arXiv:2608. 12529v1 Announce Type: cross Abstract: Motivation: LinkML is a suitable language for the representation of the structural and content constraints of different kinds of biomedical data.
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.
arXiv:2606. 07094v1 Announce Type: cross Abstract: Scientific workflows increasingly generate structured JSON data that is easy to exchange but difficult to interpret consistently across systems due to lacking semantic interoperability.
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.
arXiv:2607. 24512v1 Announce Type: new Abstract: Mathematical models are central to formalizing research problems, yet their documentation often falls short of FAIR principles.
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.
The paper introduces an end‑to‑end pipeline that harvests, validates, and models links between scholarly articles and their source code from journals such as JOSS, SoftwareX, and IPOL, as well as SIGMOD ARI reproducibility reports. It produces a curated set of 4,397 DOI‑repository pairs and defines two Wikidata‑based application profiles—one for articles and one for software—aligned with schema.org and CodeMeta. Using these profiles, the authors created 4,182 new Wikidata software items linked to their papers, while only 82 repositories were previously represented, and they demonstrate compatibility with the COAR Notify protocol for future live enrichment.
arXiv:2606. 05415v1 Announce Type: cross Abstract: Real-world data spans tables, documents, and semi-structured files with implicit semantics.
arXiv:2607. 11464v1 Announce Type: cross Abstract: Retrieval-Augmented Generation (RAG) addresses the limitations of Large Language Models (LLMs) when providing responses to domain-specific questions.
arXiv:2607. 21610v1 Announce Type: cross Abstract: Schema graphs are an upstream bottleneck of schema-grounded information extraction and knowledge graph construction, yet most extraction systems assume the schema is already available.
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.
arXiv:2607. 29677v1 Announce Type: new Abstract: Enterprise workflows increasingly rely on agents for \emph{schema-guided extraction}: given a document and a user-defined schema, the agent faithfully follows the schema to produce the correct output with source evidence as grounding metadata.
arXiv:2604. 03496v2 Announce Type: replace Abstract: Knowledge graph generation typically relies either on predefined ontologies or on schema-free extraction.