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Related Concept Videos

Methods of Documentation I: Source-Oriented Records01:18

Methods of Documentation I: Source-Oriented Records

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Source-oriented records, or SOR, are medical record-keeping organized by the data source. The SOR system was first developed in the mid-1900s to organize the growing patient data in hospitals and other healthcare facilities.
In an SOR, each discipline involved in patient care maintains a separate medical record section. This record-keeping method enables easy tracking of patient progress and ensures healthcare staff have access to up-to-date information.
Key Attributes include the following:
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Methods of Documentation VII: EMR01:30

Methods of Documentation VII: EMR

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Electronic Medical Records (EMRs) primarily center around electronically documenting patients' health information within a single healthcare organization or practice. They contain essential clinical data related to a patient's medical history, diagnoses, medications, treatment plans, lab results, and other pertinent information relevant to the specific encounter or episode of care. EMRs are designed to streamline documentation and workflow processes within individual healthcare...
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NMR Spectrometers: Overview01:20

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NMR spectrometers consist of a strong magnet, a radiofrequency transmitter, and a detector attached to a computer console for recording spectra of samples containing NMR-active nuclei. In first-generation NMR instruments called continuous-wave spectrometers, the resonance frequencies of the nuclei are determined by frequency-sweep or field-sweep methods. The magnetic field strength is fixed and the rf signal is swept in the former, while the radiofrequency signal is fixed and the magnetic field...
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Methods of Documentation V: CBE01:23

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Charting by Exception, or CBE, is a method of documentation used in healthcare, particularly in nursing, that focuses on documenting only significant or abnormal findings rather than recording every detail. This approach aims to streamline the documentation process, improve efficiency, and ensure that healthcare providers can quickly identify deviations from normalcy in patient assessments.
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Methods of Documentation III: PIE01:21

Methods of Documentation III: PIE

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Problem-intervention-evaluation (PIE) is a systematic approach to documentation used in healthcare settings for clinical decision-making and patient care planning. It is a structured approach to organizing patient data based on problems, interventions, and evaluations. Here's a breakdown of its key features and considerations:
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Synthetic Biology02:55

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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Related Experiment Video

Updated: Oct 5, 2025

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
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Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

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Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation.

Max Schröder1,2, Susanne Staehlke3, Paul Groth4

  • 1Institute of Communications Engineering, University of Rostock, Rostock, Germany. max.schroeder@uni-rostock.de.

Journal of Biomedical Semantics
|February 1, 2022
PubMed
Summary
This summary is machine-generated.

Electronic Laboratory Notebook (ELN) protocols can be semantically documented to represent research data provenance. This enables machine-interpretable data sharing and analysis, enhancing research reproducibility and discoverability through linked data.

Keywords:
Electronic laboratory notebooksFAIRKnowledge acquisitionProvenanceRO-CrateResearch dataSemantic documentation

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Area of Science:

  • * Scientific data management
  • * Biomedical research informatics

Background:

  • * Electronic Laboratory Notebooks (ELNs) document wet-lab experiments and protocols.
  • * ELN protocols detail experimental steps, data, and reproducibility information.
  • * Investigating ELN protocols for semantic data provenance documentation.

Purpose of the Study:

  • * To determine if ELN protocols can generate semantic documentation of research data provenance.
  • * To explore the use of ontologies and linked data methodologies for this purpose.

Main Methods:

  • * Manually engineered a retrospective provenance model from a biomedical ELN protocol.
  • * Developed an automated, structure-based knowledge acquisition approach for ELN protocols.
  • * Created ready-to-publish bundles adhering to FAIR principles, including data and semantic documentation.

Main Results:

  • * Manual modeling proved the concept for one protocol.
  • * Automated approach generalized to seven ELN protocols.
  • * SPARQL queries demonstrated the ability to answer questions about experimental processes and data.

Conclusions:

  • * Semantic documentation of ELN protocols enables machine-interpretable research data provenance.
  • * Research Object Crate (RO-Crate) bundles facilitate sharing and searching of data with documentation.
  • * Enhanced data sharing and inter-experiment relationships are enabled.