A systematic approach to chemical information is older than any of us and what we are trying to do with chemistry data and information today is not too far off from what has been desired for many generations. Even engaging computers to assist us with this data, actively pursued in very sophisticated efforts since mainframes. While we may think our workflows and information activities are different today than previous generations, the fundamentals that the informed human needs to manage to use the computer are really not that different in principle. I mention this as what I would perceive as a core lesson of the course content.
Regarding the course design, I found the lack of cohesive learning objectives and syllabus a significant challenge for pulling together a course, as opposed to a loosely themed series of 'visiting lecturers'. I have experienced as a student (UG and grad), a TA and an instructor various courses taught by multiple lecturers, even in disparate locations via various connecting technologies (my library degree was one of the early online programs). They all suffered this challenge, everyone taught to their own perception of the content and delivery and very little coordination was feasible given limited time. Now as a professional, I have come to appreciate the value of the seminar series style, in person, online, in real-time, as needed. I have my education fundamentals and professional training, and I am looking for different ideas and approaches to augment my knowledge and experience. If I was seeking background and solid foundation in a new area I would search for a cohesive course experience, building material sequentially. There is a forthcoming column on chemistry related MOOCs that looks a bit at this question that we may want to consult.
I support the premise that one useful learning goal is the ability of the students to design and conduct ongoing projects. Perhaps a future version could generally scope the type of projects available and target supporting skills to cover in the modules. There is a lack of such a foundation course in chemical information, especially designed to engage 'regular' chemistry majors more directly in the digital culture. They may be brought up surrounded by it, but I have yet to appreciate how much 'under-the-hood' and 'information-as-a-computer-sees-it' learning may be available, even as far as many of us educated in the 'early' days of computer program design that are hacking the informatics space now. New interfaces and tools are more available for lower barrier than ever before, can we marry these with the best practices that are useful to understand behind the scenes for forthcoming chemists to engage more scientifically?
Discussion
With the pubchem identifier
With the pubchem identifier exchange service we can convert pubchem IDs to inchi keys as well as other things. It can be found at <a href="https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi">https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi</a>
New files for the library
I've uploaded a first draft of an overview of how I think the mining of the PubChem and Wikipedia Chemboxes can help us work with chemical safety information that is available on the web. The numbers in the paper are based on my "spare time", manual review of the 88 or so chemicals named in the 1995 edition of Prudent Practices last week. It would be great if we could double check them electronically and expand the number that are reviewed using the XML data from PubChem and scraping of the ChemBoxes.
Solubility Dataset and Solubility Unit Conversion Scripts
Here's this solubility database: <a href="https://figshare.com/articles/Open_Notebook_Science_Challenge_Solubility_Dataset/1514952">https://figshare.com/articles/Open_Notebook_Science_Challenge_Solubility_Dataset/1514952</a>
See here for scripts and webservices to convert between solubility units x,M, etc.: <a href="http://onswebservices.wikispaces.com/solubility">http://onswebservices.wikispaces.com/solubility</a>
Changing student expectations
>What type of online material best engages 21st century students?
I've been thinking about this a fair amount of a variety of purposes, so I'll share some random thoughts that might be relevant to the question:
1. When we did the OLCC on chemical safety in 2004(?), it felt pretty exciting to connect students and campuses nationally and I seem to remember greater participation in the on line materials. Whether this was due to the novelty of the opportunity or the topics discussed, I can see where the greater availability of all information in 2015 would require a different medium to keep one's attention these days.
2. Talking to my son about his experience as an undergrad at a high end liberal arts college (graduating in 2013), he would talk about what was said in classes, or reading he did (he likes to talk about ideas), but not about any on-line experiences. That was for entertainment.
3. I have had success with using on line content to prepare students for lecture by pre-loading jargon, but they still needed conversation to incorporate logic that connects those pieces of jargon. Maybe the authors of the OLCC papers could develop quizzes that provide that aspect of the topic?
02/09/16
02/09/16
Hello, everyone
It has been a little while since any discussions on this project have taken place and now that I am back I think we can resume discussions. First, I would like to mention that I wrote a paper about this project last semester in my cheminformatics class and I will upload the document soon (It should be at the very bottom). The paper explains the project and it gives some information about what I've accomplished so far on this project (which isn't much).
I had a skype session today with Dr. Belford as well as Dr. Muzyka and we had some interesting discussions about what direction this project is taking. Dr. Belford suggested that a critical part of this project is that we add tools to the solubility spreadsheet that allows users to enter solubility values. The problem is that different solubility databases will have solubility values in different units and so it is important that we find a web API for unit converter that will allow us to convert the values so that they all have the same units, making comparisions easier. I hope I am on the right track explaining the problem. If not, Dr. Belford please feel free to add.
Additionaly, a third dimension can also be added to the problem if we realize that the different solubility databases will have different solubility values depending on which solvent was used to determine the value. For example, you will notice that some databases will have the solubility values based on solubility in water. Other databases will base there solubility values on other solvents. Although this is a problem, I think it is secondary to the unit problem that we will encounter.
I have found a couple of databases on the internet already (links are below) and you will notice that all three of the databases have different units for solubility. The goal is to process these values so that they all have the same units. Please feel free to provide ideas on how to do this and Dr. Belford, if I am missing any part of the problem please add so we can all be on the same page.
Also, if you happen to stumble upon some solubility databases, please add them on this page.
Links:
<a href="http://www.chem.wisc.edu/deptfiles/genchem/sstutorial/Text11/Tx112/tx112.html">http://www.chem.wisc.edu/deptfiles/genchem/sstutorial/Text11/Tx112/tx112.html</a>
<a href="https://www.organicdivision.org/orig/organic_solvents.html">https://www.organicdivision.org/orig/organic_solvents.html</a>
<a href="http://cool.conservation-us.org/coolaic/sg/bpg/annual/v03/bp03-04.html">http://cool.conservation-us.org/coolaic/sg/bpg/annual/v03/bp03-04.html</a>
Thank You
Parijat Sharma
LCSS List
Ive uploaded an excel page with the list of chemicals from the LCSS. There are four tabs, Sheet0, Sheet1, Sheet2, and Sheet3. Sheet3 is the filtered down list in alphabetical order. The other sheets are just part of the filtering process. There are many duplicates which I can get rid of and there are many chemicals listed by pubchem as numbers.
Small Excel File
I just uploaded the file to the page. "Structured" is a little generous - it was more a note taking device with some calculations at the bottom. But I think that it gives us an idea of how to generate interesting data for SD.
- Ralph
Small Excel File
Ralph,
Can you upload the file to this page, or the Google drive I just shared with you. It would be nice to see how you structured the file.
Cheers,
Bob
Several attempts were made to bring up the JavaScript libraries within the ELN today. The HTML shows up as needed in the source, but the visual display is still not showing up. Tomorrow I will determine where the link to a reference is broken and apply a fix so charts display properly. This will get the initial integration where it needs to be to start working with handling spectral data.