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Bad PMIDs in downloads/iptmnet/current/ptm.txt #630

Closed rykahsay closed 1 year ago

rykahsay commented 1 year ago

It looks like the following PMIDs from downloads/iptmnet/current/ptm.txt are invalid -- please check these to confirm

1629231415665377 1733095019823750 1840795619684113 1840795619779198 1977919816844691 1977919817563356 1982375019795423 2019027818407956 2117749518407956 2117749519684113 2117749519779198 2117749520702584 31745324 33428935 33431121 33451558 33451567 33451735 33453820 33453904 33453959 33455663 33473134 33498134 33516355 33516356 33516365 33526191 33563945 33580028

jeet-vora commented 1 year ago

Hi Hongzhan and Chuming, Hope you are doing well.

While processing iPTMnet data from ptm.txt file for GlyGen we found out there are few PMIDs (at least for the species data we integrate) to be invalid/obsolete, attached below. The first 12 PMIDs are 16 digits long and are invalid, however if you split them into 8 digits and perform a search they are valid PMIDs. e.g.1629231415665377 > 16292314 | 15665377 16292314 - Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae15665377- Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway The rest of the 18 PMIDs are invalid or obsolete and thus yield no result.  All these PMIDs are also visible in your frontend aswell. There could be other similar PMIDs which could be invalid/obsolete in the file. Can you please review these PMIDs and make necessary changes in the ptm.txt file. Many thanks.

1629231415665377 1733095019823750 1840795619684113 1840795619779198 1977919816844691 1977919817563356 1982375019795423 2019027818407956 2117749518407956 2117749519684113 2117749519779198 2117749520702584 31745324 33428935 33431121 33451558 33451567 33451735 33453820 33453904 33453959 33455663 33473134 33498134 33516355 33516356 33516365 33526191 33563945 33580028

jeet-vora commented 1 year ago

Aug 22, 2023 Hello Jeet,

Thanks for letting us know about these issues. Please remove those problematic PMIDs for now. We have just checked those 16 digit PMIDs. They actually came from a source data file. We will look into this problem.

Best,

Hongzhan