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Used for issue tracking of data curation efforts.
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Curating Matt's hotspot list + a list from a Nanture review paper #100

Open ritikakundra opened 8 years ago

jjgao commented 8 years ago

@ritikakundra @chenh4 I converted the file into a check list. Maybe you can check off the ones that are already imported and put them into a separate group.

ritikakundra commented 8 years ago

Sure, Thanks!

chenh4 commented 8 years ago

Need to get DOI number from Matt Got the MAF file from Matt, there are 60 studies in total.

chenh4 commented 8 years ago

Already separate them into per study per folder/maf file

ritikakundra commented 8 years ago

NCBI has a tool to convert the DOI to PMID. Will change them to PMIDs

chenh4 commented 8 years ago

Could you please convert these DOI numbers to pmid id for me? And what else information can you get from the conversion? Or only pmid is fine.

Thanks a lot, Annice

From: ritikakundra notifications@github.com<mailto:notifications@github.com> Reply-To: cBioPortal/curation reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, March 24, 2016 at 3:56 PM To: cBioPortal/curation curation@noreply.github.com<mailto:curation@noreply.github.com> Cc: "Chen, Hsiao-Wei/Sloan Kettering Institute" chenh4@mskcc.org<mailto:chenh4@mskcc.org> Subject: Re: [curation] Curating Matt's hotspot list (#100)

NCBI has a tool to convert the DOI to PMID. If you can attach the DOI list, I can give you the PMIDs

— You are receiving this because you were assigned. Reply to this email directly or view it on GitHubhttps://github.com/cBioPortal/curation/issues/100#issuecomment-200992915

doi:10.1038/ng.2246 doi:10.1126/science.1239947 doi:10.1038/ng.2323 doi:10.1038/nature11284 doi:10.1038/ng.2468 doi: 10.1126/science.1206923 doi:10.1073/pnas.1314608110 doi:10.1172/JCI64400 doi:10.1038/ng.2493 doi:10.1038/ng.2396 doi:10.1038/ng.2359 doi: 10.1038/ng.1032 doi:10.1038/ng.2529 doi:10.1016/j.cell.2013.03.021 doi: 10.1016/j.cell.2012.08.029 doi:10.1016/j.cell.2012.04.023 doi:10.1038/nature10910 doi:10.1016/j.ccr.2013.12.015 doi: 10.1038/ng.2291 doi:10.1038/ng.2611 doi:10.1016/j.cell.2012.06.024 doi:10.1038/nature11154 doi:10.1038/nature11412 doi:10.1038/nature10166 doi:10.1038/nature11282 doi:10.1126/science.1200609 doi:10.1038/nature11125 doi:10.1038/ng.2508 doi:10.1038/ng.2938 doi:10.1038/nature10496 doi:10.1038/ng.1041 doi: 10.1016/j.cell.2013.01.019 doi:10.1038/ng.2279 doi: 10.1016/j.cell.2013.09.034 doi:10.1038/nature10738 doi:10.1038/nature10351 doi:10.1038/ng.2405 doi:10.1038/ng.788 doi:10.1038/nature11213 doi: 10.1038/nature12222 doi: 10.1038/nature11329 doi:10.1038/nature11404 doi:10.1038/nature12477 doi:10.1126/science.1196333 doi:10.1038/ng.2591 doi:10.1038/ng.2643 doi:10.1126/science.1226344 doi:10.1038/nature11547 doi: 10.1126/science.1208130 doi: 10.1038/nature13176 doi: 10.1038/ng.1014 doi:10.1038/nature11252

doi: 10.1056/NEJMoa1301689

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ritikakundra commented 8 years ago

MattsPMID_LIst.xlsx

IT"S PERFECT! THANKS! (by Annice)

ritikakundra commented 8 years ago
ritikakundra commented 8 years ago

Also:

chenh4 commented 8 years ago

This is the validation paper pmid validation_paper_pmid.txt

ritikakundra commented 8 years ago

I guess we have a list to go forward.

chenh4 commented 8 years ago

@ritikakundra @jjgao I compared the PMID list above with the ones existing in cBioPortal, and we only have 13 new studies to curate!!!

PMID: 22237025 22197930 22683710 23202128 23583981 24705251 22923433 20826764 23143597 23945592 22608083 23263491 22484628

And I compared these 13 PMID with the ones in Niki's list (16 studies), here is the union set (27 in total): 22237025 22197930 23202128 23583981 24705251 22923433 20826764 23143597 23945592 22608083 23263491 22286061 21248752 22683710 22484628 22722193 21822264 22561517 22922871 22817890 21995386 21670202 21642962 22150006 21390126 21804550 21430775

ritikakundra commented 8 years ago

Annice:

@ritikakundra Ritika:

Nik's list (whole new studies):

chenh4 commented 8 years ago

@ritikakundra
Studies.zip

All the 13 paper with individual mutation maf files. Let me know how do you want to divide the works. Thank you!