Sixty-Four Free Chemistry Databases Part 7: Manage Your Spectra and Chromatograms Online with mylims.org
Our tour of free chemistry databases and services on the Web continues with mylims.org, a spectrum and chromatogram management system. What sets mylims.org apart from the other services we've looked at to date is the ability to upload and manage research data from individual users.
Painless Account Setup
mylims.org is a free service, but to upload your own data, you'll need to create a free account. Simply provide your email address, follow the link in the email the system sends you, add your password, and you're done.
Entries and Notebook Pages
mylims.org is organized around the concept of the "entry." You first create a new entry and then associate data with it. Although entries can be mapped to a variety of concepts in most research organizations, one of the most familiar will be notebook pages.
To create a new entry, go to Add Entry and then click on the "+" symbol on the left of the table. You'll need to supply "reference" and "batch" numbers.
In many labs it's standard practice to manage the products you create by referring to a notebook number and page/subpage. For example, if your notebook number is "1881", your working page is "223", and the sample giving rise to the spectrum you're uploading is the first one you've created on the page, you could fill in the field as shown below:
Clicking on the green checkmark icon saves the entry.
Add an NMR Spectrum
To add an NMR spectrum, click on the "+" symbol under the NMR column. This will generate a "Choose file" button. Clicking on it will allow you to browse to the file on your system. You can use this example JCAMP-DX file to get started.
After choosing your file, click the green checkmark button to save your selection. You've just uploaded a spectrum to your account.
View the Spectrum
To view your NMR spectrum, click on the green magnifying class icon. A popup window will appear containing a live spectrum that you can zoom, integrate, and even generate a PDF from.
Conclusions
mylims.org is an excellent example of using the power of the Web to create solutions to the information management problems chemists face. This review only scratches the surface of what is possible. For example, you can share your spectra with everyone who uses the service, or a select group of collaborators. mylims.org may not be the perfect solution for your lab, but it is well worth the time to set up an account and see for yourself.
Kudos
- Simple, hassle-free signup.
- Integrated tools (structure editor and spectrum viewer).
- One of the few chemistry databases that accepts user data.
- Workable system for sharing information publicly or in groups.
- Lightweight approach to LIMS software.
Ideas for Improvement
- Provide a method to delete individual entires after creation.
- "Delete All" redirected to a page with a button labeled "Delete". Pressing it gave no response.
- Simplify and streamline entries table.
- Give each entry its own summary page and URL to enable even more effective sharing.
- Hover popups have scrollbars that are impossible scroll because moving the mouse disposes the popup.
Luc Patiny and his group are the same ones who provide the NMRDB service. They do move fast based on feedback (http://www.chemspider.com/blog/nmrdborg-nmr-predictor-already-improved.html)
It wasn't clear that once data are submitted that they can then be downloaded? Also, any comments around licensing you have seen ..Open Data labels etc? As you are likely aware Peter Murray-Rust hit ChemSpider pretty hard regarding his judgment that we were laying claim to copyright for submitted data (http://www.chemspider.com/blog/?p=208) ...it was never true. We feed up the majority of spectral data on ChemSpider (chosen to be Open Data by the submitters) via the www.spectralgame.com website. This is a great reuse of the data we believe.
Do you have any ideas about whether the spectra are freely downloadable? PMR would have a field day with this if they aren't.
Some suggestions for improvement..
1) label 1D vs 2D in the table. 2) The applet didn't display for me under Firefox on a couple of occasions 3) Add a feed regarding new spectra available: Example: http://www.chemspider.com/blog/one-more-rss-feed-added-to-chemspider-spectral-data.html 4) Collaborate with other databases of spectral data to allow mutual sharing. We could provide a dump of our Open Data to Luc and vice versa. I will approach him to discuss 5) Consider licensing and Open Data labels
@Tony,
>It wasn't clear that once data are submitted that they can then be downloaded?
and
>Do you have any ideas about whether the spectra are freely downloadable?
Provided the data are public, they can be downloaded. Whether they can be downloaded in bulk is another question, but each individual public spectrum can be viewed.
>Also, any comments around licensing you have seen ..Open Data labels etc?
Not that I know of. However, the service appears to be geared toward letting individual scientists manage their own data and share them with a select group of collaborators.
Thanks for your nice review ! Concerning Deleting an entry, if you click on a line at the level of Ref or Batch a little trash will appear and you may delete the entry. You can give a direct link to a specific page using: http://www.mynmrdb.org/search/entryid/421645.html Where the number of the record can be found using the mouse over popup window over the INFO icon. Best regards, Luc
@Luc,
Thanks for the info. I was able to delete an entry by clicking on a Ref or Batch id and then clicking on the trashcan icon.
Unfortunately, I'm not able to copy the record number from the popup because the popup disappears when I move the mouse. But I see how you'd construct a URL from it.
Care to offer any thoughts on your future plans for mylims.org?
Looking for the data and results for LMWH NMR thanks