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Extraction: Advanced Methods

Extraction: Advanced Methods

Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is formed in...

Extraction: Effects of pH

Extraction: Effects of pH

Consider a neutral form of an amine, B, with a partition coefficient, K, in a liquid mixture containing organic and aqueous phases. The pH of the aqueous phase affects the charge on acidic and basic solutes, and the charged form is usually more soluble in the aqueous phase. Suppose the conjugate acid form of the amine is soluble only in the aqueous phase while the base form is soluble in both phases. Then the distribution coefficient, D, can be given as the ratio of amine concentration in the...

Atomic Force Microscopy

Atomic Force Microscopy

Atomic force microscopy (AFM) is a type of scanning probe microscopy that can analyze topographic details of various specimens like ceramics, glass, polymers, and biological samples. AFM offers over 1000 times more resolution than the optical imaging system. Images generated from AFM are three-dimensional surface profiles, offering an advantage over the flat, two-dimensional images from other imaging techniques.
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Scanning Electron Microscopy

Scanning Electron Microscopy

A scanning electron microscope (SEM) is used to study the surface features of a sample by using an electron beam that scans the sample surface in a two-dimensional manner. Typically, areas between ~1 centimeter to 5 micrometers in width can be imaged. SEM can be used to image bacteria, viruses, tissues as well as larger samples like insects. Conventional SEM gives a magnification ranging from 20X to 30,000X and spatial resolution of 50 to 100 nanometers.
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Extraction: Partition and Distribution Coefficients

Extraction: Partition and Distribution Coefficients

The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
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Western Blotting

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Western blotting is an analytical technique for protein identification. It has various applications in immunology and medicine, including detecting diseases like bovine spongiform encephalopathy, mad cow disease, and human and feline immunodeficiency virus from biological samples.
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Related Experiment Video

Updated: May 22, 2026

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

Published on: September 20, 2018

Layout-aware text extraction from full-text PDF of scientific articles.

Cartic Ramakrishnan¹, Abhishek Patnia, Eduard Hovy

¹Information Sciences Institute, University of Southern California, 4676 Admiralty Way, Suite 1001, Marina del Rey, CA, 90292-6695, USA. cartic@isi.edu.

Source Code for Biology and Medicine

|May 30, 2012

Summary

This study introduces a new system for extracting text from PDF scientific articles. The Layout-Aware PDF Text Extraction (LA-PDFText) system accurately identifies and classifies text blocks for improved text mining.

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Area of Science:

Computational Biology
Bioinformatics
Scientific Publishing

Background:

Portable Document Format (PDF) is the standard for online scientific publications.
Extracting text from PDFs in a layout-aware manner is challenging for text mining and biocuration systems.
Existing methods struggle to accurately process the structural information within PDF scientific articles.

Purpose of the Study:

To introduce the Layout-Aware PDF Text Extraction (LA-PDFText) system.
To facilitate accurate, layout-aware text extraction from PDF research articles for text mining applications.
To provide a baseline system for future research in multi-modal content extraction.

Main Methods:

The LA-PDFText system employs a three-stage process: detecting contiguous text blocks using spatial layout, classifying blocks into rhetorical categories via a rule-based method, and stitching blocks in the correct order.
Spatial layout processing is used to identify and group text blocks.
A rule-based classifier categorizes text blocks into logical units such as title, abstract, and body text.

Main Results:

The LA-PDFText system achieved high performance in identifying text blocks and classifying them into rhetorical categories, with Precision=0.96, Recall=0.89, and F1=0.91.
Evaluated the accuracy of the block detection algorithm and compared text extraction accuracy against the PDF2Text system and PubMed Central.
Demonstrated the system's effectiveness in extracting text from section-wise grouped blocks.

Conclusions:

LA-PDFText is an open-source tool that enables accurate text extraction from full-text scientific articles.
The system provides a foundational solution for enhancing biomedical text mining and biocuration.
The source code is publicly available for further development and application.