A framework for integrating biomedical knowledge in Wikidata with open biological and biomedical ontologies and MeSH keywords
Bibliographic record
Abstract
This study presents a comprehensive framework to enhance Wikidata as an open and collaborative knowledge graph by integrating Open Biological and Biomedical Ontologies (OBO) and Medical Subject Headings (MeSH) keywords from PubMed publications. The primary data sources include OBO ontologies and MeSH keywords, which were collected and classified using SPARQL queries for RDF knowledge graphs. The semantic alignment between OBO ontologies and Wikidata was evaluated, revealing significant gaps and distorted representations that necessitate both automated and manual interventions for improvement. We employed pointwise mutual information to extract biomedical relations among the 5000 most common MeSH keywords in PubMed, achieving an accuracy of 89.40 % for superclass-based classification and 75.32 % for relation type-based classification. Additionally, Integrated Gradients were utilized to refine the classification by removing irrelevant MeSH qualifiers, enhancing overall efficiency. The framework also explored the use of MeSH keywords to identify PubMed reviews supporting unsupported Wikidata relations, finding that 45.8 % of these relations were not present in PubMed, indicating potential inconsistencies in Wikidata. The contributions of this study include improved methodologies for enriching Wikidata with biomedical information, validated semantic alignments, and efficient classification processes. This work enhances the interoperability and multilingual capabilities of biomedical ontologies and demonstrates the critical role of MeSH keywords in verifying semantic relations, thereby contributing to the robustness and accuracy of collaborative biomedical knowledge graphs.
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 distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".