arXiv subjects

Josef Hardi

Publications and source records attributed to Josef Hardi.

7 recordsLinked to original sources

arXiv2026

Automated Standardization of Legacy Biomedical Metadata Using an Ontology-Constrained LLM Agent

Descriptive scientific metadata in public repositories are often incomplete and inconsistent with community standards and ontologies, limiting data FAIRness. Large language models (LLMs) offer a promising approach to automatically standardizing such metadata when provided with relevant standards in machine-actionable form, such as metadata templates from the CEDAR Workbench. Prompt engineering, however, provides only fixed snapshots of these standards and relies on an LLM's pretrained knowledge to interpret and satisfy their constraints. We evaluate whether giving an LLM access to metadata specifications and authoritative terminology at runtime improves automated metadata standardization. Methods: We present ARMS, a tool-augmented LLM agent that retrieves complete CEDAR metadata templates and dynamically queries authoritative biomedical terminology services at execution time. We compared ARMS with a prompt-based approach on 839 legacy metadata records from the Human BioMolecular Atlas Program (HuBMAP), using expert-standardized records as the reference standard. Results: ARMS outperformed the prompt-based approach, increasing precision from 0.56 to 0.93 and recall from 0.51 to 0.85, with improvements across all field categories and assay types. The largest gains occurred for ontology-constrained fields, where precision increased from 0.36 to 0.92. Conclusion: LLMs cannot convert legacy metadata to standards-adherent form without knowledge of the relevant standards. ARMS improves metadata standardization by providing runtime access to authoritative resources that define valid metadata. Machine-actionable metadata standards enhance LLM-based rectification of legacy metadata, especially when they can be queried dynamically.

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arXiv2025

HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues

The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multimodal, multi-scale spatial and single-cell data from healthy human tissues. As of August 2026, the portal hosts 9,316 public datasets from 26 data types spanning 29 organ classes across 501 donors. Portal infrastructure and user interfaces support data search and discovery, visualization, and analysis directly in web browsers. These capabilities include metadata- and data-driven search, collaborative Workspaces with access to high-performance compute, and interactive Vitessce visualizations across non-spatial, 2D, and 3D spatial datasets. Data-type-specific uniform processing pipelines and rigorous quality control processes ensure comparability of results across laboratories, organs, and donors, while externally processed community-contributed datasets provide complementary perspectives. Here we describe portal functionality, infrastructure, and design, and highlight its role as a platform for large-scale spatial single-cell research across diverse data types, organs, and scales.

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arXiv2025

Knowledge engineering for open science: Building and deploying knowledge bases for metadata standards

Scientists strive to make their datasets available in open repositories, with the goal that they be findable, accessible, interoperable, and reusable (FAIR). Although it is hard for most investigators to remember all the guiding principles associated with FAIR data, there is one overarching requirement: The data need to be annotated with rich, discipline-specific, standardized metadata. The Center for Expanded Data Annotation and Retrieval (CEDAR) builds technology that enables scientists to encode metadata standards as templates that enumerate the attributes of different kinds of experiments. These metadata templates capture preferences regarding how data should be described and what a third party needs to know to make sense of the datasets. CEDAR templates describing community metadata preferences have been used to standardize metadata for a variety of scientific consortia. They have been used as the basis for data-annotation systems that acquire metadata through Web forms or through spreadsheets, and they can help correct metadata to ensure adherence to standards. Like the declarative knowledge bases that underpinned intelligent systems decades ago, CEDAR templates capture the knowledge in symbolic form, and they allow that knowledge to be applied in a variety of settings. They provide a mechanism for scientific communities to create shared metadata standards and to encode their preferences for the application of those standards, and for deploying those standards in a range of intelligent systems to promote open science.

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arXiv2024

Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets

Scientists increasingly recognize the importance of providing rich, standards-adherent metadata to describe their experimental results. Despite the availability of sophisticated tools to assist in the process of data annotation, investigators generally seem to prefer to use spreadsheets when supplying metadata, despite the limitations of spreadsheets in ensuring metadata consistency and compliance with formal specifications. In this paper, we describe an end-to-end approach that supports spreadsheet-based entry of metadata, while ensuring rigorous adherence to community-based metadata standards and providing quality control. Our methods employ several key components, including customizable templates that represent metadata standards and that can inform the spreadsheets that investigators use to author metadata, controlled terminologies and ontologies for defining metadata values that can be accessed directly from a spreadsheet, and an interactive Web-based tool that allows users to rapidly identify and fix errors in their spreadsheet-based metadata. We demonstrate how this approach is being deployed in a biomedical consortium known as HuBMAP to define and collect metadata about a wide range of biological assays.

cs.DL↗

arXiv2023

A Comprehensive Approach to Ensuring Quality in Spreadsheet-Based Metadata

While scientists increasingly recognize the importance of metadata in describing their data, spreadsheets remain the preferred tool for supplying this information despite their limitations in ensuring compliance and quality. Various tools have been developed to address these limitations, but they suffer from their own shortcomings, such as steep learning curves and limited customization. In this paper, we describe an end-to-end approach that supports spreadsheet-based entry of metadata while providing rigorous compliance and quality control. Our approach employs several key strategies, including customizable templates for defining metadata, integral support for the use of controlled terminologies when defining these templates, and an interactive Web-based tool that allows users to rapidly identify and fix errors in the spreadsheet-based metadata they supply. We demonstrate how this approach is being deployed in a biomedical consortium to define and collect metadata about scientific experiments.

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arXiv2022

Modeling community standards for metadata as templates makes data FAIR

It is challenging to determine whether datasets are findable, accessible, interoperable, and reusable (FAIR) because the FAIR Guiding Principles refer to highly idiosyncratic criteria regarding the metadata used to annotate datasets. Specifically, the FAIR principles require metadata to be "rich" and to adhere to "domain-relevant" community standards. Scientific communities should be able to define their own machine-actionable templates for metadata that encode these "rich," discipline-specific elements. We have explored this template-based approach in the context of two software systems. One system is the CEDAR Workbench, which investigators use to author new metadata. The other is the FAIRware Workbench, which evaluates the metadata of archived datasets for their adherence to community standards. Benefits accrue when templates for metadata become central elements in an ecosystem of tools to manage online datasets--both because the templates serve as a community reference for what constitutes FAIR data, and because they embody that perspective in a form that can be distributed among a variety of software applications to assist with data stewardship and data sharing.

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arXiv2019

Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases

Metadata-the machine-readable descriptions of the data-are increasingly seen as crucial for describing the vast array of biomedical datasets that are currently being deposited in public repositories. While most public repositories have firm requirements that metadata must accompany submitted datasets, the quality of those metadata is generally very poor. A key problem is that the typical metadata acquisition process is onerous and time consuming, with little interactive guidance or assistance provided to users. Secondary problems include the lack of validation and sparse use of standardized terms or ontologies when authoring metadata. There is a pressing need for improvements to the metadata acquisition process that will help users to enter metadata quickly and accurately. In this paper we outline a recommendation system for metadata that aims to address this challenge. Our approach uses association rule mining to uncover hidden associations among metadata values and to represent them in the form of association rules. These rules are then used to present users with real-time recommendations when authoring metadata. The novelties of our method are that it is able to combine analyses of metadata from multiple repositories when generating recommendations and can enhance those recommendations by aligning them with ontology terms. We implemented our approach as a service integrated into the CEDAR Workbench metadata authoring platform, and evaluated it using metadata from two public biomedical repositories: US-based National Center for Biotechnology Information (NCBI) BioSample and European Bioinformatics Institute (EBI) BioSamples. The results show that our approach is able to use analyses of previous entered metadata coupled with ontology-based mappings to present users with accurate recommendations when authoring metadata.

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