Demo Data from SIGIR 2026 / reviewers in the wild / expert
Favour James
dblp:428/3233
· DBLP profile ↗
1ranked-venue papers
1as first author
1since 2021 · last 2026
0009-0005-9299-2442ORCID · reported
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 1 heaviest of 1, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology
biomedical text mining |
1.0 | 1 | 2026 | textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape · Bioinform. 2026 |
Methods — techniques the papers use, named apart from their topics
large language model · 1.0biological expression language · 1.0
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2026 | textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in CytoscapeabstractMOTIVATION: Knowledge graphs (KGs) are powerful tools for structuring and analyzing biological information due to their ability to represent data and improve queries across heterogeneous datasets. However, constructing KGs from unstructured literature remains challenging due to the cost and expertise required for manual curation. Prior works have explored text-mining techniques to automate this process, but have limitations that impact their ability to capture complex relationships fully. Traditional text-mining methods struggle with understanding context across sentences. Additionally, these methods lack expert-level background knowledge, making it difficult to infer relationships that require awareness of concepts indirectly described in the text. Large Language Models (LLMs) present an opportunity to overcome these challenges. LLMs are trained on diverse literature, equipping them with contextual knowledge that enables more accurate information extraction. RESULTS: We present textToKnowledgeGraph, an artificial intelligence tool using LLMs to extract interactions from individual publications directly in Biological Expression Language (BEL). BEL was chosen for its compact, detailed representation of biological relationships, enabling structured, computationally accessible encoding. This work makes several contributions. (i) Development of the open-source Python textToKnowledgeGraph package (pypi.org/project/texttoknowledgegraph) for BEL extraction from scientific articles, usable from the command line and within other projects, (ii) an interactive application within Cytoscape Web to simplify extraction and exploration, (iii) a dataset of extractions that have been both computationally and manually reviewed to support future fine-tuning efforts. AVAILABILITY AND IMPLEMENTATION: https://github.com/ndexbio/llm-text-to-knowledge-graph. Favour James, Dexter Pratt, Christopher Churas, Augustin Luna |
Bioinform. | 1 |