Evaluating biomedical data production with text mining

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Estimating biomedical data

Evaluating the impact of a scientific study is a difficult and controversial task. Recognition of the value of a biomedical study is widely measured by traditional bibliographic metrics such as the number of citations of the paper and the impact factor of the journal.

However a more relevant critical success criteria for a research study likely lies in the production itself of biological data, both in terms of quality and also how these datasets can be reused to validate (or reject!) hypotheses and support new research projects. Although biological data can be deposited in specific repositories such as the GEO database, ImmPort, ENA, etc., most data are primarily disseminated in articles within the text, figures and tables. This raises the question – how can we find and measure the production of biomedical data diffused in scientific publications?

To address this issue, Gabriel Rosenfeld and Dawei Lin developed a novel text-mining strategy that identifies articles producing biological data. They published their method “Estimating the scale of biomedical data generation using text mining” this month on BioRxiv.

Text mining analysis of biomedical research articles

Using the Global Vector for Word Representation (GloVe) algorithm, the authors identified term usage signatures for 5 types of biomedical data: flow cytometry, immunoassays, genomic microarray, microscopy, and high-throughput sequencing.

They then analyzed the free text of 129,918 PLOS articles published between 2013 and 2016. What they found was that nearly half of them (59,543) generated 1 or more of the 5 data types tested, producing 81,407 data sets.

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Estimating PLOS articles generating each biomedical data type over time (from “Estimating the scale of biomedical data generation using text mining“, BioRxiv).

This text-mining method was tested on manually annotated articles, and provided a valuable balance of precision and recall. The obvious next  – and exciting – step is to apply this approach to evaluate the amount and types of data generated within the entire PubMed repository of articles.

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Estimating PLOS articles generating each biomedical data type over time (from “Estimating the scale of biomedical data generation using text mining“, BioRxiv).

A step beyond data dissemination

Evaluating the exponentially growing amount and diversity of datasets is currently a key aspect of determining the quality of a biomedical study. However in today’s era of bioinformatics, in order to fully exploit the data we need to take this a step beyond the publication and dissemination of datasets and tools, towards the critical parameter of improving data reproducibility and transparency (data provenance, collection, transformation, computational analysis methods, etc.).

Open-access and community-driven projects such as the online bioinformatics tools platform OMICtools, provide access not only to a large number of repositories to locate valuable datasets, but also to the best software tools for re-analyzing and exploiting the full potential of these datasets.

In a virtual circle of discovery, previously generated datasets could be repurposed for new data production, interactive visualization, machine learning and artificial intelligence enhancement, allowing us to answer new biomedical questions.

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