Biology subjects

Lopez Gomez, F.

Publications and source records attributed to Lopez Gomez, F..

3 recordsLinked to original sources

bioRxiv2026

AI semantics for biomedical data integration

Researchers increasingly need to explore hypotheses that span multimodal data across different scales, organisms, and domains. In practice, this requires connecting knowledge across fragmented databases with incompatible APIs and heterogeneous annotation practices. Large language model (LLM) agents can automate this data integration process, but grounding LLM agent outputs in scientifically correct sources of truth remains a significant challenge. Here we describe our deployment of a novel AI semantics workflow using LLM agents to enable scalable data integration, grounded in biological knowledge in the form of ontologies. Our workflow comprises (1) a multi-agent system curating scientific knowledge across ontologies using the Ontology Lookup Service (OLS) as grounding; (2) an LLM embedding service to enable interoperability between scientific databases by mapping ontology terms; and (3) GrEBI, a knowledge graph and Model Context Protocol (MCP) server enabling LLM agents to conduct cross-cutting, multi-omic biomedical queries.

bioinformatics↗

bioRxiv2025

International Mouse Phenotyping Consortium: Investigating gene function and providing insights into human disease.

The International Mouse Phenotyping Consortium (IMPC; https://www.mousephenotype.org/) web portal contains phenotype data for mouse protein-coding genes derived from analysis of data obtained in a systematic and high-throughput fashion from knock-out lines produced by IMPC. The project has produced >1,400 mouse models of human disease that recapitulate phenotypes observed in patients. Over 8000 papers rely on data or reagents generated by IMPC, demonstrating the impact of the project on the research and clinical communities, and IMPC data is incorporated into other resources, such as MGI, Open Targets and UniProt. Data release (DR23.0, 2025) contains > 100 million data points from 9,277 genes and identified 113,803 significant phenotypes. To manage efficient access to this quantity of high dimensional data the IMPC web portal has been rebuilt using a cloud native architecture. The modern user interface retains the look and feel of the original portal with improvements identified through a usability study. New data visualisation and training materials for large scale data access through the API have also been developed to make the resource easier to use. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/681205v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@199243borg.highwire.dtl.DTLVardef@119c12forg.highwire.dtl.DTLVardef@1da1a27org.highwire.dtl.DTLVardef@1eb141d_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

Establishing Comprehensive Transthoracic Echocardiography Reference Ranges for Mouse Models: Insights into the Impact of Anesthesia, Sex, and Age

Mouse models play a critical role in cardiology research, offering valuable insights into the molecular mechanisms, genetics, and potential treatments for cardiovascular diseases. However, the ability to transfer findings in mice between studies is limited by the absence of standardized protocols and valid reference values for the assessment of normal cardiac function in mice. This study aims to establish comprehensive transthoracic echocardiography (TTE) reference ranges for mice, particularly focusing on C57BL/6N wildtype controls. The study, which includes data from over 15,000 mice through the International Mouse Phenotyping Consortium (IMPC), highlights how variables such as sex, age, body weight, and anesthesia affect TTE parameters. The findings showed that anesthesia is the primary predictor of variability in cardiac function. Isoflurane and tribromoethanol anesthetized mice presented with modified cardiac function compared to conscious mice. Additionally, we observed minimal sex differences in cardiac morphology and function, except for small variations influenced by anesthesia. The effects of aging on cardiac function were modest, characterized by a decrease in heart rate and subtle changes in ventricular dimensions without evidence of pathological remodeling, likely attributable to disease-free cardiovascular aging. Validation of the reference ranges across multiple mouse strains showed that these values provide a reliable baseline for experiments involving cardiac function in mice. The data underscore the importance of using anesthesia-specific reference values when interpreting TTE results, ensuring robust comparisons in genetic and pharmacological studies. These reference ranges serve as quality assurance tools for future cardiac studies in mice, offering insights into typical TTE parameter values, supporting the detection of experimental perturbations, and contributing to more effective translation of findings from mouse to human.

genetics↗