Embedded Files
At Maptamer.org, we are dedicated to creating a comprehensive and permanent database of aptamers for use in biomedical and bioengineering projects. This database should include a list of molecules, cells, and tissues that have publicly-available aptamers, and references for these aptamers can be in the form of patents, catalogs, and private correspondence.
You can contribute to this effort by adding new aptamers, removing duplicates, updating references with DOI URLs where possible, adding common target names and species, and correcting any typos. By promoting Maptamer.org on your lab, company, or institution website and through social media, we can make this database more visible and accessible to the global research community and industry. The more support we receive, the more valuable Maptamer.org will become as a hub for aptamer-based research.
A draft of the Aptamer List (V2) is now available as a static download!
The original, community-editable Aptamer List V1 is still available below.
How to open the file
This can be opened easily in Google Sheets. If opening as a .csv, use tab-delimited cells and double-quotation marks (") as the string delimiter to ensure it displays correctly.
Maptamer.org now hosts about 3,500 aptamer targets, more than triple our previous record!
Here, we scraped all "aptamer"-keyword papers from Scopus on 4 April 2023, identified the targets in the abstracts using validated ChatGPT target calling techniques and traditional natural language processing, and clustered them into natural groups, finding 3,638 non-generic clusters.
Ideally, each cluster should represent either a unique single specific chemical or cellular target, or a natural grouping of such targets. Examples include "MS2 phage coat protein", "CD28", and "Tumor necrosis factor alpha (TNF-α)." In practice, there may in some cases be more than one cluster per target, or more than one target per cluster. Occasionally, some clusters incorporate distinct targets that have very names, such as "Vaspin" and "Vasopressin." Despite these challenges, we expect this list will be useful in its current form and can be refined over time.
High-throughput, validated ChatGPT-based text mining for high accuracy target calls
Most target calls have not been manually validated for accuracy, but instead, the text processing and clustering techniques have been manually validated and shown to have a high degree of specificity, such that papers grouped in clusters should reliably be correctly associated with their target.
The Aptamer List (V1) contains nearly 1,000 aptamers as of 13 April 2023, and was already by far the largest list of aptamer targets online. The problem of duplicates aside, this new updated list likely represents a tripling of the number of aptamer targets, using our finding of 3,638 unique target clusters as an approximation for the true number of targets.
Planned improvements include solving the duplicates problem, further validation of clustering accuracy, scraping targets from paper bodies and patents, adding additional target aliases, grouping targets according to molecular or tissue type and disease or commercial relevance, bibliometric analysis, and ultimately an open-source release of the entire informatics pipeline we are using to process this information on github. The new version will be made community-editable by 30 April 2023.
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