blueobelisk / bodr Goto Github PK
View Code? Open in Web Editor NEWBlue Obelisk Data Repository - your one stop place of element and isotope data.
Home Page: https://doi.org/10.1021/ci050400b
Blue Obelisk Data Repository - your one stop place of element and isotope data.
Home Page: https://doi.org/10.1021/ci050400b
and likely some extra info
Which Wikidata already does, but is merged into one file in elements.xml
in BODR.
Tasks:
It still says MIT on this line: https://github.com/BlueObelisk/bodr/blob/master/bodr/elements/elements.xml#L22
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.
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
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?
and several other files (bc https://github.com/BlueObelisk/bodr/blob/master/bodr/elements/elements.xml contains a lot more than Wikidata currently has)
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