arXiv:2608. 08056v1 Announce Type: new Abstract: Medical data, by its nature, exhibit a high degree of heterogeneity on multiple levels ranging from (a) different modalities like images, text and time series, (b) diverse tabular schemata introduced by institutions and (c) completely unstructured textual information data provided by healthcare professionals.
By Ioannis N. Tzortzis, Georgia Kapetadimitri, Agapi Davradou, Nefeli Kousta, Nikolaos Bakalos, Ioannis Rallis, Dimitrios Kalogeras, Nikolaos Doulamis, Anastasios Doulamis
OptimusKG is a multimodal biomedical labeled property graph that integrates structured and semi‑structured resources to preserve detailed, type‑specific metadata across molecular, anatomical, clinical, and environmental domains. The graph contains nearly 191,000 nodes, over 21.8 million edges, and more than 67 million property instances derived from 18 ontologies, with a top‑level schema that enforces node and edge constraints while retaining granular provenance. Validation using the PaperQA3 agent found that 70.0% of sampled edges are supported by literature evidence, and the graph offers a standardized resource for machine learning, knowledge‑grounded retrieval, and hypothesis generation in biomedical research.
By Lucas Vittor, Ayush Noori, I\~naki Arango, Joaqu\'in Polonuer, Sam Rodriques, Andrew White, David A. Clifton, Marinka Zitnik
arXiv:2608. 14228v1 Announce Type: new Abstract: Life science knowledge graphs make large collections of structured data available through SPARQL, but each resource uses its own schema, identifiers, and links.
By Yiming Zhang, Koji Tsuda
arXiv:2604. 08552v2 Announce Type: replace-cross Abstract: Scientific metadata are often incomplete and noncompliant with community standards, limiting dataset findability, interoperability, and reuse.
By Josef Hardi, Martin J. O'Connor, Marcos Martinez-Romero, Jean G. Rosario, Stephen A. Fisher, Mark A. Musen
arXiv:2607. 18029v1 Announce Type: cross Abstract: Researchers need to answer ad-hoc questions about the contents of domain-specific archives but often lack the expertise to write structured queries on the metadata.
By Blake G. Fitch, Cato Elia Kurtz
arXiv:2506. 01232v2 Announce Type: replace-cross Abstract: Deriving OWL ontologies from relational database schemas supports semantic interoperability and downstream tasks such as knowledge graph population, ontology-based data access, graph-based learning, and automated reasoning.
By Nadeen Fathallah, Mojtaba Nayyeri, Athish A Yogi, Ratan Bahadur Thapa, Hans-Michael Tautenhahn, Anton Schnurpel, Steffen Staab
arXiv:2607. 22592v1 Announce Type: new Abstract: Graph-based retrieval-augmented generation (GraphRAG) grounds answers in structured knowledge, but current systems extract entities and relationships exhaustively, producing graphs whose size and construction cost scale with corpus length rather than with the reasoning a query requires.
By Marc Saouda (Boston Consulting Group), Rajprakash Bale (Boston Consulting Group), Eren Aldis (Boston Consulting Group), Cloves Almeida (Boston Consulting Group)
The paper introduces EXYGEN, a framework that enables conversational access to large knowledge graphs by combining VoID descriptions, ShEx schemas, retrieved triples, and example question‑query pairs in a retrieval‑augmented generation pipeline. On the SciQA benchmark, this approach achieves an exact‑match score of 0.419 without fine‑tuning any large language model, and shows that larger general‑purpose LLMs can outperform smaller code‑specialized ones when provided sufficient context. To scale metadata generation for very large KGs, the authors propose a predicate‑coverage‑aware parallel graph sampling strategy that preserves structural diversity, reduces runtime by over 80× on OpenCitations Meta and GESIS, and is the only tractable method for obtaining complete metadata on ORKG.
By Harshdeep Singh, Yurui Zhu, Giovanni Colavizza, Matteo Romanello
LingShu is a large-scale, symptom‑centric knowledge graph that bridges Traditional Chinese Medicine (TCM) and modern biomedicine. It contains 17.33 million entity records and 39.47 million relation records, combining 17.19 million semantic triples with 22.29 million contextualized quadruples to encode conditional medical associations. The graph integrates data from electronic medical records, TCM texts, biomedical ontologies, and curated knowledge bases, and is supported by a web platform offering visualization, reasoning, and evidence‑grounded question answering.
By Rui Hua, Zixin Shu, Kai Chang, Dengying Yan, Jianan Xia, Hui Zhu, Shujie Song, Shurui Yang, Tongxin Wang, Yue Yin, Yu Wei, Lijuan Pei, Yunhui Hu, Hao Xu, Mingzhong Xiao, Xiaodong Li, Haibin Yu, Runshun Zhang, Wenjia Wang, Baoyan Liu, Xuezhong Zhou
EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.
By Chang Zong, Jinyu Chen, Sicheng Lv, Si-tu Xue, Huilin Zheng, Jian Wan, Lei Zhang
arXiv:2607. 12310v1 Announce Type: cross Abstract: While modern question answering (QA) systems excel on clean, schema-aligned corpora, real-world knowledge is rarely so neatly packaged.
By Michael Solodko, Steven Gong, Guangwei Yu, Satya Krishna Gorti, Jesse C. Cresswell, Victor Zhong
arXiv:2604. 25605v2 Announce Type: replace-cross Abstract: Introduction: Semantic search, which retrieves documents based on conceptual similarity rather than keywords, offers advantages for retrieval of clinical information.
By Faith Wavinya Mutinda, Spandana Makeneni, Anna Lin, Shivaji Dutta, Irit R. Rasooly, Patrick Dibussolo, Shivani Kamath Belman, Hessam Shahriari, Kevin Murphy, Alex B. Ruan, Barbara H. Chaiyachati, Sanjay Chainani, Robert W. Grundmeier, Scott M. Haag, Jeffrey M. Miller, Heather M. Griffis, Ian M. Campbell