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Discussion

Damon Ridley's picture
Damon Ridley | Sun, 04/02/2017 - 22:19

Amita Greetings from Sydney! I am on a different time zone so was unable to reply earlier, although I note Anja and Dr Kim have commented on your project. Everything they have said is absolutely correct, and, in particular, that you need to refine the project a little. A comment here is that there are a few steps in any search: first, define the question; second, understand the search landscape; third, then proceed with the search(es).

Let me start from the third part first. Here you almost invariably need to trial a few searches first, so don't just do a single search and then stop.

The second part (the landscape) means that you need to have some idea what is in the database(s) and then start to think of searches based on that knowledge.

Which brings me to the first part, where my suggestion is that you focus on two general problems:
1. How to find relevant substances and then specific properties on them. I suggest you choose QUAT 188 (perhaps also include some related quaternary ammonium salts) and find biological activity information on them.

2. How to formulate and execute a (text) search relating to "removal and recovery of phosphorus and heavy metals (Selenium, Arsenic, cobalt, lead etc.) from waste water using renewable resources based nanomaterials prepared from wood or cellulose". In starting this search, you need to define the concepts then formulate a search based on a few of the concepts (the ones for which you feel you can search more efficiently).

Since you probably have not had a lot of experience with general strategies for the second problem, let me start you off with the concepts I see (and comments on how to search them):

- removal/recovery (authors/indexers would use all sorts of terms here, so I don't think this would be a good concept at least initially);

- phosphorus (problem here is that you don't mean 'phosphorus' (the element) at all - rather you mean phosphate. Herein lies a common problem in this field. Yes, I know that fertilisers are often defined in N:K:P content and I know some authors would write about phosphorus and mean phosphate - but the question is how to search for it. Again, I don't think this would be a good concept at least initially);

- heavy metals (similar problem. Some authors/indexers would talk about heavy metals, but others would be more specific - as you suggest: Se, As, Co, Pb etc. So yet again, I don't think I'd be searching for this concept at least initially);

- waste water (at last - something that is quite specific and commonly mentioned, although you have to think about searching wastewater/wastewaters and so forth);

- nanomaterials ('synonyms' may be nanosponges, nanoparticles, nano materials and so forth. These probably could be included in an initial search, and there is a very simple way to search them - right? :-) );

- wood/cellulose (this concept also would be worth considering in an initial search).

So, what do you think? If you agree with my suggestions, then the next thing I suggest you do is formulate specific search strategies in PubChem and in Reaxys, and then get them checked by Dr Kim and Anja/me. Damon

OLCC S197 | Sun, 04/02/2017 - 19:42
please how can i get IUPAC - condensed biological line notation because all i can see in the compound summary page of both is only the IUPAC. please i need help.

Sunghwan Kim | Sat, 04/01/2017 - 20:30
Submicromolar means "less than (or below) micromolar". For the purpose of homework, you can use the link with the phrase "at/below 1 microM" for submicromolar. (Strictly speaking, the term "submicromolar" does not include "at (or equal to) 1 microM".) For your information, subnanomolar means less than (or below) nanomolar.

Olcc S15 | Sat, 04/01/2017 - 19:33
Dr Kim, while working on question 4 d and e, after reading the directions i couldn't retrieve AIDs. My "related data" didn't have any section for submicromolar potency. Could you please explain to me what i'm missing? Thanks

Olcc S14 | Sat, 04/01/2017 - 14:03
Thank you. I will follow the instructions that you, Dr. Kim and Dr. Damon have provided me so far. I will keep in touch.

Anja Brunner | Sat, 04/01/2017 - 13:12
Hello Amita, I concur with Dr. Kim with regards to his advice to define specific information for your research that you would like to find and then explore PubChem and Reaxys to see what kind of answers they can provide. PubChem and Reaxys were designed for different objectives and thus, I think that you will find them to be complementary -- one being better for one kind of search and the other for another type. The key is first to know what specific type of information you want to find. Above you list the following: (1) What are the reactivity and toxicity properties of quat-188, sodium hydroxide, metal chlorides, ammonium hydroxide and cellulose? (2) What reactions occur in your synthesis of nanocomposites (you need to define which syntheses/nanocomposites)? (3) What work has already been reported in the literature and patents on "removal and recovery of phosphorus and heavy metals from waste water using cellulose-based nanomaterials"? Each of those questions calls for a different type of search. 1 is a search for specific property data. 2 is a search for reactions that lead to a specific product, o maybe even the elucidation of new reactions that could lead to that specific product. And 3 is broader search for literature on a topic. Maybe it would make sense to start with one question, define the specific information you are looking for (e.g., toxicity of ammonium hydroxide) and then perform the search in PubChem and then Reaxys. You already have experience using PubChem from the excellent modules Dr. Kim prepared and we have provided some detailed instructions on the search functionalities of Reaxys. Then, compare the two systems-- you could do so in terms of the information you found in each, or in terms of the functionality each affords. It might make sense to first sit down and think of specific evaluation criteria you could use to assess the search and results in each of the systems. Those criteria should be important to you as a researcher and in terms of what advances your research. So, for example, is it more important to have comprehensive answers or specific information that has been excerpted from source documents? See how it goes with one question and write down what works well in each system, what surprises you about the answer sets you get, what helps with your research. Then perhaps, you can tackle another question that requires searching differently and compare the two systems. The best thing you can do is to define your question and dive in! When you get stuck, contact us and we can try to help you along. I hope that helps! Anja

Olcc S14 | Fri, 03/31/2017 - 16:18
Sorry for the confusion. My goal for my research work as well as for class projects is to find out chemical reactions occur in my synthesis of nanocomposites. I use chemicals like quat-188, sodium hydroxide, metal chlorides, ammonium hydroxide and wood (cellulose). The information I am looking from PubChem and Reaxys are properties of these chemicals such as reactivity and toxicity. And I am also looking for the reported documents which are related to my research work " removal and recovery of phosphorus and heavy metals (Selenium, Arsenic, cobalt, lead etc.) from waste water using renewable resources based nanomaterials prepare from wood or cellulose. So I am looking papers related to this topic. It's not my research topic but it is quite similar. I know I can find properties of the chemicals that I am using but I am not sure about the documents. So can I find documents related to my research topic? Looking forward to hearing from you. Thank you Amita

Sunghwan Kim | Fri, 03/31/2017 - 14:23

It seems that you are having hard time figuring out where to start from. To help you get started, let me tell you how you should approach. Typically, a project has a specific goal or specific questions to answer and needs to have tasks/steps that you will need to take to achieve that goal.

I guess your goal is to compare PubChem and Reaxys, but what tasks should you do to achieve the goal?  One issue here is that your goal is somewhat broad, making it difficult to identify necessary tasks.  A questions that you answered in your comment above is a process to narrow down the scope of your study, probably making your goal is more specific.

You asked how you can use the two databases to get useful information for your research on waste water treatment using nanomaterials.  However, you did not really say "what specific information" (or specific analysis tools/services) you need for your research.  Once you can identify specific pieces of information relevant to your study, now you can compare the two databases in the context of that information content.  Does both databases provide what you need?  Does one database have incorrect information?  Is a particular type of information found in one database, but not in the other?  So, essentially, you need to identifiy a set of specific questions that you can use when comparing the two databases.

Actually, you have asked me a series of questions, including:

  • how can I use these two databases to get useful information for my research work?
  • Does PubChem search useful for my research?
  • Does PubChem search document related to my research work?
  • Does PubChem draw chemical reactions?

While some of these questions are very subjective and ambiguous, I think they are a sort of good starting point.  Please define your questions more narrowly.  For example, in the fist question, what do you mean by "useful information"?  By narrowing down your questions and searching for answers to them, you will be able to compare two information resources.

Sunghwan Kim | Fri, 03/31/2017 - 13:32

Yes, I believe the link contains the information that we should start with. Please map drug names with PubChem CIDs (and other necessary information for next step). I see some couple issues here:

(1) The list contains biologics (e.g., monoclonal antibody and protein drugs) as well as small molecule drugs. So, it's likely that you will fail to map these drugs with CIDs, because PubChem primarily contains small molecules. Do not worry even if you get many failed search. We will focus on small molecules.

(2) The list contains thousands of drugs, while Google Sheet cannot make that many web service request, so you will need to use MS Excel for this task. Once you have a shorter list of drugs (after removing biologics and duplicates), it may be possible to use Google Sheet (depending on the size of the data set).