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Show source/evidence for features on mouse over #2231
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Some of the features from UniProt have an evidence qualifier that includes a PubMed ID:
In that case we should use that as the reference instead of the UniProt paper. |
Yes definitely but that links to the comment in this this ticket: "First, I think we need to extend our MOD data format file to include an "assigned by" column so that all of these have "assigned_by" UniProt" so that we can capture the experimental source, and the source of the curation. |
I've implemented that for the annotations created directly from the UniProt data file. That's the lipidation sites, glycosylation sites, disulfide bonds and modifications from Those annotations will have the There are also some UniProt annotations that were put in After that I'll work on display the assigned_by in the display. |
I've now added an "Assigned_by" column to |
Only for modifications for now. Refs pombase/website#2231
We now get the reference from the data file and just annotated assigned_by UniProt. Refs pombase/website#2231
I'm working on storing and displaying the PubMed ID . Some features from UniProt have more than one evidence code and reference. For example csx1 / SPAC17A2.09c:
For now the code is just using the first evidence code and reference. Most of the processing and display code can only handle one evidence code and one reference per annotation so we would need to split these cases into multiple annotations if we want to capture them. |
These look like: /evidence="ECO:0000269|PubMed:24352239" Previously we were just storing the evidence code. Refs pombase/website#2231
This is great. Will we be able to see the PubMed ID in the pop-up on the protein feature viewer? This would be very useful. |
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I'll add it. It will be a little annoying that you can't click on it though.
There is no filtering yet. |
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Do you mean the example in the screenshots? It was https://www.pombase.org/gene/SPAC26H5.10c (I think). Sorry, I should have included a link. |
Is the PubMed ID best? We could put the citation as well or instead? |
Maybe the citation would be better than the PMID
we can chat about the longer term options on the next call. I have some vague ideas.... |
I think we should add this. It seems a bit odd not to....
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