Current challenges in microbiome metadata collection

Rosenfeld, Gabriel; Angelova, Angelina; Shin, Chris; Quiñones, Mariam; Hurt, Darrell E.

doi:10.1101/2021.05.05.442781

Cited by 2 publications

(2 citation statements)

References 16 publications

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“…During metadata collection, we encountered difficulties in locating African metadata in public repositories, even with advanced query keywords, prompting us to extend data searches through the literature. This is probably due to the inadequate annotation and erroneous terms in the public repositories, as stated previously ( 39 , 40 ). Furthermore, a major investment was required to complete and harmonize the information before integration in the AHMP.…”

Section: Discussionmentioning

confidence: 87%

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The African Human Microbiome Portal: a public web portal of curated metagenomic metadata

Kiran,

Hanachi,

Alsayed

et al. 2024

Database

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There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user’s applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.

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Section: Discussionmentioning

confidence: 87%

“…Rosenfeld et al. ( 40 ) reported the predominance of missing information, particularly regarding the age, ethnic group and gender of the participants. This is pertinent when it deals with metadata related to the African populations, which represent different genetic, geographical and environmental backgrounds.…”

Section: Discussionmentioning

confidence: 99%

The African Human Microbiome Portal: a public web portal of curated metagenomic metadata

Kiran,

Hanachi,

Alsayed

et al. 2024

Database

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Automated Harmonization and Large-Scale Integration of Heterogeneous Biomedical Sample Metadata Using Large Language Models

Higashi,

Nakagawa,

Yamada

et al. 2024

Preprint

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The exponential growth of biomedical data has created an urgent need for efficient integration and analysis of heterogeneous sample metadata across studies. However, current methods for harmonizing and standardizing these metadata are largely manual, time-consuming, and prone to inconsistencies. Here, we present a novel computational framework that leverages large language models (LLMs) to automate the harmonization and large-scale integration of diverse biomedical sample metadata. Our approach combines semantic clustering techniques with LLM-driven natural language processing to extract, interpret, and standardize metadata from various sources, including research papers, supplementary tables, and text data from public databases. We demonstrate the efficacy of our framework by applying it to thousands of human gut microbiome papers, successfully extracting and integrating metadata from over 400,000 samples. Our method achieved a 50% recovery rate of manually curated metadata, significantly outperforming traditional rule-based methods. Furthermore, our framework enabled the creation of a unified, searchable database of standardized metadata, facilitating cross-study analyses and revealing previously obscured patterns in microbiome composition across diverse populations and conditions. The scalability and adaptability of our approach suggest its potential applicability to a wide range of biomedical fields, potentially accelerating meta-analyses and fostering new insights from existing data. This work represents a significant advancement in biomedical data integration, offering a powerful tool for researchers to unlock the full potential of accumulated scientific knowledge.

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Current challenges in microbiome metadata collection

Cited by 2 publications

References 16 publications

The African Human Microbiome Portal: a public web portal of curated metagenomic metadata

The African Human Microbiome Portal: a public web portal of curated metagenomic metadata

Automated Harmonization and Large-Scale Integration of Heterogeneous Biomedical Sample Metadata Using Large Language Models

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