Put 583 remaining compounds in Wikidata

[egonw]

By creating a Bacting script that takes PubChem CIDs and adds the corresponding compounds to Wikidata.

[egonw]

@petermr, where can I find the list of 200 CIDs?

[petermr]

on https://github.com/gilienv/EssOilDB/tree/master/tables/chemistry/ It's a bit messy as we have split / forked the chemistry and the disambiguation and cleaning is going on there. Ambarish Kumar is doing a good job, but he's not working on CEV. See gilienv/EssOilDB#76 which has 100 comments and look at the latest. It may be easiest just to download the tables. from /tables/chemistry/ I have posted an html table today. Do you need access? I'll post something.

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On Wed, Aug 28, 2019 at 11:27 AM Egon Willighagen ***@***.***> wrote: @petermr <https://github.com/petermr>, where can I find the list of 200 CIDs? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AAFTCS7XWSVT3XIPHLEOZF3QGZHJ5A5CNFSM4IRB6WNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5KUVEQ#issuecomment-525683346>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFTCS4F4VZAOEYDMGS2HALQGZHJ5ANCNFSM4IRB6WNA> .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[egonw]

I need to part this until at least next week, I'm afraid. I got some urgent stuff to solve first :(

[petermr]

There's no rush

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On Wed, Aug 28, 2019 at 2:57 PM Egon Willighagen ***@***.***> wrote: I need to part this until at least next week, I'm afraid. I got some urgent stuff to solve first :( — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AAFTCSYS5FU2K7RVTTX3PS3QGZ76HA5CNFSM4IRB6WNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5LGZOQ#issuecomment-525757626>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFTCS5AV663QZXN3XGGI4LQGZ76HANCNFSM4IRB6WNA> .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[egonw]

Sorry, there are too many files in that folder... I have no idea at this moment how to see which compounds have not been found in Wikidata yet (and that I should add).

Help/suggestions welcome.

[petermr]

We have copied the 2112 EssoilDB compounds to CEVOpen. @ambarish Kumar <ambari73_sit@jnu.ac.in> is working on them. We found far too many synonyms in PubChem and ChEBI so we've dropped those to about 300 which were found in EssoilDB 1.0 Ambarish , do we have a simple list of compounds in CEVOpen that do not have Wikidata entries?

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On Tue, Sep 10, 2019 at 8:50 AM Egon Willighagen ***@***.***> wrote: Sorry, there are too many files in that folder... I have no idea at this moment how to see which compounds have not been found in Wikidata yet (and that I should add). Help/suggestions welcome. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AAFTCS6OH3AOGXBURWACJM3QI5GSVA5CNFSM4IRB6WNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6KF3FY#issuecomment-529816983>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFTCS6XPN6MJBIIXSTFHRDQI5GSVANCNFSM4IRB6WNA> .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[petermr]

Yes sir. Please check the list of compounds which does not has Wikidata Id. notFoundWikidata.csv - https://github.com/petermr/CEVOpen/blob/master/notFoundWikidata.csv Total number of records 583. On Tue, Sep 10, 2019 at 4:11 PM Peter Murray-Rust < peter.murray.rust@googlemail.com> wrote:

…

We have copied the 2112 EssoilDB compounds to CEVOpen. @ambarish Kumar ***@***.***> is working on them. We found far too many synonyms in PubChem and ChEBI so we've dropped those to about 300 which were found in EssoilDB 1.0 Ambarish , do we have a simple list of compounds in CEVOpen that do not have Wikidata entries? On Tue, Sep 10, 2019 at 8:50 AM Egon Willighagen ***@***.***> wrote: > Sorry, there are too many files in that folder... I have no idea at this > moment how to see which compounds have not been found in Wikidata yet (and > that I should add). > > Help/suggestions welcome. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#5?email_source=notifications&email_token=AAFTCS6OH3AOGXBURWACJM3QI5GSVA5CNFSM4IRB6WNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6KF3FY#issuecomment-529816983>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AAFTCS6XPN6MJBIIXSTFHRDQI5GSVANCNFSM4IRB6WNA> > . > -- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

-- *AMBARISH KUMAR* *M.Tech - 2014-2016* *SC&IS ; Jawaharlal Nehru University,* *New Delhi, INDIA* *+91 - 8377964303* *ambari73_sit@jnu.ac.in <http://goog_1594941533>* *er.ambarish@gmail.com <er.ambarish@gmail.com>*

[petermr]

Thanks Ambarish, Egon does this look tractable? (I suspect that some of these - especially the esters which may have missing spaces - are not what the authors intended, but that doesn't alter the validity of linking Wikidata to Pubchem - it just means they may not get used frequently. On Tue, Sep 10, 2019 at 12:29 PM Ambarish Kumar <ambari73_sit@jnu.ac.in> wrote:

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Yes sir. Please check the list of compounds which does not has Wikidata Id. notFoundWikidata.csv - https://github.com/petermr/CEVOpen/blob/master/notFoundWikidata.csv Total number of records 583. On Tue, Sep 10, 2019 at 4:11 PM Peter Murray-Rust < ***@***.***> wrote: > We have copied the 2112 EssoilDB compounds to CEVOpen. @ambarish Kumar > ***@***.***> is working on them. We found far too many > synonyms in PubChem and ChEBI so we've dropped those to about 300 which > were found in EssoilDB 1.0 > > Ambarish , > do we have a simple list of compounds in CEVOpen that do not have > Wikidata entries? > > > On Tue, Sep 10, 2019 at 8:50 AM Egon Willighagen < > ***@***.***> wrote: > >> Sorry, there are too many files in that folder... I have no idea at this >> moment how to see which compounds have not been found in Wikidata yet (and >> that I should add). >> >> Help/suggestions welcome. >> >> — >> You are receiving this because you were mentioned. >> Reply to this email directly, view it on GitHub >> <#5?email_source=notifications&email_token=AAFTCS6OH3AOGXBURWACJM3QI5GSVA5CNFSM4IRB6WNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6KF3FY#issuecomment-529816983>, >> or mute the thread >> <https://github.com/notifications/unsubscribe-auth/AAFTCS6XPN6MJBIIXSTFHRDQI5GSVANCNFSM4IRB6WNA> >> . >> > > > -- > Peter Murray-Rust > Founder ContentMine.org > and > Reader Emeritus in Molecular Informatics > Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK > -- *AMBARISH KUMAR* *M.Tech - 2014-2016* *SC&IS ; Jawaharlal Nehru University,* *New Delhi, INDIA* *+91 - 8377964303* ***@***.*** <http://goog_1594941533>* ***@***.*** ***@***.***>*

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[egonw]

Yes, thanks!

[egonw]

Processing the file...

[egonw]

This looks promising :)

====================
C₁₇H₂₈O₂ is not yet in Wikidata
====================
====================
C₁₅H₂₀O is not yet in Wikidata
====================
====================
C₁₇H₂₄O₂ is not yet in Wikidata
====================
====================
C₁₆H₂₂O₂ is not yet in Wikidata
====================
====================
C₁₀H₁₆O is not yet in Wikidata
====================
====================
C₉H₁₆ is not yet in Wikidata
====================
====================
C₁₅H₂₆O is not yet in Wikidata
====================
====================
C₁₅H₂₂O is not yet in Wikidata
====================
====================
C₁₅H₂₄O is not yet in Wikidata
====================
====================
C₁₅H₂₆O is not yet in Wikidata
====================

[egonw]

And so does the next step! :) The first 10 missing entries are in (573 to go ;)

[egonw]

For the next batch, I do find hits in Wikidata, tho. But that's not a problem.

[egonw]

Okay, this is the workflow. On the above linked CSV file, I run this script: https://github.com/egonw/ons-wikidata/blob/master/EssOil/prepareInput.groovy This prepares the content for https://github.com/egonw/ons-wikidata/blob/master/Wikidata/createWDitemsFromSMILES.groovy which I run after that. The first (new) script fetches the SMILES for the compounds from PubChem.

[egonw]

I'm now doing the remaining batch: https://tools.wmflabs.org/quickstatements/#/batch/18772

[petermr]

Egon this is great We are writing a paper for mat todd and would be great to put all this in

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On Wed, 18 Sep 2019, 15:59 Egon Willighagen, ***@***.***> wrote: I'm now doing the remaining batch: https://tools.wmflabs.org/quickstatements/#/batch/18772 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AAFTCS4IEXJXKENAXQDFU4LQKI64NA5CNFSM4IRB6WNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ALXUY#issuecomment-532724691>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFTCS2NPURYQCK2RM2MNJ3QKI64NANCNFSM4IRB6WNA> .

[egonw]

Hi all, so what is next for this issue?