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[SOLVED] Add number of compounds to Record Index page #175

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schymane opened this issue Apr 27, 2019 · 12 comments
Open

[SOLVED] Add number of compounds to Record Index page #175

schymane opened this issue Apr 27, 2019 · 12 comments
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@schymane
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@schymane schymane commented Apr 27, 2019

The number of compounds in MassBank is not available anywhere ... we should have basic stats on how many compounds by unique InChIKeys and a number of records without InChIKeys (for instance).
A total number of spectra would also be good (and the answer is not >186,000, see #174) :-) but can be calculated relatively easily by adding pos and neg numbers - this is not the case for compounds (e.g. adding by name - due to naming inconsistencies, and the number of letters/numbers there in the range...

@egonw

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@egonw egonw commented Apr 27, 2019

Indeed, useful as "Reference URL" here:

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@ChemConnector

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@ChemConnector ChemConnector commented Apr 27, 2019

Good idea. And you and I have exchanged on the need for some of the chemicals to be collapsed together too so the curation effort would affect those numbers. If you want me to do anything re looking for duplicates with mapping exercise let me know. I will dedicate a little time every day.

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@schymane schymane commented Apr 29, 2019

On that note we could add the number of compounds by unique InChIKeys and also the numbers by unique first block to collapse down the (stereo)isomers ... would be an interesting statistic to have.

@meier-rene

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@meier-rene meier-rene commented Apr 30, 2019

Implemented with 50fb7ca and rolled out on the dev server server. I added 3 numbers: Unique Spectra corresponds to the the total number of accessions, Unique Compounds is the count of unique InChI-keys and Unique Isomers is the count of unique first blocks of InChI-keys. I have not added a section of records without InChI-keys which is around 3000 atm. With some work it will come down to less than 900. This can be closed with the next rollout of the official MassBank server.

@meier-rene meier-rene changed the title Add number of compounds to Record Index page [SOLVED] Add number of compounds to Record Index page Apr 30, 2019
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@egonw egonw commented Apr 30, 2019

I updated the entry in Wikidata: https://www.wikidata.org/wiki/Property:P6689

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@schymane schymane commented Apr 30, 2019

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@schymane schymane commented Apr 30, 2019

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@schymane schymane commented Feb 10, 2020

So ... this appears only on the msbi.ipb-halle record index still it seems, but is there an issue with the numbers? More isomers than compounds? What do we mean with "isomer" vs "compound"? Can we name them more accurately?
Unique Compounds (with stereoisomers)
Unique Compounds (without stereosiomers) or Unique Compounds (same skeleton)?
(better ideas welcome, I realise there is space limitation)

https://msbi.ipb-halle.de/MassBank/RecordIndex

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@tsufz

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@tsufz tsufz commented Feb 10, 2020

yep, should he solved next weekend. I am relactant to change the sever in the week because of the service availability. And we have still some issues with the deployment...

@tsufz tsufz closed this Feb 10, 2020
@tsufz tsufz reopened this Feb 10, 2020
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@meier-rene meier-rene commented Feb 11, 2020

So ... this appears only on the msbi.ipb-halle record index still it seems

Yes, thats true but @tsufz is working on that issue. 👍

, but is there an issue with the numbers? More isomers than compounds? What do we mean with "isomer" vs "compound"? Can we name them more accurately?

I implemented my understanding of the topic:
Lets have two Spectra, one from L-Alanin and one from D-Alanin. Than we have one unique compound (Alanin) and two unique Isomers. Do you find this logic irritating? Should we name it differently? Should we count different things?

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@schymane schymane commented Feb 11, 2020

Well the problem is that isomers are defined on many different levels, and most would count a unique stereoisomer as a unique compound - hence the confusion.
I would propose something like Compounds (with stereoisomers) and Compounds (without stereoisomers) to clarify more exactly what you mean. Most users will not really know the InChIKey first block assumption (although many do in the meantime).

@egonw

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@egonw egonw commented Feb 11, 2020

Interesting ontological discussion :)

So, the IUPAC Goldbook does not have a definition of chemical compound or compound, but Wikipedia defines a compound as follows: Chemical compounds have a unique and defined chemical structure held together in a defined spatial arrangement by chemical bonds.

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