software that is sometimes used to emphasize the fact that research organizations may need to track data, documents and assets and project management tasks in a 21CFR11 compliant way, even if they are not actually performing any discovery research. The “Records” variant tends to be more commonly used in healthcare environments where HIPAA and other compliance issues may be as important or more important than 21CFR11.
Electronic Research Notebook. Another name for an Lab Notebook software that is sometimes used to emphasize the idea that research does not necessarily take place in a laboratory.
File Cabinet Editor
CERF user role that has the same privileges as a metadata editor and can also edit a Resource, version a Resource, add a Resource to a File Cabinet (required to initiate signing), and remove a Resource. A File Cabinet Editor can also copy and paste as a new resource or version and can save manual sort order. In the context of a Notebook, this role has the same privileges as Annotator.
File Cabinet Manager
CERF user role that has the same privileges as a File Cabinet Editor and can also create File Cabinets, delete a Resource (if policy permits), archive, and set resource access. A File Cabinet Manager can also save the Sort order for a Folder. In the context of a Notebook, this role is the same as Annotator.
The portion of a filename that defines the file type. CERF is able to ingest data of all file types.
A CERF resource (file, entry, page, etc.) that can no longer be edited. A finalized record is stored in a read-only state and may be locked according to business policy. Resources that are submitted initially to CERF as Uneditable are in a Final state by default.
If permitted by business policy, a CERF flexible notebook allows the user to move (cut/paste) resources within the notebook, to save sort order, delete page content, and empty Notebooks or Sections.
File Transfer Protocol. This is a standard protocol for transferring files between a client and server over a computer network.
General Data Protection Regulation. Established to improve data protection and regulation within the European Union.
Good Data and Record Management Practices. Guidelines established by the WHO regarding the collection, quality, security and accuracy of data and records.
Good Laboratory Practice. Guidelines geared towards laboratories. CERF was designed to promote a critical good laboratory practice- archiving and protecting data.
Good Manufacturing Practice. Established systems for regulating quality of pharmaceutical products.
GxP (Good Practices)
The general term for Good Practice guidelines. CERF can be an important tool for your organization to make sure that you can follow and document appropriate GxP guidelines. Subsets of guidelines include GCP (Good Clinical Practices), GLP (Good Laboratory Practices), and GMP (Good Management Practices). A full list is available at: http://en.wikipedia.org/wiki/GxP#List_of_GxPs.
CERF user role with same privileges as Resource Identifier plus the privilege of viewing Resources as read-only copies. The right-click menu for a user with the role of Guest includes View Resource, View Resource Info, and Copy (but there are no Paste Options).
Graphic User Interface. Pronounced /’gu:i/ (“gooey”) is a program interface that uses your computer’s graphics capabilities to let users interact with electronic devices through icons, buttons, and visual indicators as opposed to text-based interfaces, typed command labels or text navigation. This allows users to accomplish complex tasks without using or needing to learn complex command languages.
Health Insurance Portability and Accountability Act of 1996. Important rule set that governs how electronic patient information can be stored in an IT environment. CERF can be used for HIPAA information provided that the host on which it is stored is created, configured, maintained and validated as meeting all HIPAA guidelines. Lab-Ally’s relationship with http://www.validatedcloud.com allows us to deploy HIPAA ready systems.
A graphic image or symbol, visible on the screen, that performs an action or opens a menu when selected by the user.
The study of computer information systems where processed data is stored and accessed.
The process of converting a file in a CERF notebook page into a preview that can be seen inline, without opening it as an attachment. An example is the conversion of Microsoft office documents into .PDF previews. This conversion is useful because it sidesteps the question of whether or not a valid version of the appropriate external viewer application is available on the user’s local machine. Inline rendering helps scientists see the content of most common files regardless of the locally available software.
The ability to view non-standard Notebook Entries directly within the Notebook Page, rather than having to open in an external window or program. CERF is unique in it’s ability to render more file types inline than other ELNs, including Microsoft Word and Excel documents.
IP (Intellectual Property)
A concept that has commercial value, which has a unique set of exclusive rights under law.
IRB (Institutional Review Board)
Institutional (or Internal) Review Board is tasked with approving, monitoring, and reviewing biomedical and behavioral research involving humans with the aim to protect the rights and welfare of the research subjects. CERF SOP management features can researchers meet and document compliance with the requirements of the IRB and any associated SOPs.
A boundary across which two separate systems interact.
ISO (International Organization for Standardization)
Responsible for quality and management standards pertaining to laboratory processes and production.
IUCAC (Institutional Animal Care and Use Committee)
An IUCAC has a similar role to the IRB except that it is concerned only with studies using animals. CERF SOP management features can help researchers meet and document compliance with the requirements of your IUCAC and any associated SOPs.
A primary record of research used to document hypotheses, experiments, analysis and interpretation. Lab notebooks are used to organize and record information and also serve a primary role in proving intellectual property under federal guidelines by documenting inventions and their reduction to practice. The maintenance of accurate Lab Notebooks is a proud tradition in science.
LIMS (Laboratory Information Management System)
Another type of electronic laboratory management software, largely used in managing samples, instruments and workflow automation. ELNs and LIMS are increasingly overlapping in functionality as scientific laboratories become more modern and look for solutions from single sources.
LIS (Laboratory Information System)
The distinction between a LIS and a LIMS is pretty arbitrary and the functional differences between them have become blurred. ELNs and LIS are increasingly overlapping in functionality as scientific laboratories become more modern and look for solutions from single sources.
Especially applicable to SOP and controlled document compliance, and for recording maintenance to precision instruments involved with regulated research. All of the functions of a paper logbook can be performed with significantly increased efficiency and accuracy using CERF SOP management.
LRB (Laboratory Record Book)
Another name for a Lab Notebook, but in some cases a LRB may be a more formal, collaborative tool used less to record speculative hypotheses and more to maintain detailed records of the purpose, background, materials, equipment, samples, method, actions taken, results, and outcome of a scientific experiment.
Additional information, such as tags, keywords, descriptions, creation date and author, about a digital resource used to further describe the resource, its content, and its relationship to other resources. CERF includes a rich semantic metadata system and semantic search engine that lets you quickly pinpoint the data you need from within a potential vast body of data your organization has accumulated over many years. This will save your organization time and money.
CERF user role with the same privileges as Annotator plus the ability to edit metadata. Note that metadata editors can put a resource under version control and can make it final. In the context of a Notebook, this role is the same as Annotator.
A file which contains the metadata describing the contents of another file.
A software program designed to function on multiple operating systems.
A claim guaranteeing that the source of the documentation cannot later deny that he or she was the author.
A collection of all research records created or used in an experiment or unified set of experiments. A Notebook may be shared with others in a workgroup according to their access roles. A Notebook can be organized into Sections as well as holding individual Pages and inserted Files.
CERF user role that has the same privileges as File Cabinet Manager, plus the ability to create Notebooks.
In the context of File Cabinets, a Notebook Editor has the same privileges as a File Cabinet Editor. In the context of Notebooks, a Notebook Editor can add resources and edit them, save manual sort order in Flexible Notebooks, and rename Notebooks.
CERF notifications are like a secure internal email between CERF users. A notification can be sent to one or more people and can have comments and a link back to the source file. CERF notifications can be used to let users know that a file exists and where, or that some action has occurred that may need attention (ready for next steps, needs signed, needs reviewed, etc.).
In the context of scientific research, an ontology defines a set of keywords, metadata or concepts with which to organize a domain of knowledge. The vocabulary pool typically includes synonyms and related words, taxonomies, classes, attributes (properties), and relationships. In this context (as opposed to its use in Computer Science), ontologies are closer in structure to spoken language than computer languages used to create databases. For this reason, these ontologies are called “semantic,” whereas computer ontologies are called “logical.” Semantic Ontologies are used extensively in online search functions (Semantic Web) to help people find results that are related to what they mean to find. Ontologies are needed in research to find and identify related resources: for example, there are almost 30 different terms for one Drosophila gene (1). Ontology is closely related to terms like Shared Vocabulary and Controlled Vocabulary.
OOB / OOTB
Out-of-the-box. OOB / OOTB or Out of Box also seen as OTS (Off-the-Shelf) is a product or feature thereof that works immediately after installation without modification or further configuration.
Software and/or the code behind it that is distributed free of charge and made publicly available. Open Source Software may be free, but it is often subject to special licensing agreements that specify distribution methods and usage guidelines.
A CERF container for one or more entries related to an experiment (introduction, materials, actions, etc.) that mimics the traditional paper page in a laboratory notebook. There is no limit to page length. Pages are created in Notebooks and can be stand-alone or organized into Sections and subsections. Pages typically represent some defined unit of work such as a single day or a single shift. Currently, pages are loaded into the CERF page viewer one at a time.
A set of rights granted to an inventor for a period of time, in exchange for a public disclosure of the invention.
An ISO standard format for archiving information.
PI (Principle Investigator)
– The “head scientist” of a laboratory or collaborative study.
An extension that adds features to a software application.
Objective standards to access the quality, performance, functions, and protocols or an organization and its data.
The qualitative method investigates the why and how of decision making, not just what, where, when. Data tends to be in the form of interview transcripts, video segments, and descriptions of scenarios and events. CERF handles this type of data well because its semantic metadata technologies can be used to socially construct and ascribe or code rich meaning onto free-form text.
Quality Risk Management
A standard set of steps to investigate quality risks during a product’s life cycle.
RAID (Redundant Array of Independent Disks
A collection of hard drives used together to keep all data as multiple copies, protecting the data from a drive failure, or used to increase performance, or both. RAIDS may be configured in a variety of ways, and may include almost any number of drives. RAID arrays are recommended for housing the file store (raw data) held inside a CERF server.
Resource Description Framework. A hierarchic metadata management technology used widely in the industry and the basis for CERF’s semantic metadata capabilities.
A designated location for the management and storage of data. CERF acts as a repository for laboratory projects.
Files of all types that have been uploaded into CERF. In addition, File Cabinets, Folders, Notebooks, Sections, Pages, Resource Pages, and Entries are also CERF Resources.
Able to see the title of Resources in a CERF File Cabinet, Search Results, or in the Version History list. May not view contents of a Resource. There is no right-click menu, and this user cannot create File Cabinets, set access level on Resources, submit Resources, export Resources, edit, or sign Resources.
RFI (Request for Information)
An early stage document issued by the customer to suppliers requesting technical details about the product. There is no strong expectation that an RFI will actually lead to deployment of a selected product.
RFP (Request for Proposal)
A document issued by the customer to suppliers requesting technical, pricing and deployment details about the product. Vendors assume that an RFP will actually lead to deployment of the selected product.
A Rigid Notebook does not allow resources to be moved (cut/pasted) within the Notebook, sort order cannot be saved, and nothing can be deleted. This is often required under stringent compliance guidelines.
ROI (Return on Investment)
In the context of an ELN project, this is a measure of the increased productivity and financial gain and / or savings realized by your lab as a result of deploying CERF data management software.
Software that is hosted online using cloud-computing techniques.
SDMS or Scientific Data (or Document) Management System.
SDMS is a generic term that may be used to describe either a standalone scientific document management software system (see also EDMS), or a system that captures, catalogs and archives data, in some cases directly from laboratory instruments as unstructured (heterogeneous) data. An SDMS may also be used to facilitate the capture and visualization of data or data streams and / or the conversion of these streams into files for storage within an ELN or LIMS, or similar system.
SDIMS or Structured Data Information Management System.
The CERF SDIMS module consists of sets of pre-configured forms also called “cards” that can be used to register and manage multiple instances of some defined resource such as a sample or type of experiment.
A way to organize contents within a CERF Notebook much like Folders do within File Cabinets. Sections may contain other sub-sections and Notebook Pages.
Software tools that encode the meaning of objects separately from the application code. Designed to imbue data with hierarchic, categorical meaning that mimics human understanding and makes it easier for computers to locate information intelligently and leverage relationships between objects and concepts.
A designated set of cosigners having specific signing roles. A Signature Workflow is selected for each File Cabinet and Notebook at the time it is created.
SOP (Standard Operating Procedure)
A document that describes a common process at your organization. SOPs may be informal or may be formal controlled documents that must be read and approved by authorized users before they can be used in an experiment.
SSL (Secure Sockets Layer)
A standard protocol used for transmitting private data. SSL uses a cryptographic system to encrypt data “in flight,” making it difficult for unauthorized parties to intercept and read it. CERF is compatible with SSL and SSL (or some other secure connection) is recommended whenever the CERF user and server are not located within the same secure network.
Static Record Format
Rigid record formats that only permit a user to have minimal interaction with the data.
A type of metadata. Tags are annotations that can be quickly added to CERF notebook pages and other resources to make them easier to locate and identify. By using tags in conjunction with saved searches, dynamically updated bundles of related resources may be identified.
A pre-arranged set of placeholder entries or other documents that can be re-used each time an experiment is performed in order to minimize repetitive tasks and ensure all of the necessary information is collected.
Thin Client refers to a specific type of web-based program that only requires the user to have an ordinary web browser to use it.
Also referred to as the java client, desktop client or desktop app). Usually refers to an application that runs independent of a web browser. CERF currently supports desktop clients for Mac OS and Windows.
The date and time that a resource was created or edited. In CERF, the time stamp resides in a database and points indelibly at an associated resource held in the secure file system.
The part of a computer system with which the user interacts.
The formal process of using a detailed step-by-step analysis to make sure that a specific system, lab, or process meets (complies with) all of the rules and requirements of a specified rule set such as 21CFR11. This process can generally only occur in-situ because it usually includes training, operational, procedural and enforcement portions that can only be met by the entire system as a whole. Technically, software like CERF is “21CFR11 ready” but cannot be fully 21CFR11 compliant until it is deployed and validated as such in a specific organizational setting by a qualified third party. Lab-Ally has partners who can perform this validation process for you. Full validation of entire lab can be labor intensive and expensive. Once completed, it may not be easy to make even small changes to your procedures without triggering the need to re-validate.
A version is a new instance of an edited file or entry in CERF. The previous instance is retained and the new version has the new date and timestamp information to comply with audit trails and electronic record guidelines. Resources in CERF may be “final” meaning that new versions cannot be created, “versionable” meaning that the current version can be replaced with a new version, or “version controlled” meaning that a complete version history can be browsed, and older versions can be examined and are available for re-editing or re-deployment elsewhere in CERF.
A recording of spoken information stored in CERF, which includes a built in recording tool for capturing Voice Notes as new entries. Users can also email voice notes to CERF from a suitably equipped mobile device.
VPN (Virtual Private Network)
A way to create a secure wide area network (WAN) that may span a large geographic area. VPNs are used to provide site-to-site connections to branch offices and to allow mobile users to dial up their company LANs. CERF is compatible with VPN and this is the preferred method used by most CERF users to access their CERF server securely from outside their organization’s network.
The sequential processes work goes through until a project is complete. CERF is key for tracking every part of a workflow to ensure that data smoothly transitions to the next step.
A designated group created for collaborative purposes. In CERF, workgroups are used to control access to data. All resources in CERF are owned not by individuals but by workgroups. A workgroup CAN correspond to a single individual, but workgroups can also contain any number of users, each with specific roles within that workgroup.