Final ACS Abstract: This project was designed to create an open solubility resource for the larger organic chemistry community. This project seeks to allow for solubility information to become more easily accessible, and provide information such as which compounds are soluble in which solvents, and to what degree. The information required for this project will be procured by combining data on solubility and solvents from publicly available databases and recent literature. In addition to providing a large open dataset of solubility values, the project seeks to create a webservice that can report measured and predicted solubilities directly from structure.
Nov 12: Belford asked Davis to contact Lang with following:
Dr. Lang,
I'm trying to get a project outline finalized for the Cheminformatics class. I've looked at this data: http://figshare.com/
I see columns N-AF are mostly empty; is there something there I could add to the data?
I've also looked through this data set: http://figshare.com/
and found it very interesting. Is there something I can add to this research.
I have about 2 weeks before I have to present my project. I understand that this is a very short time period, but what in these areas would you suggest would be a feasible project for me? Another student at Centre college is grouped with me and is going to continue the project in the spring to present at ACS.
I will greatly appreciate any input you provide.
Nov. 13: Lang replied:
Hi Brandon,
I would suggest working through: http://figshare.com/
A quick project would be to analyse the names and the structures to see if they match? Then you could give examples and statistics on the accuracy of the database. Why are the structures wrong? Missing stereochemistry? etc.
Then you would correct the structures (all the names are correct - well at least they are the names according to the sources from which the solubility data was extracted) and update the other identifiers: CSID (column AA), etc to agree with the name column and then republishing as an updated dataset to figshare (which will now include you as a co-author). I think this would be a good two-week project.
Furthering this would be to add the new data I (and Bill Acree - UNT) have been collecting for about a year that needs converting to molar units and inputting. Then working working on a open solubility model (using the CDK) and then publishing this new dataset with the model in ChemistryCentral journal or other appropriate OA journal.
The columns you mentioned are not necessarily needed anymore, column AA is needed CSID is the Chemspider ID. Adding an additional column with the PubChem ID would be useful for the community.
How does that sound?
Nov 15: Belford sent everyone following:
The 5 of us went in on the abstract that Perry is going to present, and I had created a discussion page, and would like everyone to subscribe themselves to it, so we can use this, instead of emails, to discuss the project. Here is the direct link:
There have been some discussions going over email, and I am going to take the liberty to post to the body of the above page their content. One of these deals with curating solubility data that has been uploaded to figshare.
As we included predicting solubilities in the abstract I am having Brandon give a presentation to my lecture class on the Abraham's equation, and we can share his powerpoint presentation on the above site.
Now, with regard to the data curation, I have an idea, which I would like to discuss on the above web page, but I need you all to subscribe. With Jennifer and Perry's approval, this may be something that would be appropriate for Perry.
One of the things we did with the WikiHyperGlossary was take an IUPAC glossary, you NIH and ChemSPider services to generate an InChI, and figure if they generated the same InChI, the word was a chemical. (We then associated the InChI with the "word" and used that for various software tasks). That is, we needed to know which words were chemicals, and which were not.
Now, we published this work here,
Additional file 1 (http://youtu.be/ptX9tIrqcEE. )shows why we did this,
But Additional file 4
describes this process using additional 5 as a spreadsheet.
Now, I have not looked at figshare (I am very busy and still have to upload the last part of module 8), but I understand we need to make sure the sturcutres and names match. So my question is, can we do something like we did with the WikiHyperGlossary, where we convert the names to InChI, and the Stuructures to InChI, and then match the InChI (or more accurately, flag when they do not match).
OK, Please subscribe to the project page. Also, please realize that there are two, potentially 3 projects going on. That is, both Brandon and Perry are doing their own project for this class, which will be over withing 4 weeks, and we are all doing a project that will be presented at the ACS meeting. Hopefully we can synch Brandon and Perry's class projects for their respective schools with the overall project.
So I thought if Brandon tackled the Abraham's eq., and maybe Perry tackle a script using web APIs to convert structures and names to InChI and compare them. He can possibly use the spreadsheet in file 5 of the supporting documents as a template.
If so, we probably need to acknowledge Andrew Cornell, as he spent quite a bit of time on the project.
Cheers,
Comments 13
IUPAC-NIST Solubility Database
Abstract
Clarification
Response to clarification
Broken Excel File
Excel file and J Chem Inf
Interesting and maybe worth noting
The Excel file seems zipped (so the extension is wrong)
More data
02/09/16
Solubility Dataset and Solubility Unit Conversion Scripts
PHP Scripts
PHP Scripts