arXiv subjects

Sierra Moxon

Publications and source records attributed to Sierra Moxon.

5 recordsLinked to original sources

arXiv2026

Agents for Everyone: A Workshop Framework for Building Agentic AI Capabilities in a Distributed Curation Community

Agentic AI has the potential to accelerate curation of biological databases and knowledge bases. However, uptake has been hindered by a number of challenges and obstacles, including access to agents and appropriate training. Here we describe how we have attempted to address and mitigate these challenges and obstacles through the deployment of a cloud-based agentic environment, and the development of an interactive training workshop for the Gene Ontology Consortium. Our cloud environment for agentic-assisted curation was based on the JupyterHub platform, and utilized Claude Code as a universal harness. This allows curators to interact with an agent session through a terminal running in the browser, and has additional benefits such as centralization of access through a single API gateway, removing the need for participants to manage subscriptions or install software locally. We created four training modules, walking participants through basic agentic tool use first and then working up to agentic biological pathway curation using the existing GO-CAM (GO Causal Activity Model) curation tool. Thirty-seven participants took part in the four-hour workshop. Our key takeaway from this workshop is that building community capability with agentic AI is primarily a problem of access, workflow design, and training. Removing technical barriers, introducing capabilities gradually, grounding exercises in familiar curation tasks, and giving curators direct experience evaluating agent output can provide a practical route toward building shared agentic AI capability in distributed scientific communities.

cs.AI↗

arXiv2025

Why we need all the organisms: an exploration of the Monarch knowledge graph to aid mechanism discovery

Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for experiments to enhance understanding of biological mechanisms conserved across the evolutionary tree. Decades of model organism research has generated vast amounts of data; however, this data is split across many domains, organisms, and biological fields of research. Knowledge graphs (KGs) are a computational way to aggregate and compile disparate information in a parsable format. By unifying data across studies, organisms and time points, KG researchers can create novel targeted hypotheses. Here we demonstrate how model organisms are connected to humans and other organisms through genes, diseases and phenotypes allowing for a broader understanding of genetic biology than just one organism alone can provide. Utilizing resources such as the Monarch KG is a great way to reduce redundant experiments and find directions previously unexplored.

q-bio.QM↗

arXiv2023

MapperGPT: Large Language Models for Linking and Mapping Entities

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is the process of determining correspondences between entities across these resources, such as gene identifiers, disease concepts, or chemical entity identifiers. Many tools have been developed to compute such mappings based on common structural features and lexical information such as labels and synonyms. Lexical approaches in particular often provide very high recall, but low precision, due to lexical ambiguity. As a consequence of this, mapping efforts often resort to a labor intensive manual mapping refinement through a human curator. Large Language Models (LLMs), such as the ones employed by ChatGPT, have generalizable abilities to perform a wide range of tasks, including question-answering and information extraction. Here we present MapperGPT, an approach that uses LLMs to review and refine mapping relationships as a post-processing step, in concert with existing high-recall methods that are based on lexical and structural heuristics. We evaluated MapperGPT on a series of alignment tasks from different domains, including anatomy, developmental biology, and renal diseases. We devised a collection of tasks that are designed to be particularly challenging for lexical methods. We show that when used in combination with high-recall methods, MapperGPT can provide a substantial improvement in accuracy, beating state-of-the-art (SOTA) methods such as LogMap.

cs.CL↗

arXiv2022

Recommendations for extending the GFF3 specification for improved interoperability of genomic data

The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing re-use of annotation data, this flexibility has become an obstacle for standardized downstream processing. Common software packages that export annotations in GFF3 format model the same data and metadata in different notations, which puts the burden on end-users to interpret the data model. The AgBioData consortium is a group of genomics, genetics and breeding databases and partners working towards shared practices and standards. Providing concrete guidelines for generating GFF3, and creating a standard representation of the most common biological data types would provide a major increase in efficiency for AgBioData databases and the genomics research community that use the GFF3 format in their daily operations. The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome further discussion of these recommendations. We request the genomics and bioinformatics community to utilize the github repository (https://github.com/NAL-i5K/AgBioData_GFF3_recommendation) to provide feedback via issues or pull requests.

q-bio.OT↗

arXiv2021

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Are they associated in some other way? Such relationships between the mapped terms are often not documented, leading to incorrect assumptions and making them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Also, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. The Simple Standard for Sharing Ontological Mappings (SSSOM) addresses these problems by: 1. Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. 2. Defining an easy to use table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data standards. 3. Implementing open and community-driven collaborative workflows designed to evolve the standard continuously to address changing requirements and mapping practices. 4. Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases, and survey some existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable, and Reusable (FAIR). The SSSOM specification is at http://w3id.org/sssom/spec.

cs.DB↗