KoExPubMed: A Tool for Effective and Customized Knowledge Extraction from PubMed
Bibliographic record
Abstract
An exponential growth in the literature in general and the medical literature in particular raises a need for effective intelligent analysis strategies and tools to provide valuable insights to researchers about the current evolving literature. While existing applications provide more specific approaches to the problem, such as focusing on particular genome or protein information, in this paper, the proposed application provides effective and detailed analysis of PubMed. The developed tool, named KoExPubMed, follows a more generalized and holistic way by taking into consideration different types of information such as authors, countries, genes, and the interactions between them. The developed application consists of four main components; (1) keyword search and ID extraction, (2) PubMed article information and abstract retrieval, (3) country and address extraction, and (4) gene information extraction. In addition to the fundamental components, the tool provides a variety of visualization options for showing the extracted information and the related associations, including line charts for densities and countries, chord charts for collaborations of authors, network graphs for the genes mentioned together, bubble charts for gene frequencies, etc. By addressing the need for a generalized data mining tool, we propose a comprehensive application which is capable of employing data mining and machine learning techniques to extract from PubMed knowledge valuable to researchers and practitioners who are interested in closely investigating the achievements of others.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.016 |
| Meta-epidemiology (narrow) | 0.003 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.017 | 0.011 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.004 |
| Open science | 0.002 | 0.005 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.032 | 0.016 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".