1. Fall 2015 Course
  2. Discussion

Discussion

Olcc S14 | Fri, 03/31/2017 - 09:20
Sorry for late reply. I was not registered to this topic previously so I didn't see yours' comments. Regarding my class project, I want to connect with my research work. Yes, I am working on nanomaterials and waste water purification. I am making nanocomposites from waste materials like wood chips and utilize it in waste water purification. So my research is based on utilization of renewable resources based nanomaterials for waste water treatment. I am trying to remove heavy metals and some inorganic compound from waste water. So I wonder how can I use these two databases to get useful information for my research work? I have search document related to my project on Reaxys but I don't know about PubChem. Does PubChem search useful for my research? Does PubChem search document related to my research work? In my research, there is some chemical reaction occurs during preparation and phosphorous treatment so I want to use these databases to get information on those chemical reactions. I know Reaxys can be used to draw chemical structures and reactions but I am not sure about PubChem. I know PubChem can also draw chemical structure but I am not sure about reactions. Does PubChem draw chemical reactions? Looking forward to hearing from you. Thank you Amita

Robert Belford's picture
Robert Belford | Thu, 03/30/2017 - 12:16
I know Amita is involved with a research group, and she can orient this to assist her graduate research work. I do not believe Nwume is involved with research. The bottom line, is there is so much in Reaxys and PubChem, that they can work on total different projects that have no overlap. So I am not seeing a problem, as long as they pick different topics, that take them through different information spaces. I also know that Amita's work is more material sciences oriented, and there may not be significant usage of PubChem, while Nwume can pick a topic more in line with PubChem's mission and resources.

Sunghwan Kim | Thu, 03/30/2017 - 10:57

Hi, Amita and Nwume,

Thank you for showing interest in this project.  By the way, it seems that both of you are from UALR and Professor Belford (at UALR) told me that each student at UALR would be required to work on different project (for grading purposes), while it is okay for him or her to work with students at other schools.  Considering that both of you are from UALR, I suggest that both of you discuss this issue with Professor Belford before starting working on it. Because your school is getting closer to the end of semester, I recommend you to do it as soon as possible (if both of you are still interested in this project).

 

Sunghwan Kim | Thu, 03/30/2017 - 09:46

Currently, both adding and removing a legacy designation are being done manually.

  

It is true that we have *automated* check if legacy depositors submit new data into PubChem. However, the final decision whether to remove a legacy designation is manually done.

 

[It is expected to be (and really is) extremely rare for a legacy depositor to start submitting new data because it stopped data submission for a reason (mostly money-related issues, e.g., discontinued funding or product, strategic priority changes, business gone under, etc.) and this reason is not likely to be changed by PubChem's legacy designation.]

OLCC S66 | Wed, 03/29/2017 - 22:38
I've been looking through several different sources and may be overlooking the answer, but I was wondering what the time frame is for a depositor to be considered inactive and for their records to take on the legacy designation? Also, when it comes to removing the legacy designation, is that a manual process of the depositor making contact with PubChem? Or is that in some way semi-manual and semi-automatic as well? For example, if a depositor (previously considered inactive) again adds information to PubChem, would that automatically make the other records lose the legacy designation, or would that depositor have to make contact with PubChem prior to adding a new record? Basically, I'm slightly confused about the order, but I'm not sure exactly how to phrase the question.

Sunghwan Kim | Wed, 03/29/2017 - 20:00
You need to sort both matrices by CID, so that you can compare them with each other more easily. How to do this is explained in the comment you happened to reply to.

olcc s16 | Wed, 03/29/2017 - 19:39
Dr. Kim, While doing this question, I realized that the CID orders in 2D and 3D are not the same. So, calculation of delta will be incorrect due to different pairs. How would you resolve this problem? I have uploaded the picture and Excel files (those are raw data before doing anything) of my problem too. Thanks Phuc

Sunghwan Kim | Wed, 03/29/2017 - 13:49

Detailed information on non-live records can be found at one of the papers listed at the beginning of Question 1.

But the bottom line is that you *can't* find non-live records because, by definition, they are not searchable. However, it is still accessible if you know "where the record is".

Probably, somewhat confusing to understand, so let me explain it this way. Essentially, a URL, which stands for "Uniform Resource Locator", is the address of the record you are interested in. When you modify the address of CID 60823 to that of 733692, it means that you already know where CID 733692 is. (You just told your web browser the address of CID 733692. This is not the same as searching for the record.) With that said,......

>>> How would one know to search a certain number to find a non-live record?

Again, non-live records are not searchable. You should know the existence of a particular non-live record and what its web address is.

>>> Is it only used if one had previously used that CID and it later became non-live.

All records in PubChem Compound (whether live or non-live) entered into PubChem as live records because at least one depositor provided information on associated substances. Each compound record is assigned to its own address. To access that record, you would (metaphorically) search *an address book* for that record. However, once you know where the record is, you can get that record even if it is dropped out of the address book (that is, not searchable but still accessible).

OLCC S69 | Wed, 03/29/2017 - 10:52
As I was going through the assignment for this module I went through the section in Part 1 where we are instructed to change the URL for the search of compound 60823 to find the non-live compound 733692. How was the CID for the non-live record determined. How would one know to search a certain number to find a non-live record, or is it only used if one had previously used that CID and it later became non-live. Then, the person could alter the URL to go back and find that compound they had previously searched for?