user uberstrain or barcode as the key field for user upload curations
Issue #80
resolved
on top of accessions ?
Comments (6)
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- attached octavia.txt
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- marked as blocker
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- changed status to resolved
Fixed Issue 80: user uberstrain or barcode as the key field for user upload curations
→ <<cset 0abfbd18bc1a>>
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See commit 0abfbd1
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Fixed Issue 80: user uberstrain or barcode as the key field for user upload curations
→ <<cset 0abfbd18bc1a>>
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From Mark :
Martin, here is another file that cannot be uploaded to S enterica. When you are working on EnteroBase again, please inform me why these files cannot be uploaded. Also please give me an indication of when these problems will be fixed and put up an FAQ with that information on the help page. Finally, please upload it when the problem is fixed and notify me.
You should probably read RefMan 11956 to see what we are missing. This paper describes a variety of serial isolates from carriers that need to contain that information in EnteroBase. So we need a clickable link to the PubMed ID. We need a way of grouping strains from a single patient in an Ueberstrain but in such a way that we can readily compare the SNPs differentiating them from each other. A typical Ueberstrain would not be appropriate, unless we expand its tools.We also need to look at the original records to find out what these strains are because the strain names differ from what is in the publication.
It is not that this paper is particularly important but it reveals some of the missing functionality that EnteroBase should be providing.
Zhemin, there is a second paper from Octavia in RefMan 11957 describing a phage-like plasmid. We should really check just how much of that plasmid we were able to assemble ourselves and include the plasmid genome within the appropriate ueberstrain. So this is another problem of how to add just a plasmid genome to the ueberstrain.