Plasmid and Strain - reference import guide

[pfey03]

It's important that we do NOT import any of Jakob's internal references, like d456, NOR should we have any Alternative References Fields anymore.

Jakob went overboard and got the two fields, maybe in the early days we could not add >1 PMID into the ref field.

IF POSSIBLE: Jakob sometimes entered a second PMID into Alternative refs. When I see it I add to other PMID after comma. But for those still trapped in the Alternative reference field would be nice to add to the list of PMIDs, so those don’t get lost. Only if possible.

Thanks!

[pfey03]

The fields in the annotation tool are as follows and labeled Y or N:

Strain: Pubmed ID (Enter multiple references separated by a comma) YES Franke Reference Library reference ID NO Additional references NO

Plasmid: Pubmed ID YES Internal literature reference ID NO Additional references NO

[pfey03]

BUT, Probably we need to add DOI:

Could we have it in same field or a separate?

• PMID or DOI or 2 fields?

Our internal DSC ref that we need to add, I believe we can create a DOI for that?

[pfey03]

@cybersiddhu, could you remind me, where can I create a DOI reference? And is this the way to create a DSC reference to cite these phenotypes: https://github.com/dictyBase/migration-data/blob/master/strain/DSC_phenotypes_import.tsv

Also are you on track importing these? The original file is here: https://github.com/dictyBase/migration-data/blob/master/strain/DSC_phenotypes_orig.tsv

Thanks!

[cybersiddhu]

To get a free doi for internal references go here and upload the reference. It will be a good practice to have a doi for all of our internal references. And i think we can do the same for any of our public presentations. After that, i could add doi for any record. I think the phenotypes are exported as planned, nothing is really left behind, i don't see any phenotype import related issue(s). You can check them here https://github.com/dictyBase/Migration/issues?q=is%3Aissue+is%3Aopen+label%3A%22DSC+import%22 and here https://github.com/dictyBase/Migration/issues/31 (this is the master tracker)

[pfey03]

This issue has too many topics. I add a new issue for DOI. This should be just about the current messy references to clean up in the NEW database. See the TOP 2 COMMENTS

[cybersiddhu]

• Give me a strain/plasmid id with alternate PMID.
• Verify if the export script is looking for PMID in the alternative field.

[pfey03]

Here is a strain ID with a PMID in the alternate ID field: DBS0236808 The PMID buried there is: 559083

[cybersiddhu]

55