The Aptamer Database

As a potential off bench project, I mentioned updating the aptamer database. The original publication should be read first to figure out what the database is all about. It hasn't been updated in nearly 4 years and is missing a wealth of current journals. A former member of the Aptamer Stream began updating it, but did not send me her final product and I've lost contact with her, so I guess we should start over again. Aptamer literature is fairly easy to search for on PubMed, but much more difficult to find exactly what you are looking for so having a database of all things aptamer is useful.

For an idea of what we can do with an up-to-date database, check out this article. Basically, we can mine the database for all sorts of information that isn't readily apparent by cursory glance. For instance, we could tell what the most common selection buffer is, or we could look for the most common 4 nucleotide sequence or the most common random region that produces aptamers. We could also find out if a skewed pool or random pool is more beneficial for screening aptamers.

Any of you can begin this project at any time. The first step is to get articles that aren't in the database. To begin finding primary articles, I would first suggest looking at a few of the reviews I've given you. In them are tables of selected aptamers with references. Look up those selections on pubmed and download the articles into Mendeley. Then you should find articles where people have used aptamers and find out the original aptamer publication for the particular aptamer. We are interested in the original selections of aptamers. The database does not include reviews, applications, patents etc. We may look to add these in the future. If you are off campus, you must append the following proxy address before the article: thus an article from NAR for instance would be:

I have created a Mendeley account for this purpose. Download Mendeley Desktop and use the account with the room number as the password. This way, we can keep the collection of pdf files synced up. It is easy to incorporate articles you find in the web using the Mendeley Bookmarklet. Just remember you have to be signed in and turn off your popup blocker for these sites. Then within Mendeley desktop if you double click the article it will download the PDF. I'm not a fan of Mendeley for PDF organization though after using for Mac. In searching, a similar option is available for Windows called "I, Librarian". Haven't used or installed, but it seems cross platform and merges the best of Papers with the online collaboration of Mendeley. Sound off in the comments if you like I, Librarian.

Every time you go into Mendeley, sync with the server and then start searching for new stuffs. The sycn makes sure that anyone working on this project will have the most up to date links possible.

As for the database itself, you can and and modify citations from the website directly with the proper credentials. The database is set up like figure 1. Alternatively, we can grant you special access to the sandbox database through MySQL Admin, a graphical front end will be installed through phpMyAdmin, a graphical front end like MS Access that interfaces with the actual database and runs on your computer.
I have also created a webform in Google that allows you to add effectively add information for curation later.
Figure 1. Database table layout

If you find that the information should be displayed differently or that more information should be included, then feel free to tell me. For instance, there is another aptamer database called RiboaptDB and discussed in in this PDF. You may find they do things better or different than we do. Whereas they copied a lot from us, we may find they have implemented information searching or viewing slightly different that makes it easier to use. We can certainly re implement our site better or completely differently so please be aware.

You should also learn a bit about database setup. The aptamer database is hosted from MySQL on a linux virtual machine in the Ellington Lab. You should probably understand a bit about relational databased such as MySQL, so here is a nice tutorial from I have a complete copy of the database that can be imported into Microsoft Access if you want to play around with your own ways of adding information (i.e. making a new form or something).

Lastly, the project should include some type of website redesign and database input redesign. Using mendeley you should realize that Mendeley uses a database in the back end. If we can create some type of "referenced input" such as BibTeX or RIS format, we wouldn't have to input all the citation information manually. Additionally, if you know web programming (or know of someone who does) and want to try your hand at redesigning the site, please let me know. You could even interface it with some of the blogs or content management systems that are available if you know how to program PHP code. I can get you started on a scratch site to play around with before changes are moved over to the real site.

  1. Find new literature - Articles detailing the original selection of aptamer binding species. You can also include different techniques, reviews or applications/uses of that aptamer in therapeutic/diagnostic capacity, but separate those into different folders in Medeley. We just want the aptamer sequence for now and the conditions it was selected under.
  2. Input all literature into Mendeley - You should label/organize into original selections, other catagories. We don't care much about the potential application for now. We also don't care much about
  3. Transfer literature from Mendeley to Database - probably an XML file of some sort.
  4. Add sequence information into database
  5. Redesign input method
  6. Redesign website
  7. Do cool things with the data


Adaobi Anyiwo said...

Thanks Brad for the info...I've already saved some articles from PubMed and downloaded Mendeley Desktop. Like you said, the instructions are quite easy to follow. I plan to read more on the MySQL tutorial

Jason said...

Hey can the database be altered so you can search by sequence, so to compare sequence motifs?

Brad Hall said...


Maybe. It is certainly something that would help, good thinking! The correct answer is yes, of course, but would take some programming to get right. Especially for motif searching because that would require some RegEx knowledge and likely an interface so you don't have to remember the backend RegEx language.

Do you know PHP/MySQL? Wanna help rewriting the pages in Ruby with a better interface?

Jason said...

Hey Brad,

Sorry i am only just starting to learn Python. But i did learn about a recently built database

Seems like they got a pretty good head start with programming

Brad Hall said...

Good find Jason! The site seems interesting and would prevent much of the programming to get something like this started. they don't have a lot of aptamers linked Ted, but well on their way. And a much different layout/concept than I was thinking.