Discussion

OLCC S31's picture
OLCC S31 | Sun, 05/07/2017 - 16:23
Bob Belford, I apologize for how long it took me to get back to you. I am in the process of moving, and lost my internet. I am interested in a component of webchem that allows me to access the chemspider database. This is great, because it allows me to create lists using R to access multiple chemical properties with a single command, where the CIR Identifier does not. Dr. Walker is currently assisting me in aquiring the API key for the chemspider database. I will ask Dr. walker what he feels is sufficient for the project. Am I correct in my understanding that the format of the submission is in the form of a presentation of my usage of R to access chemical data? If so, I could be ready to give a presentation to Dr. Walker by weeks end at the very latest. All the best, Aiden

Bob Belford's picture
Bob Belford | Wed, 05/03/2017 - 13:04
I note Dr. Walker is now subscribed to this module and think you need to communicate with him on what it is you would like to do, the idea was to open up the option for students to work with R, and the students sort of need to identify the projects they want, and get the green light from their facilitator, as that is the one who gives them their grades. You should feel free to comment here on ideas, and hopefully, there would be someone subscribed that could help. My personal feeling as that since we have PubChem people on board, projects involving PubChem would be easiest to get support with. Have you tried doing anything with R shiny,<a href="https://shiny.rstudio.com/">https://shiny.rstudio.com/</a> ? Also, one of my students made a spreadsheet in Excel that she uploaded boiling and melting points from PubChem depositors to, and used the API to get molar masses, and then set it up to filter results based on the values of an "unknown". That is, sort of the opposite of what we have been doing (you are not searching the physical property of a molecule, but the molecule that has the physical property). the issue we ran into is that many of them do not come up over the API, in fact if I understand right, only computed values come through the API. But you can still get the actual data sets from the depositors, and then maybe do some task with that. The bottom line is you need to pick a project that interests you, and that your faciliator approves, and hopefully we can find someone who can help. Cheers, Bob

Bob Belford's picture
Bob Belford | Wed, 05/03/2017 - 09:39
Hi Aiden, I apologize for not getting back quicker, but our school has a different schedule than yours, and my students gave their presentations on April 13, 20, 25 & 27. One student did do a data visualization project using R, and although he is still subscribed to this module, his semester is also over and I fear it is just too late to join in on a project (he gave his presentation April 13). Cheers, Bob

Anja Brunner | Fri, 04/28/2017 - 05:19
Hello! Sorry for the delay in my response. So, good observation. The specific kind of safety and hazard information that you would find on an MSDS (so, standard GHS Hazard statements, precautionary statement codes and such) is not covered in Reaxys. I talked to some of our colleagues about this and there are lengthy historical reason for this (that we don't need to discuss). Having said that, Reaxys covers toxicity and environmental toxicity, for example, very nicely. And if you are specifically looking for H&S information, Reaxys links directly to substance records in third party databases where you DO find that kind of information. So, look up a substance, go to the hit list of Substance Records, and in the upper right corner you will find a dropdown menu titled "Database:". The menu will most likely be set to "Reaxys". You can change that to, for example, "PubChem". This will show you records available in PubChem and links you directly to the records where you can find that information (as you mentioned). While you are there, you might also want to look at the linked records in eMolecules. This is a database designed for the sourcing (purchase and supply) of chemicals. Their records may also contain interesting information. This is a good example of how Reaxys tries to bring together information across multiple sources and position them in one location so they can all be easily accessed and used. I hope this answers your question! Anja

OLCC S31's picture
OLCC S31 | Thu, 04/27/2017 - 22:57
Hello! My name is Aiden Farragher-Gnadt, a student of SUNY Potsdam. I am interested in this project. I have had some luck using the Webchem R package with the R console to search for chemical data. My use of this has been limited to the chemical identifier resolver tool, as I do not have an API key for chemspider. I must admit that my expertise with R is very limited, and I would like to know what kind of materials I would be submitting for this project. I am currently enrolled in two credits of this course, any help or information about this project would be greatly appreciated. Thank you very much!

Olcc S14 | Tue, 04/25/2017 - 11:10
While using Reaxys and PubChem for compound search, I found "safety and hazard" on PubChem but I am unable to find that in Reaxys. So does Reaxys give an information about safety and hazard of searched compound?

Damon Ridley's picture
Damon Ridley | Sun, 04/23/2017 - 03:45
Hi OLCC197 You have asked a very general question and I think you have to tell us more precisely what you want to do. Thus I presume you are well aware that there are a number of naturally occurring amino acids and that the biosynthesis of each one of them is done in a number of steps, each one of which involves a very specific enzyme. So can you think about what you really want to find and then let us know? Another suggestion I have is that you read the general documents published in Part IV: Exploring Reaxys, in particular the one on Substance Records and the one on Text Searches. These largely teach the "search mechanics" and when you have a good grasp of these then you can try a few of the workflows and see what you get. Then you will better understand why you need to narrow your search intent. Having said that, on Reaxys you can easily find the substances (=inhibitors) that have been tested on an enzyme. In the first instance you can try to search for the enzyme in the Substance Basic Index (available through Query builder => Search properties: Substance Basic Index, then click, drag and drop the field into the main work space) involved in the (bio)synthesis . So please define your question more precisely. Damon

OLCC S197 | Sun, 04/23/2017 - 00:54
please how can i search for drugs that inhibit amino acids synthesis using reaxys or pubchem

OLCC S197 | Sun, 04/23/2017 - 00:54
please how can i search for drugs that inhibit amino acids synthesis using reaxys or pubchem

OLCC S197 | Sun, 04/23/2017 - 00:54
please how can i search for drugs that inhibit amino acids synthesis using reaxys or pubchem