Some errors to correct - Githubissues

bigbio / proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

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Some errors to correct #132

Closed ypriverol closed 2 years ago

ypriverol commented 4 years ago

[x] I think the source names are not correct in https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD002088/sdrf.tsv they differ between fractions
[x] in https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD004452/sdrf.tsv it also does not contain the enzyme
- [x] https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD005940/sdrf.tsv does not contain a fraction identifier
- [x] https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD005946/sdrf.tsv replicates are not annotated should have a column
- [x] https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD006401/sdrf.tsv source name changes between fractions
- [x] in https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD006675/sdrf.tsv source name changes between fractions
- [x] https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD008840/sdrf.tsv has associated file uri but not file uri
- [x] In https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD010154/sdrf.tsv entries with
  AC=MS:1002631;EThcd/ETD are missing the "NT="
- [x] https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD012203/sdrf.tsv seems to contain multiple tabs or whitespaces (I guess there should be "not available" instead)
- [x] https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/annotated-projects/PXD000561/sdrf.tsv here also the source name changes between fractions

StSchulze commented 4 years ago

In PXD011799 the label column indicates that TMT16plex was used but in the modification parameters TMT6plex is given.

In general, is there any plan to implement a system that tries to guarantee the accuracy of the information provided in the SDRF files? E.g. it could be required to have every SDRF file checked by at least two members of the community before accepting it?