5 Reasons Not to Use GEO Datasets

Shrushti Joshi
June 26, 2023

Gene Expression Omnibus (GEO) is one of the largest open-source repositories. It is a valuable resource for various data applications. This includes exploring gene expression studies, genome methylation, chromatin structure, and genome-protein interactions. Moreover, GEO is a platform that facilitates researchers and scientists working in these fields by providing them with relevant and readily available data.

Datasets in GEO are not standardized, making them hard to use for experiments. The query search and data downloadability are tedious and complex in nature. When considering the utilization of GEO datasets for research purposes, it's crucial to acknowledge the limitations.

Here is a quick read that can help you with it. By understanding these limitations, researchers can make informed decisions about the suitability and applicability of GEO datasets to their specific research objectives.

Here are Five Reasons:

  1. Data Quality and Reliability Concerns: The quality and reliability of the data in GEO datasets can vary significantly. While efforts are made to ensure data accuracy, inconsistencies, errors, or biases may still exist. Relying on datasets with questionable quality can lead to unreliable or misleading results.
  2. Lack of Experimental Control: GEO datasets primarily comprise data from experiments conducted by different researchers or research groups. The lack of control over the experimental design, protocols, or conditions introduces confounding factors. The data is difficult to download as the annotation on which set refers to which state is missing. This creates a load on the user to download each and every dataset and cross-verify the sets.
  3. Limited Data Availability: Not all research questions or domains may have relevant or sufficient data in GEO datasets. The existing datasets may not be accurately labeled and stored, leading to mining issues. This creates gaps in dataset availability.
  4. Lack of Contextual Information: GEO datasets often provide limited contextual information about the samples or experiments. Essential details such as demographic characteristics, clinical history, treatment protocols, or other relevant variables may be missing or insufficiently documented. This can hinder the interpretation and analysis of the data, making it challenging to draw robust conclusions.
  5. Complex Query Syntax and Ambiguity in Terms: Constructing queries in GEO often requires familiarity with the platform’s syntax or language. The syntax can be complicated, and researchers not well-versed in it may struggle to express their search criteria accurately. This leads to difficulties in retrieving the desired data.  Similarly, the search terms or keywords used in the query can significantly impact the results obtained. However, ambiguous or imprecise query terms may yield irrelevant or incomplete results, making finding the desired datasets or information within GEO challenging.

How Polly Helps Use GEO Datasets Better?

GEO primarily focuses on providing access to gene expression datasets. Polly by Elucidata offers a broader range of functionalities for multi-omics data analysis.

Polly has close to 50,000 Bulk and Single Cell Datasets that are ingested from GEO on a weekly basis and transformed into a clean structured and usable format. It curates both public and proprietary biomedical data into a F.A.I.R (Findable, Accessible, Interoperable, Reusable) resource, leveraging Bio-NLP technology that cleans and links data with unprecedented speed and accuracy. This makes data more findable and analysis-ready.

Polly overcomes the limitations of GEO datasets in the following ways-

  1. Sample Diversity Assessment: Polly offers tools for researchers to assess the representativeness of GEO datasets by analyzing sample characteristics, demographics, and experimental conditions. Researchers can gain insights into the suitability of the data for their specific research questions and determine if additional data collection or alternative sources are necessary.
  2. Quality Control and Assurance: GEO datasets undergo a rigorous quality check before it is made available to users on Polly. The curation process ensures that all data and metadata associated with the dataset are available and complete. Researchers can leverage data quality metrics, visualization tools, and statistical analyses to identify and mitigate potential issues related to inconsistencies, errors, or biases. This helps ensure that reliable and trustworthy data are used for analysis.
  3. Simplified Query Construction: Polly provides an intuitive interface that simplifies the process of constructing queries. Researchers can leverage user-friendly tools and workflows, reducing the complexity of query syntax and facilitating accurate search results.
  4. Advanced Query Options: Polly expands the query options beyond the limitations of GEO's interface. It supports advanced filtering, complex Boolean operations, and customized queries, empowering scientists to precisely define their search criteria and retrieve the most relevant datasets for their research questions.
  5. Reliable Performance: Polly is built to deliver reliable performance, minimizing technical challenges during query execution. It offers efficient response times, minimizing delays and errors researchers may encounter when using the GEO platform, ensuring a smooth and uninterrupted research experience.

Using Polly, researchers can fully leverage the wealth of data contained in big data repositories such as GEO. You can focus on insight derivation via data analysis and visualization instead of data wrangling and engineering. Incorporating Polly into your existing data infrastructure and analysis/visualization is pretty straightforward.

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