pubchem issueshttps://git-r3lab.uni.lu/eci/pubchem/-/issues2023-07-07T18:04:47+02:00https://git-r3lab.uni.lu/eci/pubchem/-/issues/40Convert Transformations.R into RMarkdown2023-07-07T18:04:47+02:00Emma SchymanskiConvert Transformations.R into RMarkdownhttps://git-r3lab.uni.lu/eci/pubchem/-/issues/37Add PFAS for DW to PFAS Tree2023-06-19T12:59:51+02:00Emma SchymanskiAdd PFAS for DW to PFAS TreeAdd 20 & 24 PFAS relevant for drinking water into the PubChem PFAS Tree (ZeroPM webinar 19 June 2023)Add 20 & 24 PFAS relevant for drinking water into the PubChem PFAS Tree (ZeroPM webinar 19 June 2023)Emma SchymanskiEmma Schymanskihttps://git-r3lab.uni.lu/eci/pubchem/-/issues/36Split downloading sources into a separate service2022-11-19T10:26:52+01:00Todor KondicSplit downloading sources into a separate serviceTransfer the Build System to a Separate Repositoryhttps://git-r3lab.uni.lu/eci/pubchem/-/issues/35Ensure the build machines know about the move2022-11-19T10:26:05+01:00Todor KondicEnsure the build machines know about the moveeci-02, pf0322eci-02, pf0322Transfer the Build System to a Separate Repositoryhttps://git-r3lab.uni.lu/eci/pubchem/-/issues/34Move pubchemlit build system2022-11-19T10:25:08+01:00Todor KondicMove pubchemlit build systemTransfer the Build System to a Separate Repositoryhttps://git-r3lab.uni.lu/eci/pubchem/-/issues/33Split depositor into a new repo2022-11-19T10:24:16+01:00Todor KondicSplit depositor into a new repoTransfer the Build System to a Separate Repositoryhttps://git-r3lab.uni.lu/eci/pubchem/-/issues/31New eval4pub info request2022-01-31T22:00:12+01:00Emma SchymanskiNew eval4pub info request@todor.kondic do you think it would be possible to add to the PCL evaluation tracking:
- Total number of entries in PCL
- Total number of entries per annotation category
(and if we can get this overview for earlier versions - great!)
T...@todor.kondic do you think it would be possible to add to the PCL evaluation tracking:
- Total number of entries in PCL
- Total number of entries per annotation category
(and if we can get this overview for earlier versions - great!)
This would help greatly to track dramatic shifts in annotation content - that may not necessarily affect the overall ranking performance.https://git-r3lab.uni.lu/eci/pubchem/-/issues/28Update GitLab paths2022-11-19T10:18:53+01:00Emma SchymanskiUpdate GitLab pathsNeed to replace `git-r3lab.uni.lu` with `gitlab.lcsb.uni.lu` in many locations...Need to replace `git-r3lab.uni.lu` with `gitlab.lcsb.uni.lu` in many locations...https://git-r3lab.uni.lu/eci/pubchem/-/issues/27"Chemical Class" lists in SLE2021-09-09T15:15:02+02:00Emma Schymanski"Chemical Class" lists in SLEFigure out which SLE lists would have information suitable for the "Chemical Class" section (eg like PFAS and PMT). E.g. CyanoMetDB: https://pubchem.ncbi.nlm.nih.gov/compound/155802454#section=Chemical-Classes
Reasses whether some of "...Figure out which SLE lists would have information suitable for the "Chemical Class" section (eg like PFAS and PMT). E.g. CyanoMetDB: https://pubchem.ncbi.nlm.nih.gov/compound/155802454#section=Chemical-Classes
Reasses whether some of "Use Classification" (currently under properties) could be better placed as "Use Classes" under "Chemcial Classes". What subheader is appropriate for chemicals classified according to properties (PFAS, PMT) rather than use?Emma SchymanskiEmma Schymanskihttps://git-r3lab.uni.lu/eci/pubchem/-/issues/25Haz and Expo Scores into PCL2021-07-05T11:12:01+02:00Emma SchymanskiHaz and Expo Scores into PCLIt would be useful to merge the KEMI Haz and Exposure scores into PCL once we have XlogP3 (see #19 #24) tidied up and CCS #18 added (still WiP). @emma.schymanski needs to find most suitable file to merge in ...It would be useful to merge the KEMI Haz and Exposure scores into PCL once we have XlogP3 (see #19 #24) tidied up and CCS #18 added (still WiP). @emma.schymanski needs to find most suitable file to merge in ...https://git-r3lab.uni.lu/eci/pubchem/-/issues/22multiple-CIDs in extractAnnotations.R2021-05-08T18:07:30+02:00Emma Schymanskimultiple-CIDs in extractAnnotations.RFor now a placeholder issue, here is the reference to the code affected:
https://git-r3lab.uni.lu/eci/pubchem/-/blob/master/annotations/tps/extractAnnotations.R#L196
A long discussion went on in emails May 5-7 (with Paul T, plus Asta,...For now a placeholder issue, here is the reference to the code affected:
https://git-r3lab.uni.lu/eci/pubchem/-/blob/master/annotations/tps/extractAnnotations.R#L196
A long discussion went on in emails May 5-7 (with Paul T, plus Asta, Jeff, Evan) and is summarized here:
https://git-r3lab.uni.lu/mira.narayanan/transformation-products/-/issues/2https://git-r3lab.uni.lu/eci/pubchem/-/issues/21Stereochemistry functions2021-05-06T14:32:27+02:00Emma SchymanskiStereochemistry functionsSome inputs about stereochemistry from Paul:
https://www.ncbi.nlm.nih.gov/pccompound?cmd=Link&LinkName=pccompound_pccompound_parent_isotopes_pulldown&from_uid=445
and
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/445/cids/JSO...Some inputs about stereochemistry from Paul:
https://www.ncbi.nlm.nih.gov/pccompound?cmd=Link&LinkName=pccompound_pccompound_parent_isotopes_pulldown&from_uid=445
and
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/445/cids/JSON?cids_type=same_parent_isotopes
will give the same list, the query CID will always come first in the list, but the ordering of the others is basically arbitrary.
...
>“get me a stereochemistry neutral parent”
First get the parent, e.g.
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/44229196/cids/JSON?cids_type=parent
… and then take the result of that (cid 9899562) and get stereo variants with
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/9899562/cids/JSON?cids_type=same_isotopes
same as this if you want to just look at the list visually:
https://www.ncbi.nlm.nih.gov/pccompound?cmd=Link&LinkName=pccompound_pccompound_sameisotopic_pulldown&from_uid=9899562
OR
with PUG REST in two steps.
First get the (7) stereo variants of the parent like above, but store the list for use in a second call:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/9899562/cids/JSON?cids_type=same_isotopes&list_return=listkey
```
{
"IdentifierList": {
"ListKey": "1550642116508648379",
"Size": 7,
"EntrezDB": "pccompound",
"EntrezWebEnv": "MCID_6093c529f6ba3b5f61217454",
"EntrezQueryKey": 1,
"EntrezURL": "https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&hinit=true&db=pccompound&WebEnv=MCID_6093c529f6ba3b5f61217454&query_key=1"
}
}
```
Then use that listkey to get stereo atom (sp3) and bond (sp2) information:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/listkey/1550642116508648379/property/AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount/JSON
Note that CID 445 is the only one with fully undefined (undefined count = total) atom stereo:
```
{
"CID": 445,
"AtomStereoCount": 2,
"DefinedAtomStereoCount": 0,
"UndefinedAtomStereoCount": 2,
"BondStereoCount": 0,
"DefinedBondStereoCount": 0,
"UndefinedBondStereoCount": 0
}
```https://git-r3lab.uni.lu/eci/pubchem/-/issues/18CCS into PCL2021-11-08T10:01:44+01:00Emma SchymanskiCCS into PCL@todor.kondic this is currently a placeholder issue ... CCSbase will provide a new input file for us to merge into our Jan 1, 2021 Exposomics file, and then we can work on how to do this automatically ...
My preference would be to have a...@todor.kondic this is currently a placeholder issue ... CCSbase will provide a new input file for us to merge into our Jan 1, 2021 Exposomics file, and then we can work on how to do this automatically ...
My preference would be to have a separate Zenodo record for the CCSbase version (the file is quite a bit bigger), and we will have to figure out how to run updates our side.
> If it is just a few hundred or thousand, batch prediction function should work well. Or you can write a script to access the web interface to integrate with your other programs.
[https://ccsbase.net/predictions](https://ccsbase.net/predictions)
[https://ccsbase.net/about](https://ccsbase.net/about)
Our current first version:
[https://zenodo.org/record/4081057](https://zenodo.org/record/4081057)