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Sabrina Toro

Publications and source records attributed to Sabrina Toro.

5 recordsLinked to original sources

Engaging the scientific community in high-quality biocuration: a report on the International Society for Biocuration workshop, 'Maximizing community curation for the benefit of all'

Biological knowledgebases traditionally rely on expert, professional curation of the research literature to maintain up-to-date collections of data organized in machine-readable form. However, despite the increasing amount of curatable biomedical knowledge, support for knowledgebases is declining, leaving these resources no alternative but to explore additional ways of updating and maintaining content. One way in which knowledgebases have addressed this problem is by engaging researchers to help curate their published papers, a process generally known as 'community curation'. As helpful as community curation can be, though, it is not universally adopted and, for groups that do have it, there is a wide range of approaches. To learn about existing community curation pipelines and explore possibilities for working towards a common approach, we organized a workshop, Maximizing Community Curation for the Benefit of All, at the 18th International Biocuration Conference, hosted by the Stowers Institute for Medical Research. Our aim was to examine the different strategies that groups use, share successes, failures, and ongoing challenges, and produce suggested deliverables for broader adoption of common best practices and tools for effective community curation. Representatives from 18 different resources, ranging from model organism and specialty knowledgebases to journals and literature resources, presented their work. The result was a comprehensive assessment of the state-of-the-art for community curation and an in-depth discussion on how community curation can become standard practice for maintaining timely, highquality biological resources that will continue to provide scientists with the essential information they need for their research.

cs.DB

The Cell Ontology in the age of single-cell omics

Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks for data integration and annotation. The Cell Ontology (CL) has emerged as a pivotal resource for achieving FAIR (Findable, Accessible, Interoperable, and Reusable) data principles by providing standardized, species-agnostic terms for canonical cell types - forming a core component of a wide range of platforms and tools. In this paper, we describe the wide variety of uses of CL in these platforms and tools and detail ongoing work to improve and extend CL content including the addition of transcriptomic types, working closely with major atlasing efforts including the Human Cell Atlas and the Brain Initiative Cell Atlas Network to support their needs. We cover the challenges and future plans for harmonising classical and transcriptomic cell type definitions, integrating markers and using Large Language Models (LLMs) to improve content and efficiency of CL workflows.

q-bio.OT

The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization

Background: Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support advancement in diagnostics, treatments, and precision medicine. Objectives: A single, coherent, logic-based standard for documenting breed names in health, production, and research-related records will improve data use capabilities in veterinary and comparative medicine. Methods: The Vertebrate Breed Ontology (VBO) was created from breed names and related information compiled from the Food and Agriculture Organization of the United Nations, breed registries, communities, and experts, using manual and computational approaches. Each breed is represented by a VBO term that includes breed information and provenance as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence-readiness. Results: VBO is an open, community-driven ontology representing over 19,500 livestock and companion animal breed concepts covering 49 species. Breeds are classified based on community and expert conventions (e.g., cattle breed) and supported by relations to the breed's genus and species indicated by National Center for Biotechnology Information (NCBI) Taxonomy terms. Relationships between VBO terms (e.g., relating breeds to their foundation stock) provide additional context to support advanced data analytics. VBO term metadata includes synonyms, breed identifiers/codes, and attributed cross-references to other databases. Conclusion and clinical importance: The adoption of VBO as a source of standard breed names in databases and veterinary electronic health records can enhance veterinary data interoperability and computability.

q-bio.OT

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

Background: Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources and necessitate substantial collaboration between domain experts, curators, and ontology experts. We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). DRAGON-AI can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies and unstructured text sources. Results: We assessed performance of DRAGON-AI on de novo term construction across ten diverse ontologies, making use of extensive manual evaluation of results. Our method has high precision for relationship generation, but has slightly lower precision than from logic-based reasoning. Our method is also able to generate definitions deemed acceptable by expert evaluators, but these scored worse than human-authored definitions. Notably, evaluators with the highest level of confidence in a domain were better able to discern flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues. Conclusions: These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.

cs.AI

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies

Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse set of tools is required, from command line utilities to powerful ontology engineering environments such as ROBOT. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardising release practices and metadata, and establishing shared quality standards, are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardised, customisable, and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice, and describe how we envision it driving standardisation efforts in our community.

cs.DB