OLCC Project 4: Acid-Base Equilibrium

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Ben Brown (not verified) | Fri, 11/27/2015 - 20:54
I'm working on my project with Java and I was having trouble finding ways to incorporate the database I want into my code. I can figure out how to generate the right inputs, but I'm confused as to how I query the database in the first place. The modules we learned about used Javascript, but not Java. How might I go about coding in functionality that lets me access databases?

Ben Brown (not verified) | Sun, 11/29/2015 - 18:55
In module eight, we learned how to format URLs for sites like PubChem in order to look up specific pieces of information about a compound. For my project I need to look up dissociation constants online in order to use in my program. As it stands right now, I'm having to use a less robust database to search for dissociation constants. I would like to use PubChem for this search, but I don't know how to format the URL to access that information. The compounds have dissociation constants on the PubChem page, but I don't know how to access it via the PUG REST interface.

Sunghwan Kim | Tue, 12/01/2015 - 11:47
Hi, Ben, PUG-REST does not support programmatic access to pKa or pKb values. Instead, you need to use another protocol called PUG-REST-View, which allow you to access all data presented in the Compound Summary page for a particular compound. For example, the Compound Summary page of CID 91757643 can be accessed via the URL: <a href="https://pubchem.ncbi.nlm.nih.gov/compound/91757643">https://pubchem.ncbi.nlm.nih.gov/compound/91757643</a> And all the data presented in this Compound Summary page can be programatically accessed via the PUG-REST-View: <a href="https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON">https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON</a> Note that this PUG-REST-View request will give you *ALL* information on the Summary page, so you need to write a short program to extract dissociation constants from the downloaded data. Does you or your colleague have basic programming knowledge?

Sunghwan Kim | Tue, 12/01/2015 - 11:56
In my previous message, I happened to use the URL beginning with "<a href="https://testpubchem">https://testpubchem</a>..." (not "<a href="https://pubchem">https://pubchem</a>..."), which is for our test server. I've fixed the URL (in the previous message) to the correct one. By the way, you can actually download a "part" of the data displayed on the Compound Summary page through the PUG-REST-View (also called PUG-View), by suffixing the URL with an optional parameter for a particular section. For example, <a href="https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON?heading=Dissociation%20Constants">https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/91757643/JSON?heading=Dissociation%20Constants</a> This will allow you to download the "Dissociation Constants" part of the data, but you still need to parse the data.