Join GitHub today
GitHub is home to over 31 million developers working together to host and review code, manage projects, and build software together.
Sign upSubmit record to Massbank EU #54
Conversation
zzjl20
added some commits
Apr 1, 2019
This comment has been minimized.
This comment has been minimized.
Thank you for this contribution. In principle this looks quite good, but I have one issue. Although these records pass the validator they have some problems. In the "COMMENT" section i can find information like "COMMENT: Origin: Animal, CSID: 10334, SubCategory_DNP : Lipids, CASID (tmp): [18951-77-4], Fatty acids". Better would be to place things like "CSID: 10334" and "CASID (tmp): [18951-77-4]" in the CH$LINK section. Please check CH$LINK
in the recordfile. Do you think it would be possible to create the records in this way? Do you use your own software to create the record files? |
This comment has been minimized.
This comment has been minimized.
Nice work. Thank you for your contribution. |
meier-rene
merged commit 46c2ad9
into
MassBank:master
Apr 9, 2019
1 check failed
This comment has been minimized.
This comment has been minimized.
meowcat
commented
Apr 15, 2019
There's still problems here. Things listed as CH$LINK: PUBCHEM CID should really be CH$LINK: CHEMSPIDER instead! At least for the ones I checked. |
This comment has been minimized.
This comment has been minimized.
Yes @meowcat, you are right. I tested some and it was never correct. Automatic validation doesn't check this yet. Implementing test for this is on the roadmap, but I'm already a bit afraid of the numbers of mistakes I need to fix... |
This comment has been minimized.
This comment has been minimized.
meowcat
commented
Apr 15, 2019
I think it will be hard to validate this strictly, since there are multiple true and half-true answers sometimes (stereoisomers, mixtures, salts etc will all not have a simple answer). |
This comment has been minimized.
This comment has been minimized.
It should be easy to check, the ChemSpider ID and PubChem CID should be an InChIKey match, at the very least an InChIKey first block match. Everything else is clearly wrong. Entries that fail an InChIKey check should be validated. |
zzjl20 commentedApr 1, 2019
The record contains MS and MS2 records.
Already checked by .scripts/validate.sh
Contact me by:
donghan-l@nig.ac.jp