Discussion

Olcc S10 | Tue, 04/11/2017 - 15:20
My name is Emily Choate. I am a graduate student at University of Arkansas at Little Rock. I would like to work on this project. I have some minor skills with Excel and Sheets. Emily

Olcc S14 | Tue, 04/11/2017 - 15:06
I try to search Quat 188 and able find some of the data. In my search, it shows 6 bioactivities. When I clicked on it, it showed 6 hits of pharmacological data. In this section, I saw 1 of 6....., in a comment, there is reference only. So how can I know what type of bioactivity are there in quat-188? (use Reaxys for the search) Looking for your help. Thank you

Tanya Gupta | Tue, 04/11/2017 - 12:36
S04 has some very good ideas, but he was a bit disappointed. He is exploring a different project now. We need to remember that a lot of our students are new to this area. They are interested in Cheminformatics and want to learn while engaging in guided-project experiences. They will need help and guidance to develop and execute their ideas related to the project. This has been my understanding of student projects all along that students will propose an idea for a project topic and receive guidance for completing the project successfully.

Damon Ridley's picture
Damon Ridley | Tue, 04/11/2017 - 00:00
Lyndsie How would you search the topic on Google? Why don't you go ahead and do what you normally would do on Google (keep it simple, don't do anything 'complicated') and then perhaps summarise the information you get on the first two pages. Don't spend too much time on this - say no more than a few seconds on Google and then perhaps no more than 20 minutes to look through the first two pages of answers and summarise them. Since probably you don't want to record all your 'workings' on the OLCC website, then I suggest you get back to me by email (Professor Belford will give you my email address) and let me know what you did. Once I hear back from you then I'll confirm that you can go to the next step - in Reaxys, although if you are keen to try something then login to Reaxys and in the (text) search box that appears simply enter the exact same text that you did in Google and click Search. You should come to a screen of options and I'd suggest you click View Results for each of the first two and then 'play around a little' - meaning click 'Hit Data' for substances, and view a couple of the Document Records in full (that is, Title/Abstract/Index Terms). Think carefully about what you see. If you have gone to this second stage, you can include a few preliminary thoughts in the email to me. Damon PS Note that I am presently in Sydney - 15 hours ahead of you, so there could be some delay before I reply to your email if I receive it 'out of hours' (my time).

Damon Ridley's picture
Damon Ridley | Mon, 04/10/2017 - 23:14
Esther Great to hear from you. Can you ask Professor Belford to give you my email address? Yes, I am very happy to communicate with you directly. Damon

OLCC S17 | Mon, 04/10/2017 - 23:08
Hi Damon, Thank you for your message,i have read between lines. I am a graduate student. please can i request for your email, because we gonna have more conversations and it gives me direct access. Thank you.

OLCC s12's picture
OLCC s12 | Mon, 04/10/2017 - 22:20
 // This next step, retrieving the ChemSpider id, requires a server-side proxy
// because ChemSpider does not allow direct AJAX access.
// This is our server-side proxy for accessing ChemSpider.
Jmol._serverUrl = "https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php";

I took the above code from this page here, which was mentioned in example 3.2.2 above about using JSmol to get the ChemSpider ID from an InChI. This question may best be suited for my class project page, but would the server-side proxy be needed to access any external service from JSMol or is this specific just to the sources above with the asterick that mention needing the proxy. If so would this just be due to a security issue on the database side of not allowing javascript direct access or is it just a conflict with the way javascripts language talks to the code running the API?

Andrew

 

Damon Ridley's picture
Damon Ridley | Mon, 04/10/2017 - 20:45
Esther Thank you for your interest in the project: "Building and Optimising Information Search Strategies" and for your suggested topic "drug resistance in malaria". The topic clearly is a very important one, but the issue is that there are thousands of papers/patents published on the topic each year, so we need first to narrow the scope of the topic - but that in itself is one of the aspects of building search strategies! To do this, we'd first like to know a little about you and your interest in the topic. Are you an undergraduate, postgraduate, or researcher in the field? Is your interest 'a general one' or do you have a specific aspect in mind? If your interest is a general one, then to build the search strategy we first need to define the concepts and in this case there would be three concepts: "drug"; "resistance"; "malaria". Next we need to ask whether each of these concepts is (equally?) important - and in this case I think you'd probably answer: "Yes". Assuming that, the next step to build the search strategy is to think of synonyms for each of the concepts. For "drug" there would be many options including text terms such as pharmaceuticals, names of substances (e.g., chloroquine or artemisinin) or classes of substances where the classes of substances could be defined by text terms such as antimalarials or antiplasmoidals, or structures such as "substances with the artemisinin substructure". For "resistance" the most common terms would be resistance/resistant - but these could easily be searched by use of a truncated term such as resist*. Lastly you may think it would be simple to search the term "malaria" - but, no, since while that's a commonly accepted/recognised term, what scientists really are talking about are a group of Plasmodium species and in particular P. falciparum. Trouble here is that there are various strains/clones of P. falciparum, such as the Sierra Leone clone, the Indochina clone, and a bunch of other clones - named or unnamed. I am not trying to make things complicated, rather I'm being realistic and I'm pointing out to you that chemical information retrieval really is a science (hmmm... there is also an 'art' component) that needs to be studied and that researchers who rely on Google, or researchers that don't think the topic needs to be studied are almost certainly not going to get the information they need or should get. I suggest then, that we focus on a more specific aspect and that we imagine we are serious researchers who want first to understand 'everything' about what is published in that specific aspect and then develop research projects based on this understanding and knowledge. We could focus on chloroquine resistance or pyrimethanamine resistance or the like, but basically a current frontline research area is on artemisinin (and its analogues). While at present most Plasmodium species have not found a way to develop resistance to the artemisinins, the world still needs to assume that this will happen and we'd better be prepared for it. One aspect of current research in the field is to investigate artemisinin combination therapies, and this may be a good area to research for your project. If you agree then let Anja/I know and we'll put together a plan of things for you to do. If, however, you would like to research another specific aspect then that's fine - just let us know what you would like to do and we can work together on how to approach the topic. After all, what we want to do is to understand the literature in a specific area and then develop generic workflows. Looking forward to hearing from you. Damon

OLCC S17 | Mon, 04/10/2017 - 11:26
My name is Esther, I am a student in Dr. Belford's Cheminformatics class. I wish to write my project on Drug Resistance in Malaria,i feel there is more to malaria than i know. I welcome any different idea as regards to my project. Looking forward to hearing back from you shortly. Thank you.

Sunghwan Kim | Sun, 04/09/2017 - 21:22

PUG-REST does not have a way to perform a property range search (e.g., retrieving all molecules with the molecular weight between 100 and 200). This kind of search is supported by another programmatic access route, called Entrez-Utilities (E-Utils). (Actually, almost everything you do using the Entrez system can be automated using E-Utilities, but E-Utils are limited to text or numeric fielded data (e.g., chemical name search and search by numeric value like molecular weight) and cannot be used for structure searches (super/substructure search, similarity search, ...) that take a chemical structure as a query (in the form of SMILES/InChI or provided through the chemical structure sketcher).

So, depending on the type of your tasks, you need to use PUG-REST, E-Utils, or some other programmatics access routs, although this module does not cover all access routes.  If you have a particular task but you don't know what to use, feel free to contact me.