A
Access List
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.
CERF Crossreference annotation ID: access-list
Accession Number
A unique identifier assigned to a sample, specimen, record, or database entry when it is registered into a tracked system. Accession numbers are heavily used in biobanks, clinical labs, sequence databases (e.g., GenBank, UniProt), and the Protein Data Bank, and are often the value supplied to a CERF Crossreference to link a CERF record to an external database entry.
CERF Crossreference annotation ID: accession-number
ALCOA
An acronym for "attributable, legible, contemporaneous, original and accurate." ALCOA is applicable in many contexts pertaining to good lab practices and is referenced in 21 CFR Part 11, GLP, and GCP guidance.
CERF Crossreference annotation ID: alcoa
ALCOA-plus
An extension of ALCOA that adds the principles of completeness, consistency, enduringness, and availability — collectively known as ALCOA+. Together the nine principles describe the essential attributes that all regulated records, paper or electronic, must possess.
CERF Crossreference annotation ID: alcoa-plus
Alias
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.
CERF Crossreference annotation ID: alias
Aliquot
A measured sub-portion of a larger sample that is taken for analysis, testing, or storage. Aliquots are tracked with their own identifiers in laboratory information management systems and are commonly registered in CERF as Tissue Sample or Sample resources linked to their parent specimen record.
CERF Crossreference annotation ID: aliquot
Anonymization
The process of removing personally identifiable information from records so that the subject of the data can no longer be identified, either directly or indirectly. In clinical and biomedical research, anonymization is often a prerequisite for sharing data outside the originating institution. Distinct from de-identification, which is typically reversible.
CERF Crossreference annotation ID: anonymization
Annotator
CERF user role with the same privileges as Digital Signer plus the ability to add annotations to Resources. (Annotators may also copy and paste as a relation.)
CERF Crossreference annotation ID: annotator
AppleScript
A programming language exclusive to Apple products that allows for tasks to be called within applications. AppleScripts may be used to create events that transmit data directly into CERF or that can perform actions on data exported from CERF.
CERF Crossreference annotation ID: apple-script
Application
A program or group of programs designed to carry out specific tasks.
CERF Crossreference annotation ID: application
Application Programming Interface (API)
A set of guidelines, tools and standards that allows other programmers to build or alter an application.
CERF Crossreference annotation ID: application-programming-interface
API Key
A credential, typically a long random string, used to authenticate a client application when calling an API. API keys are used in place of usernames and passwords for machine-to-machine integration. They must be protected with the same rigor as a password — exposed API keys can grant attackers full access to the system the key was issued for.
CERF Crossreference annotation ID: api-key
Archive
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 back-up for long-term storage or regulations requiring record retention).
CERF Crossreference annotation ID: archive
ASCII
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.
CERF Crossreference annotation ID: ascii
Asset Management
The systematic tracking of an organization's equipment, instruments, software licenses, and other valuable items, including their condition, location, maintenance history, and calibration status. In a regulated lab, asset management overlaps with instrument qualification records, which often need to be referenceable from experimental data.
CERF Crossreference annotation ID: asset-management
Audit Trail
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 21 CFR 11, may be used to track decision-making and invention thought processes, and are central to proving ownership in Intellectual Property pursuits.
CERF Crossreference annotation ID: audit-trail
Authentication
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.
CERF Crossreference annotation ID: authentication
Authorization
Specifying the access rights of users, organizations, or systems to controlled resources and processes.
CERF Crossreference annotation ID: authorization
B
Backend
The "invisible" part of systems and programs that support the part that the user sees, which is called the "front end".
CERF Crossreference annotation ID: backend
Backup
A copy of data made for the purpose of recovery in the event of accidental loss, corruption, or destruction of the primary data. Robust backup policies — including off-site copies and tested restore procedures — are a prerequisite for any compliant electronic record system. Backups themselves must be protected with the same access controls as the primary system.
CERF Crossreference annotation ID: backup
Bandwidth
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.
CERF Crossreference annotation ID: bandwidth
Batch Record
A complete record documenting the manufacturing history of a single batch of a regulated product, including raw materials, equipment used, in-process testing, deviations, and personnel involved. Required by GMP regulations (21 CFR Part 211). Increasingly, batch records are managed electronically in MES or EBR systems and may be cross-referenced from associated R&D records held in an ELN.
CERF Crossreference annotation ID: batch-record
Biobank
A facility that collects, processes, stores, and distributes biological specimens for research. Biobanks maintain large inventories of tissue samples, blood products, DNA, and derived materials with associated clinical and demographic metadata, and serve as a critical infrastructure for translational medicine.
CERF Crossreference annotation ID: biobank
Bioinformatics
Integrating computer science and information systems with biological data to analyze and understand biological processes.
CERF Crossreference annotation ID: bioinformatics
Biometrics
Authentication based on a unique physical characteristic of the individual, such as a fingerprint, iris scan, or facial geometry. 21 CFR Part 11 specifically distinguishes biometric electronic signatures from those based on identification codes and passwords, with separate requirements for each.
CERF Crossreference annotation ID: biometrics
BLOB (Binary Large Object)
A data type used by relational databases to store arbitrary binary content — images, documents, spreadsheets — directly inside a database row. Storing files as BLOBs is convenient but locks the data into the database's proprietary format. CERF deliberately avoids BLOB storage: all files are kept in their native format in a secure filestore on disk, while the database holds only metadata and pointers.
CERF Crossreference annotation ID: blob
BPS
Bits Per Second. Measures the rate of data transmission.
CERF Crossreference annotation ID: bits-per-second
Browser-Based
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.
CERF Crossreference annotation ID: browser-based
C
CAPA
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.
CERF Crossreference annotation ID: capa
CAS Number
A unique numerical identifier assigned by the Chemical Abstracts Service to every chemical substance described in the scientific literature. CAS numbers are widely used as the canonical key for cross-referencing chemicals between databases (PubChem, ChemSpider, ChEMBL) and are commonly captured as metadata on chemical CERF resources.
CERF Crossreference annotation ID: cas-number
CDMS
Clinical Data Management System. Used here, CDMS refers to electronic data-capturing systems that capture, catalog, code and archive data directly from laboratory instruments during a clinical trial in the life sciences.
CERF Crossreference annotation ID: cdms
Certificate of Analysis (COA)
A document issued by a manufacturer, supplier, or testing laboratory attesting that a specific batch of material meets defined quality specifications. COAs are routine in regulated industries and are commonly attached to incoming raw material records, often via CERF Resource Links or formal Crossreferences.
CERF Crossreference annotation ID: certificate-of-analysis
Chain of Custody
A continuous, documented record of every person who has handled a sample, document, or piece of evidence, including dates, times, and the purpose of each transfer. An unbroken chain of custody is essential when records or samples may be used as legal evidence or in support of regulatory submissions.
CERF Crossreference annotation ID: chain-of-custody
Change Control
A formal, documented process for proposing, reviewing, approving, implementing, and verifying changes to validated systems, processes, equipment, or controlled documents. Required under GxP and ISO frameworks to ensure that no change is made without appropriate impact assessment.
CERF Crossreference annotation ID: change-control
Check In
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.
CERF Crossreference annotation ID: check-in
Check Out
When a user checks out a CERF Resource, a copy of the resource will download to a hidden CERF folder on your computer for editing. Only one user may check out a record at a time.
CERF Crossreference annotation ID: check-out
Client
A software program that accesses services from a server.
CERF Crossreference annotation ID: client
Client-Based
Typically software that is accessed using a dedicated application on the user's machine, rather than from a web browser.
CERF Crossreference annotation ID: client-based
Client/Server
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.
CERF Crossreference annotation ID: client-server
Cloud-Based
Software that runs from or on network servers typically outside of an organization's internal network.
CERF Crossreference annotation ID: cloud-based
CMC (Chemistry, Manufacturing, and Controls)
The section of a regulatory submission (e.g., an FDA New Drug Application or IND) that describes how a drug substance and drug product are manufactured, characterized, controlled, and tested. CMC documentation is a major application area for compliant content management systems.
CERF Crossreference annotation ID: cmc
CML (Chemical Markup Language)
An XML-based open standard for representing chemical structures, reactions, and properties. CERF natively reads CML files and extracts chemical metadata — molecular weight, formula, CAS number — for indexing and search.
CERF Crossreference annotation ID: cml
Compliance
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 21 CFR 11.
CERF Crossreference annotation ID: compliance
Computer System Validation (CSV)
The documented process of demonstrating that a computer system meets its specified requirements and will reliably do what it is intended to do in its operating environment. Required under GAMP and 21 CFR Part 11. Note: in this context "CSV" means Computer System Validation — not the file format of the same name.
CERF Crossreference annotation ID: computer-system-validation
Controlled Document
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.
CERF Crossreference annotation ID: controlled-document
Control Strategy
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.
CERF Crossreference annotation ID: controlled-strategy
Controlled Vocabulary
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.
CERF Crossreference annotation ID: controlled-vocabulary
CRO (Contract Research Organization)
An organization that provides outsourced research services to pharmaceutical, biotechnology, medical device, and other regulated industries. CROs often run multiple concurrent studies for different sponsors, making strict workgroup-level data segregation an important requirement in their data management systems.
CERF Crossreference annotation ID: cro
Cross-Platform
Software that can operate on multiple computer operating systems (i.e. Windows, MacOS, Linux).
CERF Crossreference annotation ID: cross-platform
Cryptographic Hash
A fixed-length string produced by running a file or message through a one-way mathematical function (e.g., SHA-256). Any change to the original input — even a single bit — produces a completely different hash, making cryptographic hashes ideal for detecting tampering. CERF uses hash digests to verify file integrity at check-in and as the basis for its PKI-based digital signatures.
CERF Crossreference annotation ID: cryptographic-hash
Cybersecurity
The protection of computer systems, networks, and data from unauthorized access, disruption, modification, or destruction. In regulated research environments, cybersecurity programs must address both the technical controls of the ELN itself (encryption, authentication, audit) and the operational environment in which it runs.
CERF Crossreference annotation ID: cybersecurity
D
Database
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.
CERF Crossreference annotation ID: database
Data Governance
The strategies employed to ensure that data entered into the software properly follows compliance regulations. CERF ELN is a true 21 CFR 11 compliant system.
CERF Crossreference annotation ID: data-governance
Data Integrity
The levels of quality, accuracy, reliability, completeness and consistency of data, as well as how thoroughly the data was collected and documented.
CERF Crossreference annotation ID: data-integrity
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 are handled according to organization standards.
CERF Crossreference annotation ID: data-life-cycle
Data Lineage
A documented record of where a piece of data came from, how it was transformed, and where it has been used. Data lineage is essential for reproducibility and for satisfying regulatory inspectors who need to trace any reported result back to its raw source. Strong audit trails and immutable version histories — as in CERF — are the technical underpinning of practical data lineage.
CERF Crossreference annotation ID: data-lineage
Data Management
The means by which a company or laboratory controls and regulates the information obtained through research projects. CERF ELN is an excellent tool to organize and safeguard your laboratory data.
CERF Crossreference annotation ID: data-management
De-identification
The removal or masking of personal identifiers from a record so that the subject is not readily identifiable, while preserving the ability to re-link the record to the subject if necessary (e.g., via a code held separately). Distinct from anonymization, which is intended to be irreversible.
CERF Crossreference annotation ID: de-identification
DICOM (Digital Imaging and Communications in Medicine)
The international standard for storing, exchanging, and transmitting medical imaging data, including pathology and radiology images. DICOM files embed extensive metadata alongside the image pixels. CERF 6 supports DICOM preview as part of its expanded image-format support.
CERF Crossreference annotation ID: dicom
Digital Cosigner
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.
CERF Crossreference annotation ID: digital-cosigner
Digital Signature
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.
CERF Crossreference annotation ID: digital-signature
Disclosure
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.
CERF Crossreference annotation ID: disclosure
Document Management System (DMS)
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).
CERF Crossreference annotation ID: document-management-system
DOI (Digital Object Identifier)
A persistent, globally unique identifier assigned to a digital object — most commonly a published article, dataset, or report. A DOI resolves to a stable URL that should remain valid even if the host moves. DOIs are widely used as the canonical reference identifier in scholarly cross-referencing.
CERF Crossreference annotation ID: doi
Domain
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 do not need or want to see.
CERF Crossreference annotation ID: domain
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.
CERF Crossreference annotation ID: drag-and-drop
DSA (Digital Signature Algorithm)
A U.S. federal government standard cryptographic algorithm for digital signatures, specified in FIPS 186. CERF uses DSA-based public key infrastructure to generate digital signatures that are mathematically tied to the signed record and cannot be separated, copied, or forged.
CERF Crossreference annotation ID: dsa
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.
CERF Crossreference annotation ID: dynamic-record-format
E
EDC
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.
CERF Crossreference annotation ID: edc
EDMS
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 21 CFR 11 compliant EDMS.
CERF Crossreference annotation ID: edms
Electronic Record
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.
CERF Crossreference annotation ID: electronic-record
Electronic Records Management
The control of the creation, maintenance, use, and disposal of electronic records.
CERF Crossreference annotation ID: electronic-records-management
Electronic Signature
Any electronic symbol, sound, or process attached to a record that an individual adopts as their signature, including typed names, scanned images of handwritten signatures, and clicked acknowledgments. Under 21 CFR Part 11, an electronic signature must be linked to its record in a way that prevents falsification. Note: an electronic signature is a broader category than a digital signature, which is a specific type of electronic signature based on cryptographic techniques.
CERF Crossreference annotation ID: electronic-signature
ELM
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.
CERF Crossreference annotation ID: electronic-lab-manager
Electronic Laboratory Notebook (ELN)
Electronic Lab Notebooks are software programs intended to replace paper notebooks used in scientific research. ELNs modernize, simplify, and strengthen note taking, record keeping, and Intellectual Property protection. Also called electronic notebook, e-notebook, lab management software.
CERF Crossreference annotation ID: electronic-laboratory-notebook
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.
CERF Crossreference annotation ID: email-to-cerf
Encryption
A method of data security involving encoding data that can only be deciphered with a designated key or password.
CERF Crossreference annotation ID: encryption
Enterprise CMS
A commercial business-level Content Management System (or Document Management System, EDMS) usually hosted onsite on local servers. (See also DMS.)
CERF Crossreference annotation ID: enterprise-cms
Entry
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.
CERF Crossreference annotation ID: cerf-entry
ERMS
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, assets and project-management tasks in a 21 CFR 11 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 21 CFR 11.
CERF Crossreference annotation ID: electronic-resource-management-system
ERN
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.
CERF Crossreference annotation ID: electronic-research-notebook
EU Annex 11
The European Union's regulatory framework for computerized systems used in GMP environments, equivalent in spirit and scope to 21 CFR Part 11 in the United States. Multinational pharmaceutical organizations must typically satisfy both standards simultaneously, which fortunately have substantial overlap in requirements.
CERF Crossreference annotation ID: eu-annex-11
Extensibility
The capacity of a software system to accept new features, integrations, or behavior without modifying its core. CERF achieves extensibility primarily through its CAM (CERF Application Module) plugin architecture, which allows new viewers, importers, and metadata handlers to be deployed without restarting the core server.
CERF Crossreference annotation ID: extensibility
F
FAIR Data
An acronym summarizing four principles for high-quality research data management: data should be Findable, Accessible, Interoperable, and Reusable. FAIR is widely adopted in academic and government research as a framework for evaluating data infrastructure.
CERF Crossreference annotation ID: fair-data
FDA
The United States Food and Drug Administration. The federal agency responsible for regulating drugs, biologics, medical devices, food, and tobacco products. 21 CFR Part 11 is the FDA regulation governing electronic records and electronic signatures across all FDA-regulated industries.
CERF Crossreference annotation ID: fda
File Cabinet
Storage unit that typically holds paper resources and folders.
CERF Crossreference annotation ID: file-cabinet
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.
CERF Crossreference annotation ID: file-cabinet-editor
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.
CERF Crossreference annotation ID: file-cabinet-manager
File Extension
The portion of a filename that defines the file type. CERF is able to ingest data of all file types.
CERF Crossreference annotation ID: file-extension
Filestore
The portion of the CERF server's storage that holds raw user files in their original, native format — preserved exactly as they were submitted. Metadata, audit trails, and pointers to filestore content live in CERF's SQL database. Keeping files in a separate filestore (rather than as BLOBs inside the database) guarantees that the underlying data can always be recovered in its original form, even if the database itself is unavailable.
CERF Crossreference annotation ID: filestore
Final Version
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.
CERF Crossreference annotation ID: final-version
FIPS
Federal Information Processing Standards. A set of publicly announced standards developed by the U.S. National Institute of Standards and Technology (NIST) for use in computer systems by non-military U.S. government agencies and contractors. FIPS 140 (cryptographic module validation) and FIPS 186 (digital signature standard) are particularly relevant to compliant ELN systems.
CERF Crossreference annotation ID: fips
Firewall
A network security system that monitors and controls incoming and outgoing network traffic based on predetermined rules. CERF servers deployed in an enterprise environment normally sit behind a firewall, with only specific ports (e.g., 8443 for HTTPS access, 61616 for ActiveMQ) opened for legitimate client traffic.
CERF Crossreference annotation ID: firewall
Flexible Notebook
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.
CERF Crossreference annotation ID: flexible-notebook
FTP
File Transfer Protocol. This is a standard protocol for transferring files between a client and server over a computer network.
CERF Crossreference annotation ID: file-transfer-protocol
G
GAMP (Good Automated Manufacturing Practice)
A risk-based framework, maintained by the International Society for Pharmaceutical Engineering (ISPE), for validating computerized systems used in regulated manufacturing. The current edition, GAMP 5, categorizes software by complexity and adapts validation effort accordingly. Widely referenced in pharmaceutical IT projects.
CERF Crossreference annotation ID: gamp
GDPR
General Data Protection Regulation. Established to improve data protection and regulation within the European Union.
CERF Crossreference annotation ID: general-data-protection-regulation
GCLP (Good Clinical Laboratory Practice)
A set of principles combining elements of GLP and GCP that governs laboratory work performed in support of clinical trials. GCLP is particularly relevant to central laboratories performing biomarker, immunology, and bioanalytical assays for clinical studies.
CERF Crossreference annotation ID: good-clinical-laboratory-practice
GCP (Good Clinical Practice)
An international ethical and scientific quality standard for the design, conduct, recording, and reporting of clinical trials involving human subjects. Compliance provides public assurance that the rights, safety, and well-being of trial subjects are protected and that clinical trial data are credible.
CERF Crossreference annotation ID: good-clinical-practice
GDRP
Good Data and Record Management Practices. Guidelines established by the WHO regarding the collection, quality, security and accuracy of data and records.
CERF Crossreference annotation ID: good-data-record-management-practices
GLP
Good Laboratory Practice. Guidelines geared towards laboratories. CERF was designed to promote a critical good laboratory practice: archiving and protecting data. In the U.S., GLP is codified at 21 CFR Part 58; the OECD maintains an internationally harmonized version.
CERF Crossreference annotation ID: good-laboratory-practice
GMP
Good Manufacturing Practice. Established systems for regulating quality of pharmaceutical products. In the U.S., codified at 21 CFR Parts 210, 211, and 820 (medical devices).
CERF Crossreference annotation ID: good-manufacturing-practice
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 Manufacturing Practices). A full list is available at Wikipedia: GxP.
CERF Crossreference annotation ID: good-practices
Guest
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).
CERF Crossreference annotation ID: cerf-guest
GUI
Graphical User Interface. Pronounced /'gu:i/ ("gooey"). 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.
CERF Crossreference annotation ID: graphical-user-interface
H
H&E Stain
Hematoxylin and Eosin stain — the most widely used staining method in histology and histopathology, providing a general overview of tissue structure. Hematoxylin stains cell nuclei blue-purple, while eosin stains the cytoplasm and connective tissue in shades of pink. H&E staining method is one of the histology-specific metadata fields available on the CERF Tissue Sample resource type.
CERF Crossreference annotation ID: he-stain
Hash Digest
The fixed-length output of a cryptographic hash function applied to a file or message. CERF stores a hash digest (e.g., MD5 or SHA-based) for every record, allowing the system — and inspectors — to detect any subsequent tampering with the file's contents.
CERF Crossreference annotation ID: hash-digest
HIPAA
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 Validated Cloud allows us to deploy HIPAA-ready systems.
CERF Crossreference annotation ID: hipaa
HL7 (Health Level Seven)
A set of international standards for the exchange, integration, sharing, and retrieval of electronic health information. HL7 is the lingua franca of clinical IT interoperability, and HL7 message types (e.g., ADT, ORM, ORU) are frequently encountered at the boundary between clinical and research systems.
CERF Crossreference annotation ID: hl7
HTTPS
HyperText Transfer Protocol Secure. The encrypted variant of HTTP used by web browsers to communicate securely with web servers, including the CERF web client. HTTPS uses TLS to encrypt traffic in transit and verify the server's identity via digital certificates.
CERF Crossreference annotation ID: https
I
ICH (International Council for Harmonisation)
The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use brings together regulatory authorities and the pharmaceutical industry to develop harmonized guidelines. ICH guidelines (e.g., ICH E6 for GCP, ICH Q9 for quality risk management) carry significant regulatory weight worldwide.
CERF Crossreference annotation ID: ich
Icon
A graphic image or symbol, visible on the screen, that performs an action or opens a menu when selected by the user.
CERF Crossreference annotation ID: icon
IND (Investigational New Drug)
A regulatory submission to the FDA that, when accepted, allows a pharmaceutical sponsor to begin clinical trials of an unapproved drug in human subjects. INDs include substantial CMC, pharmacology, toxicology, and clinical protocol content — much of it derived from records held in regulated R&D data management systems.
CERF Crossreference annotation ID: ind
Informatics
The study of computer information systems where processed data is stored and accessed.
CERF Crossreference annotation ID: informatics
Inline Rendering
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.
CERF Crossreference annotation ID: inline-rendering
Inline Viewing
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 its ability to render more file types inline than other ELNs, including Microsoft Word and Excel documents.
CERF Crossreference annotation ID: inline-viewing
Inspection Readiness
The state in which a regulated facility can produce required records, audit trails, training documents, and supporting evidence on demand — typically with very little warning — to an FDA, EMA, or other regulatory inspector. Strong inspection readiness depends on robust electronic records, well-maintained audit trails, and disciplined SOP management.
CERF Crossreference annotation ID: inspection-readiness
Installation Qualification (IQ)
Documented verification that a system has been installed correctly in its target environment, that all hardware and software components are present and at the specified versions, and that the installation environment itself meets all required specifications. The first stage of the IQ/OQ/PQ validation lifecycle. Lab-Ally provides IQ support for CERF deployments.
CERF Crossreference annotation ID: installation-qualification
Instance
A specific running deployment of a software system. An organization may operate multiple CERF instances — for example, a production instance, a validation instance, and a development instance — each with its own database, filestore, and user population.
CERF Crossreference annotation ID: instance
IP (Intellectual Property)
A concept that has commercial value, which has a unique set of exclusive rights under law.
CERF Crossreference annotation ID: intellectual-property
IRB (Institutional Review Board)
Institutional (or Internal) Review Board, 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 help researchers meet and document compliance with the requirements of the IRB and any associated SOPs.
CERF Crossreference annotation ID: institutional-review-board
Interface
A boundary across which two separate systems interact.
CERF Crossreference annotation ID: interface
ISO (International Organization for Standardization)
Responsible for quality and management standards pertaining to laboratory processes and production. Particularly relevant standards include ISO 9001 (quality management systems), ISO 17025 (testing and calibration laboratories), and ISO 27001 (information security).
CERF Crossreference annotation ID: international-organization-for-standardization
IACUC (Institutional Animal Care and Use Committee)
An IACUC 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 IACUC and any associated SOPs.
CERF Crossreference annotation ID: institutional-animal-care-use-committee
J
Java
A widely deployed object-oriented programming language and runtime platform originally developed by Sun Microsystems and now maintained by Oracle. Java's "write once, run anywhere" model makes it well suited to cross-platform desktop and server applications. CERF 6 is built on Java 25 (an LTS release) and runs in Apache Tomcat.
CERF Crossreference annotation ID: java
JP2 (JPEG 2000)
An image compression standard and file format that supports both lossy and lossless compression. JP2 is the format used by many whole slide imaging (WSI) platforms in digital pathology, and is natively supported for viewing and indexing in CERF 6.
CERF Crossreference annotation ID: jp2
JSON (JavaScript Object Notation)
A lightweight, human-readable data interchange format widely used for configuration files and API payloads. JSON is the default request and response format for most modern REST APIs and is commonly produced or consumed when integrating CERF with external systems.
CERF Crossreference annotation ID: json
K
KPI (Key Performance Indicator)
A measurable value used to evaluate progress against a defined objective. In a regulated lab context, KPIs frequently track measures such as cycle time per study, audit trail completeness, SOP compliance rate, and time-to-finalize for notebook pages.
CERF Crossreference annotation ID: kpi
L
Lab Notebook
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.
CERF Crossreference annotation ID: lab-notebook
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.
CERF Crossreference annotation ID: laboratory-information-management-system
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.
CERF Crossreference annotation ID: laboratory-information-system
Linux
A family of open-source, Unix-like operating systems widely used for server deployments. CERF servers run on Linux (typically Ubuntu LTS releases), and CERF 6 introduces a Linux desktop client in addition to the existing Windows and macOS clients.
CERF Crossreference annotation ID: linux
Locked Record
A record that has been finalized or otherwise placed in a read-only state to prevent further modification. Locking is a routine outcome of digital signing, finalization, or check-out by another user, and is an essential component of any compliant record system's data-integrity controls.
CERF Crossreference annotation ID: locked-record
Logbook
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.
CERF Crossreference annotation ID: logbook
LRB (Laboratory Record Book)
Another name for a Lab Notebook, but in some cases an 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.
CERF Crossreference annotation ID: laboratory-record-book
LTS (Long-Term Support)
A release of a software product — particularly an operating system or runtime — that is designated to receive security and maintenance updates for an extended period (typically several years). CERF deliberately builds on LTS releases of Java, MySQL, Tomcat, and Ubuntu to maximize the operational lifespan of any given deployment.
CERF Crossreference annotation ID: lts
Lucene
Apache Lucene is a robust, full-text search engine implemented in Java. CERF utilizes Lucene to deliver a powerful search engine with efficient algorithms and scalable indexing.
CERF Crossreference annotation ID: lucene
M
MD5
A cryptographic hash function that produces a 128-bit hash digest. Although MD5 is no longer considered secure against deliberate collision attacks, it remains useful and widely deployed for detecting accidental data corruption and is one of the hash functions referenced in CERF's record-integrity infrastructure.
CERF Crossreference annotation ID: md5
MES (Manufacturing Execution System)
A computerized system used by manufacturing operations to track, control, and document the transformation of raw materials into finished products. In pharmaceutical manufacturing, MES systems generate the electronic batch records required for GMP compliance and may be cross-referenced from associated R&D records.
CERF Crossreference annotation ID: mes
Metadata
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 Crossreference annotation ID: metadata
Metadata Editor
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.
CERF Crossreference annotation ID: metadata-editor
Metafile
In the context of an electronic lab notebook, a metafile is a file which contains the metadata describing the contents of another file.
CERF Crossreference annotation ID: metafile
MFA (Multi-Factor Authentication)
An authentication mechanism that requires the user to present two or more independent pieces of evidence (factors) before being granted access: typically something they know (password), something they have (a phone or token), and/or something they are (biometric). CERF 6 introduces optional TOTP-based MFA configurable via business policy.
CERF Crossreference annotation ID: mfa
Migration
The structured process of moving data, configurations, and users from one system to another — for example, from a legacy paper-based or shared-drive system into CERF, or from one CERF version to another. Successful migration preserves the original records' attributes and audit history wherever feasible.
CERF Crossreference annotation ID: migration
Multiplatform
A software program designed to function on multiple operating systems.
CERF Crossreference annotation ID: multiplatform
N
NCBI (National Center for Biotechnology Information)
A division of the U.S. National Library of Medicine that hosts a suite of databases central to molecular biology research, including GenBank, PubMed, RefSeq, and the Protein database. NCBI accession numbers and PubMed IDs are common targets for CERF Crossreferences in life-sciences deployments.
CERF Crossreference annotation ID: ncbi
Network File Link
A CERF feature that allows the system to reference and index very large files (e.g., whole slide images, raw instrument output) stored on an external SMB file server, without requiring the file itself to be ingested into the CERF filestore. Metadata, annotations, and search indexing remain in CERF while the bulk data stays on dedicated high-capacity storage.
CERF Crossreference annotation ID: network-file-link
NIST (National Institute of Standards and Technology)
A U.S. federal agency under the Department of Commerce that develops measurement standards, including cryptographic standards (e.g., the SHA family of hash functions and the FIPS digital signature standards) directly relevant to compliant electronic records.
CERF Crossreference annotation ID: nist
Non-repudiation
A claim guaranteeing that the source of the documentation cannot later deny that he or she was the author.
CERF Crossreference annotation ID: non-repudiation
Notebook
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 Crossreference annotation ID: notebook
Notebook Creator
CERF user role that has the same privileges as File Cabinet Manager, plus the ability to create Notebooks.
CERF Crossreference annotation ID: notebook-creator
Notebook Editor
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 Crossreference annotation ID: notebook-editor
Notification
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.).
CERF Crossreference annotation ID: notification
O
OAuth
An open-standard authorization protocol that allows users to grant third-party applications limited access to their resources without sharing their credentials. OAuth is the basis for many "sign in with..." patterns in modern web applications.
CERF Crossreference annotation ID: oauth
OECD (Organisation for Economic Co-operation and Development)
An international body whose Test Guidelines and Principles of Good Laboratory Practice are widely adopted by member countries for the conduct of non-clinical safety studies. The OECD GLP principles are functionally equivalent to U.S. 21 CFR Part 58 and form the basis for mutual acceptance of test data between OECD member states.
CERF Crossreference annotation ID: oecd
OME-TIFF
An open file format from the Open Microscopy Environment consortium that combines a multi-dimensional TIFF image with structured OME-XML metadata. OME-TIFF is widely used in research microscopy, especially for fluorescence and multi-channel imaging, and is natively supported in CERF 6.
CERF Crossreference annotation ID: ome-tiff
Ontology
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. Ontology is closely related to terms like Shared Vocabulary and Controlled Vocabulary.
CERF Crossreference annotation ID: ontology
On-Premises
A deployment model in which the software runs on hardware physically located within the customer's own facility — as opposed to cloud-hosted. On-premises deployment is favored where regulatory, contractual, or security constraints make external hosting impractical. CERF supports on-premises deployment, including in fully sealed (air-gapped) environments with no internet connectivity.
CERF Crossreference annotation ID: on-premises
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.
CERF Crossreference annotation ID: out-of-the-box
Open Source
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.
CERF Crossreference annotation ID: open-source
Operational Qualification (OQ)
Documented testing demonstrating that an installed system performs as designed across the range of functions critical to its intended use, under all expected operating conditions. The second stage of the IQ/OQ/PQ validation lifecycle. Lab-Ally and qualified validation partners provide OQ support for CERF deployments.
CERF Crossreference annotation ID: operational-qualification
P
PACS (Picture Archiving and Communication System)
A medical imaging technology used to store, retrieve, present, and share medical images. PACS is the dominant storage and review platform for radiology images and is increasingly common in digital pathology workflows as well. A pathology PACS may be integrated with a LIMS or ELN to provide a unified view of imaging and result data.
CERF Crossreference annotation ID: pacs
Page
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.
CERF Crossreference annotation ID: notebook-page
Password Aging
A policy that automatically expires user passwords after a defined period (e.g., 30, 60, or 90 days), forcing users to choose a new one. Password aging is explicitly required by 21 CFR Part 11 §11.300(b) and is enforced by CERF business policy.
CERF Crossreference annotation ID: password-aging
Patent
A set of rights granted to an inventor for a period of time, in exchange for a public disclosure of the invention.
CERF Crossreference annotation ID: patent
PDB (Protein Data Bank)
A worldwide repository of three-dimensional structural data for large biological molecules, including proteins and nucleic acids. Each PDB entry is identified by a four-character accession code (e.g., 1HHB), which is a common target value for CERF Crossreferences in structural biology research environments.
CERF Crossreference annotation ID: pdb
An ISO standard file format for archiving information.
CERF Crossreference annotation ID: pdf
Performance Qualification (PQ)
Documented evidence that an installed and operationally qualified system consistently performs in accordance with the user's specific study workflows and operational requirements. The third stage of the IQ/OQ/PQ validation lifecycle, typically demonstrated using realistic test data that mirrors actual production use.
CERF Crossreference annotation ID: performance-qualification
PHI (Protected Health Information)
Under HIPAA, any individually identifiable health information held or transmitted by a covered entity or its business associates. PHI must be handled with strict access controls, audit trails, and data-protection safeguards.
CERF Crossreference annotation ID: phi
PI (Principal Investigator)
The "head scientist" of a laboratory or collaborative study.
CERF Crossreference annotation ID: principle-investigator
PII (Personally Identifiable Information)
Any information that can be used, alone or in combination with other data, to identify a specific individual. Examples include name, address, social security number, biometric records, and certain combinations of demographic and clinical data. Subject to various privacy regulations including GDPR and U.S. state privacy laws.
CERF Crossreference annotation ID: pii
PKI
Short for Public Key Infrastructure, PKI refers to procedures to encrypt and decrypt content for secure information exchange, using sets of private and public keys, binary certificates, and complex hashing algorithms.
CERF Crossreference annotation ID: public-key-infrastructure
Plug-In
An extension that adds features to a software application. In CERF, the CAMs extensibility system allows new features to be deployed to CERF servers without the need to restart the service in many situations.
CERF Crossreference annotation ID: plug-in
Provenance
The documented history of a piece of data or a sample: who created it, where it came from, what transformations it underwent, and who has handled it since. Provenance is closely related to data lineage and chain of custody, and is a key driver of reproducibility and regulatory confidence.
CERF Crossreference annotation ID: provenance
Q
QA (Quality Assurance)
The systematic activities and processes implemented within an organization to provide confidence that quality requirements will be fulfilled. In a regulated lab, QA functions independently of the operational team to audit, review, and approve records and procedures.
CERF Crossreference annotation ID: qa
QC (Quality Control)
The operational techniques and activities used to fulfill quality requirements — including inspection, testing, and measurement against specifications. Distinct from QA, which audits whether the quality system as a whole is effective.
CERF Crossreference annotation ID: qc
QMS (Quality Management System)
The formal documented system describing how an organization directs and controls its quality-related activities, including responsibilities, procedures, processes, and resources. A QMS typically includes SOP management, deviation handling, change control, training records, and CAPA tracking — much of which can be supported within a compliant ELN.
CERF Crossreference annotation ID: qms
Quality Metrics
Objective standards to assess the quality, performance, functions, and protocols of an organization and its data.
CERF Crossreference annotation ID: quality-metrics
Qualitative Research
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.
CERF Crossreference annotation ID: qualitative-research
Quality Risk Management
A standard set of steps to investigate quality risks during a product's life cycle. ICH Q9 provides an internationally accepted framework for quality risk management in the pharmaceutical industry.
CERF Crossreference annotation ID: quality-risk-management
R
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.
CERF Crossreference annotation ID: redundant-array-independent-disks
RBAC (Role-Based Access Control)
An access control model in which permissions are assigned to roles rather than directly to users, and users are then assigned to one or more roles. RBAC simplifies administration and makes permission audits tractable. CERF's roles (Resource Identifier, Guest, Annotator, Metadata Editor, File Cabinet Editor, File Cabinet Manager, Notebook Editor, Notebook Creator, Digital Signer, Digital Cosigner) are an RBAC implementation tailored for laboratory workflows.
CERF Crossreference annotation ID: rbac
RDF
Resource Description Framework. A hierarchic metadata management technology used widely in the industry and the basis for CERF's semantic metadata capabilities.
CERF Crossreference annotation ID: resource-description-framework
Read-Only
A state in which a record can be viewed but not modified. In CERF, resources are read-only when they have been finalized, when they have been checked out by another user, when the current user lacks edit privileges, or when they are being viewed from a version history.
CERF Crossreference annotation ID: read-only
Repository
A designated location for the management and storage of data. CERF acts as a repository for laboratory projects.
CERF Crossreference annotation ID: repository
Resource
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.
CERF Crossreference annotation ID: resource
Resource Identifier
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.
CERF Crossreference annotation ID: resource-identifier
Retention Policy
An organizational rule specifying how long a particular class of records must be kept before they may be archived or destroyed. Retention policies are driven by regulatory requirements (e.g., FDA, OECD) and organizational risk management. CERF's "all versions forever" architecture is designed to comfortably accommodate even the longest retention requirements.
CERF Crossreference annotation ID: retention-policy
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.
CERF Crossreference annotation ID: request-for-information
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.
CERF Crossreference annotation ID: request-for-proposal
Rigid Notebook
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.
CERF Crossreference annotation ID: rigid-notebook
Risk-Based Approach
A regulatory philosophy under which the rigor of validation, testing, and oversight applied to a system is scaled to the level of risk that system poses to product quality, patient safety, or data integrity. ICH Q9, GAMP 5, and current FDA guidance all promote a risk-based approach to computer system validation.
CERF Crossreference annotation ID: risk-based-approach
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.
CERF Crossreference annotation ID: return-on-investment
Round-Trip Editing
A workflow in which a file is checked out of CERF, edited in its native external application (Word, Excel, ChemDraw, ImageJ, etc.), and checked back in — with the new version recorded under full audit-trail control. Round-trip editing is one of CERF's signature capabilities, eliminating the awkward download–edit–upload–replace cycle common to browser-based ELN systems.
CERF Crossreference annotation ID: round-trip-editing
S
SaaS (Software-as-a-Service)
Software that is hosted online using cloud-computing techniques.
CERF Crossreference annotation ID: software-as-a-service
SAML (Security Assertion Markup Language)
An XML-based open standard for exchanging authentication and authorization information between parties — typically between an identity provider and a service provider. SAML is the backbone of many enterprise single sign-on (SSO) deployments.
CERF Crossreference annotation ID: saml
SDMS — 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.
CERF Crossreference annotation ID: scientific-data-management-system
SDIMS — 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.
CERF Crossreference annotation ID: structured-data-information-management
Section
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.
CERF Crossreference annotation ID: section
Semantic Technologies
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.
CERF Crossreference annotation ID: semantic-technologies
SHA (Secure Hash Algorithm)
A family of cryptographic hash functions standardized by NIST. SHA-256 and SHA-512 are widely used today for record-integrity verification, digital signature generation, and certificate fingerprinting. SHA-1 and earlier are now considered cryptographically broken for security-sensitive applications.
CERF Crossreference annotation ID: sha
Signature Workflow
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.
CERF Crossreference annotation ID: signature-workflow
SMB (Server Message Block)
A network protocol used primarily for providing shared access to files, printers, and serial ports. CERF supports SMB 2 and SMB 3 for Network File Links — allowing CERF to reference and index files held on external SMB file servers without copying them into the CERF filestore.
CERF Crossreference annotation ID: smb
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.
CERF Crossreference annotation ID: standard-operating-procedure
Sponsor
In clinical research, the individual, company, institution, or organization that takes responsibility for the initiation, management, and financing of a clinical trial. The sponsor is the entity ultimately accountable to regulators for the integrity of the study and its records.
CERF Crossreference annotation ID: sponsor
SQL (Structured Query Language)
The standard language for managing and querying data held in relational databases. CERF stores its metadata, audit trails, and version history in an SQL database, with the customer's choice of MySQL, Microsoft SQL Server, or Oracle as the backend.
CERF Crossreference annotation ID: sql
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. SSL has been superseded in current practice by TLS (Transport Layer Security), though the term "SSL" is still commonly used as a generic label. CERF is compatible with SSL/TLS and a secure connection is recommended whenever the CERF user and server are not located within the same secure network.
CERF Crossreference annotation ID: secure-sockets-layer
SSO (Single Sign-On)
An authentication arrangement under which a user logs in once to a central identity provider and is then automatically authenticated to multiple participating applications. SSO simplifies the user experience and centralizes account lifecycle management.
CERF Crossreference annotation ID: sso
Static Record Format
Rigid record formats that only permit a user to have minimal interaction with the data.
CERF Crossreference annotation ID: static-record-format
Study Director
Under GLP regulations, the single individual responsible for the overall conduct of a non-clinical safety study. The Study Director has personal responsibility for the integrity of the study record and is named in the final study report. GLP record systems must clearly identify the Study Director's role in approving and signing relevant records.
CERF Crossreference annotation ID: study-director
T
Tag
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.
CERF Crossreference annotation ID: tag
TCP/IP
The Transmission Control Protocol / Internet Protocol suite — the foundational networking protocols that underlie almost all modern network communication, including everything between a CERF client and its server. Specific TCP ports must be opened on firewalls to allow CERF traffic (for example, 8443 for HTTPS and 61616 for ActiveMQ).
CERF Crossreference annotation ID: tcp-ip
Template
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. Users can easily create their own custom resource templates that can be shared with other users of the Domain.
CERF Crossreference annotation ID: template
Thick Client
In the context of CERF, this client is also referred to as the Java client, desktop client or desktop app. A Thick Client usually refers to an application that runs independent of a web browser. CERF currently supports desktop clients for macOS, Linux, and Windows.
CERF Crossreference annotation ID: thick-client
Thin Client
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.
CERF Crossreference annotation ID: thin-client
Time Stamp
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.
CERF Crossreference annotation ID: time-stamp
TLS (Transport Layer Security)
The current standard cryptographic protocol for securing communication between a client and a server over a network. TLS is the modern replacement for SSL, though the older term "SSL" is still commonly used colloquially to refer to TLS. CERF supports current TLS versions for HTTPS, web-client, and ActiveMQ traffic.
CERF Crossreference annotation ID: tls
Tomcat (Apache Tomcat)
An open-source Java servlet container and web server maintained by the Apache Software Foundation. Tomcat is the application server in which the CERF server-side Java application runs. CERF 6 is qualified against current LTS releases of Tomcat.
CERF Crossreference annotation ID: tomcat
TOTP (Time-based One-Time Password)
An algorithm that generates a short numeric code derived from a shared secret and the current time, used as the second factor in multi-factor authentication. TOTP codes are produced by authenticator apps such as Google Authenticator, Microsoft Authenticator, or Authy, and are the MFA mechanism supported by CERF 6.
CERF Crossreference annotation ID: totp
Traceability
The ability to follow a recorded result back through every step of the work that produced it, including the people, samples, instruments, methods, and source records involved. Strong traceability is the practical outcome of a properly implemented combination of audit trails, version control, controlled vocabularies, and cross-referencing.
CERF Crossreference annotation ID: traceability
Two-Factor Authentication (2FA)
A subset of MFA in which the user is required to present exactly two independent authentication factors. Typically a password plus a TOTP code from an authenticator app. 2FA is increasingly mandated in regulated environments as a baseline access control.
CERF Crossreference annotation ID: two-factor-authentication
U
User Interface
The part of a computer system with which the user interacts.
CERF Crossreference annotation ID: user-interface
UTC (Coordinated Universal Time)
The primary time standard used globally for civil time and computer systems. CERF audit trails record events in a consistent time reference, ensuring that a record's timestamp is unambiguous even across deployments in multiple time zones or following daylight-saving-time transitions.
CERF Crossreference annotation ID: utc
UUID (Universally Unique Identifier)
A 128-bit identifier designed to be unique across space and time without requiring a central coordinating authority. Each CERF resource carries a UUID-style internal identifier, which never changes for the life of the resource and is used throughout the system to refer to it unambiguously across versions, exports, and integrations.
CERF Crossreference annotation ID: uuid
V
Validation
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 21 CFR 11. 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 "21 CFR 11 ready" but cannot be fully 21 CFR 11 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 an 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.
CERF Crossreference annotation ID: validation
Version
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.
CERF Crossreference annotation ID: version
Virtualization
The practice of running multiple operating systems or applications as isolated guests on a single physical host, using a hypervisor. CERF is commonly deployed on virtualized infrastructure (VMware, Hyper-V, KVM) to simplify backup, snapshotting, and disaster recovery.
CERF Crossreference annotation ID: virtualization
VLAN (Virtual LAN)
A logically segmented broadcast domain within a physical local area network, used by network administrators to isolate traffic between groups of devices for security or performance reasons. CERF servers are often placed on a dedicated VLAN to limit which hosts can communicate with them at the network layer.
CERF Crossreference annotation ID: vlan
Voice Note
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.
CERF Crossreference annotation ID: voice-note
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.
CERF Crossreference annotation ID: virtual-private-network
W
WAF (Web Application Firewall)
A security appliance or service that filters and monitors HTTP/HTTPS traffic between a web application and the internet, blocking common application-layer attacks such as SQL injection and cross-site scripting. WAFs are commonly deployed in front of internet-facing CERF web clients as part of a defense-in-depth strategy.
CERF Crossreference annotation ID: waf
Web Client
A CERF user interface accessed through an ordinary web browser, with no client-side installation required. The CERF web client provides a substantial subset of CERF functionality and is particularly useful for administration, search, viewing, and signing tasks. The Java desktop (thick) client remains the primary tool for intensive editing and large-file ingestion.
CERF Crossreference annotation ID: web-client
Witness
A second qualified individual who reviews and countersigns a record to corroborate its content. Witness signatures are foundational to the intellectual-property value of a traditional paper lab notebook and are preserved in CERF through its Signature Workflow system, in which one or more cosigners can be required for a given Notebook or File Cabinet.
CERF Crossreference annotation ID: witness
Workflow
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.
CERF Crossreference annotation ID: workflow
Workgroup
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.
CERF Crossreference annotation ID: workgroup
WSI (Whole Slide Imaging)
The high-resolution digital scanning of an entire glass microscope slide into a single composite image, used in digital pathology for diagnosis, peer review, research, and education. WSI files are typically very large (multi-gigabyte) and use specialized formats such as JP2 (JPEG 2000) or OME-TIFF — both natively supported in CERF 6.
CERF Crossreference annotation ID: wsi
X
XML (eXtensible Markup Language)
A flexible, structured, text-based format for representing arbitrary hierarchical data. XML is widely used in scientific computing — CML (chemistry), HL7 (healthcare), and OME-XML (microscopy) are all XML-based. CERF supports full notebook export as open-standard XML, allowing complete records to be migrated, archived, or shared with regulators in a non-proprietary format.
CERF Crossreference annotation ID: xml
Z
Zero Trust
A modern security model that assumes no implicit trust based on network location, requiring every access request — internal or external — to be authenticated, authorized, and continuously validated. Zero Trust principles are increasingly being applied to enterprise deployments of compliant ELN systems, particularly in pharmaceutical and contract-research environments.
CERF Crossreference annotation ID: zero-trust