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structures in PDB but don't have an APPROVED session: #3456

Closed ValWood closed 1 year ago

ValWood commented 1 year ago 
          I don't know if it's useful but here's the list of publications with structures in PDB but don't have an APPROVED session:
 PMID:10801440
 PMID:11273706
 PMID:11709168
 PMID:11832950
 PMID:12018481
 PMID:14614509
 PMID:15979093
 PMID:16138082
 PMID:16777962
 PMID:16790931
 PMID:17190600
 PMID:17937917
 PMID:18381891
 PMID:18676809
 PMID:19026779
 PMID:19028693
 PMID:19307292
 PMID:19362535
 PMID:19363481
 PMID:19394293
 PMID:19474788
 PMID:19516334
 PMID:19581297
 PMID:19680239
 PMID:19884503
 PMID:20008938
 PMID:20089861
 PMID:21217703
 PMID:21444718
 PMID:21481773
 PMID:21610214
 PMID:22001694
 PMID:22081013
 PMID:22085934
 PMID:22437499
 PMID:22658721
 PMID:22971103
 PMID:23019579
 PMID:23201273
 PMID:23273506
 PMID:23481256
 PMID:23583778
 PMID:23609449
 PMID:23857276
 PMID:24449894
 PMID:24862735
 PMID:24939935
 PMID:25414009
 PMID:25428765
 PMID:25619998
 PMID:25883047
 PMID:25959226
 PMID:26062005
 PMID:26088418
 PMID:26215567
 PMID:26292707
 PMID:26673708
 PMID:26960127
 PMID:27105116
 PMID:27165520
 PMID:28162934
 PMID:28223353
 PMID:28241144
 PMID:28467824
 PMID:28533364
 PMID:28572513
 PMID:28735863
 PMID:28988770
 PMID:29160296
 PMID:29681468
 PMID:29804820
 PMID:29892076
 PMID:30051891
 PMID:30295604
 PMID:30651569
 PMID:30808655
 PMID:30911189
 PMID:31048492
 PMID:31740076
 PMID:32374864
 PMID:32518066
 PMID:32610137
 PMID:32755595
 PMID:32839613
 PMID:32958768
 PMID:33106658
 PMID:33536434
 PMID:33536435
 PMID:34100774
 PMID:34194665
 PMID:34678589
 PMID:35058438
 PMID:35512546
 PMID:35849625
 PMID:36002457
 PMID:36250672
 PMID:36423630
 PMID:36468882

Originally posted by @kimrutherford in https://github.com/pombase/pombase-chado/issues/1061#issuecomment-1426766722

ValWood commented 1 year ago

Use this list,

ValWood commented 1 year ago
kimrutherford commented 1 year ago

can you remember the difference between the first list and the second list?

One list was publications with structures but the publication isn't in Chado (that's the small list). The longer list was publications with structures that don't have an APPROVED session (there are publication that are in Chado but aren't APPROVED).

ValWood commented 1 year ago

@kimrutherford Can you paste in the IDs that are in the first list but not in the second list (or remind me where the txt file for the 2nd list is)? sorry, I initially thought the fist list was a subset of the second list.

kimrutherford commented 1 year ago

Can you paste in the IDs that are in the first list but not in the second list

All of the publications from the first list will be in the second.

(or remind me where the txt file for the 2nd list is)

Both lists are in this issue: https://github.com/pombase/pombase-chado/issues/1061

IDs not in Chado (as of Feb 12th): https://github.com/pombase/pombase-chado/issues/1061#issuecomment-1426703438

The 2nd list, of PubMed IDs from PDB that aren't APPROVED (which includes the IDs from the previous list) are in a comment that's been marked as outdated in issue 1061 but's also at the top of this issue.

kimrutherford commented 1 year ago

Would you like an updated version of either file?

ValWood commented 1 year ago

I was a bit confused because (at least) the first 2 items in the first list are not in the 2nd list (even though I didn't change them)

ValWood commented 1 year ago

Actually I did do PMID:10801440

but PMID:11273706 is not done yet, but isn't in the second list

ValWood commented 1 year ago

Anyway I don't need an updated list yet. I will continue to work through list 2, then I will request a new list of everything with a structure that has not been through approval. I don't want to start on a new list yet as I have lots of status notes in this one. I think I will be another week or two processing these papers (have done over 30- they are usually quick, but the occasional one slows me down).

kimrutherford commented 1 year ago

PMID:11273706 is not done yet, but isn't in the second list

Now I'm confused. That PMID is only in the second list, the one at the top of this issue. It's in Chado but not approved.

ValWood commented 1 year ago

RIght I'm calling the list at the top the first list. So the bottom list is a subset of the top list- that makes more sense.

ValWood commented 1 year ago
kimrutherford commented 1 year ago

PMID:36358328 not in the list so this might not be all of the structure pubs?

That one we knew about:

https://github.com/pombase/pombase-chado/issues/1061#issuecomment-1427580211

We should check why this structure isn't in https://www.pombase.org/reference/PMID:36358328 (maybe it takes pdb a while to get the structures curated...)

I mailed pdb to see why this structure is missing

On Thursday they emailed me and said:

Thank you for raising this. I have looked into it and resolved it. This should be fixed in next week's release.

The PMID wasn't associated with the structure in PDB. Sorry I forgot to comment about it on the issue.

kimrutherford commented 1 year ago

On Thursday they emailed me and said:

Thank you for raising this. I have looked into it and resolved it. This should be fixed in next week's release.

Sorry, ignore that. I emailed about PMID:35314193. I think it was you you emailed about PMID:36358328

But I've checked and I don't know why PMID:36358328 was missing from the list. I've just re-run the query and it's there. There were no other differences.

ValWood commented 1 year ago

OK, probably a synching issue. It's a recent pub.