The Aptamer Database (Final Manuscript)

Introduction and Background:

The Aptamer database is a comprehensive collection of Aptamer related articles of experiments already completed and in the works. This database would be more effective than other search engines such as PubMed, because this database will be focused only on Aptamers and aptamer related experiments which have connections to either therapeutic and diagnostic uses. This project was already begun years ago however due to some extraneous situations was discontinued, so the task that was at hand was basically continuing the database project by collecting and updating research articles, revamping the website and reorganizing the articles that were already found. Along with a fellow colleague from the Aptamer stream the years of interest were divided. Articles from 2009-2010 and

Materials and Methods:

v Laptop with internet connection

v Pre-installed internet browser (ex. Mozilla Firefox, Internet Explorer, etc.)

v Mendeley Desktop (free download—www.mendeley.com)

In order to effectively download a PDF format of the articles a Mendeley account was created with the aptamer stream email and password in order to sync all the articles found to one shared location. The search program Mendeley Desktop was also downloaded in order to effectively import the PDF form of the article once found. Also by doing so, the collection of PDF files could be synced up and other members of the lab could easily upload any articles that fit the criteria of the database. By also using the Mendeley Bookmarklet, incorporating articles was also made possible. However, for these programs to be effective, the pop-up blocker that was already installed in the laptop had to be disabled. The first step was to look into the database and collect more articles that did not already exist in the database. To begin finding primary articles, an analysis of reviews that were provided was done. The tables in the reviews presented a list of selected aptamers with references. With these references, the selections were searched for on pubmed and downloaded into Mendeley. When this was completed, more articles were located including data of people have used aptamers and the original aptamer publication for the particular aptamer were also found. The main goal for the research is the original selections of aptamers.

Progress:

With the task of focusing mainly on the years 2009 and 2010 the search for articles has been quite successful. Currently there are about 112 articles save in the Mendeley library and 50 more articles yet to be uploaded from another saved document. These articles should be completely uploaded by the end of the month. Unfortunately due to some medical circumstances, there were a couple of weeks where the uploaded of articles was kept on hold, however the process of searching for articles still continues.

Future Work

After finding about 500 articles, the next step is to create an up-to-date database which will have all sorts of information that is not immediately apparent by cursory glance. The next step is to transfer literature from Mendeley to the database in probably an XML file of some sort. The articles already found will be imported and organized with an effective organization method which involves restricted field names that limits the input to the criteria set for the database. The database would also be a beneficial tool for those interested in aptamers, or currently doing research or experimentation involving aptamers. For example, the most common selection buffer or the most common 4 nucleotide sequences, or even the most common random region that produces aptamers. This database could also be used as an informative source to determine if a skewed pool or random pool is more beneficial for screening aptamers.

Conclusion:

This project, being one of a kind was quite exciting to work on, however, it requires constant work to download and import the database manually from pubmed. The articles imported so far contains much useful information that will be beneficial for fellow scientists and researchers that are focusing on the production and uses of aptamers both in the therapeutic and diagnostic fields. Therefore, much work is yet to be done to increase the number of sources available in the Mendeley library.