blueobelisk / bodr

Blue Obelisk Data Repository - your one stop place of element and isotope data.

BODR

Blue Obelisk Data Repository - your one stop place of element and isotope data.

Download

• Ubuntu package: https://packages.ubuntu.com/bodr
• Debian package: https://packages.debian.org/bodr

How to Cite

If you use this library, please cite:

Guha, R., Howard, M. T., Hutchison, G. R., Murray-Rust, P., Rzepa, H., Steinbeck, C.,
Wegner, J., Willighagen, E. L., May 2006. The Blue Obelisk - interoperability in
chemical informatics. J. Chem. Inf. Model. 46 (3), 991-998.

See https://doi.org/10.1021/ci050400b

bodr's Issues

merge group number pull request

See https://github.com/egonw/bodr/pull/2

create script to create isotopes.xml from Wikidata

and likely some extra info

split the concept of elements and allotropes

Which Wikidata already does, but is merged into one file in elements.xml in BODR.

New source of the van der Waals radii

Currently, the Van der Waals radii values are taken from the publications of A. Bondi and S. S. Batsanov, however, a more complete source exists (S. Alvarez, 2013, "A cartography of the van der Waals territories", doi: 10.1039/c3dt50599e). Some values do differ from the ones presented in the works of Bondi and Batsanov, but overall it seems to present a more complete set. I already have the values tabulated for my own purposes and could easily add them to the xml if needed (in my own fork). Alternatively I could just provide You with the values in the preferred form (separate xml file?). Would that be of use?

ensure all articles (etc) cited are in Wikidata

Prepare release 11

create script to create elements.xml from Wikidata

and several other files (bc https://github.com/BlueObelisk/bodr/blob/master/bodr/elements/elements.xml contains a lot more than Wikidata currently has)

Update to AME2016 Atomic mass values and error?

Hello,

I'm wondering if it would be a good idea as a project to update the element and isotope data in the BODR based on the new values from the AME2016 atomic mass evaluation? If I understand correctly, I think the isotope data currently is from the AME2003 dataset. And many cheminformatics toolkits pull from this repository. Here is the new published data:

https://iopscience.iop.org/article/10.1088/1674-1137/41/3/030003

There is also a machine-readable text file of the data here. https://www-nds.iaea.org/amdc/

It is not exactly trivial to parse as some of the columns have missing values (i.e., so some rows have 16 columns, others 15, etc.). However, it is likely possible with a bit of effort.

So my question: does it make sense to update the values? Or will this cause too many issues with current calculations based on the current values in the BODR?

Lastly, if this is a reasonable project. Do you have any suggesting for a workflow to go from the parsed column data to the current XML format in this file:

https://github.com/BlueObelisk/bodr/blob/master/bodr/isotopes/isotopes.xml

I am thinking about using Python and pandas to initially read in the data. Thanks!

Vin

make the 11 release

Tasks:

1. set date in NEWS
2. update configure.ac

license outdated in elements.xml

It still says MIT on this line: https://github.com/BlueObelisk/bodr/blob/master/bodr/elements/elements.xml#L22

Isotope masses

Hi,

I wonder what is the source of the isotope mass values in the Blue Obelisk.

The most recent dataset I found is AME2012. The mass values published in AME2012 are different from the ones in Blue Obelisk.

check IUPAC updates since release 10