Comments on Download Page

[pfey03]

https://testdb.dictybase.org/downloads

1. This long reference on top is ridiculous. Why on top and so big?? Please remove for now. We should add references to the Dicty anatomy, the genome seq, maybe others and have to think how we do add them at bottom.

2. When clicking on any Download, open in new tab or window automatically? After I first clicked and it overwrote the downloads page and I couldn't even go back I now do right click to open in new tab. But maybe should do automatically?

3. I thought we decided not to have this anymore? https://betastorage.dictybase.org/downloads/44689/gene-information/DDB_G-curation_status.txt Instead we should just have a table for DDB ID mapping? Gene Prediction (Old vs Up to date (Mostly curated)like the ID Converter where it's hard to do all.

4. Maybe in 'Dictyostelium Sequences and Annotations' it should not only say what entity but what format, e.g. FastA format.

5. @cybersiddhu I think the protein domain data should be with Gene ID (DDB_G) and not Feature ID (DDB). Is that possible? I'm surprised at the DDB ID as it's proteins and those are mapped to DDB_G ID?

6. This seems too old: 'N-terminal myristoylation sites (July 2006)'. Maybe don't have here and add when we have an update?

Thanks!

[pfey03]

Other Genome Download - Reference

To be consistent with what we do for Dd, put the citation at bottom here and once we do Dd we decide what shorter format we use

[cybersiddhu]

For the references,

• If there are many of them each tied to a particular download file, have a separate page to display them. A simple(decent looking) two columns table like display should suffice.
• The citation should be shorten, first author or first three authors et.al., could make it less crowded.

[pfey03]

References for Download

Genome Sequence: Eichinger et. al 2008
AX2 Phosphoproteome: Charest et. al 2010
Anatomy ontology: Gaudet et. al 2008
dictyBase: Fey et al 2013; Basu et al 2015

Maybe we should have one Ref page for all genomes. Then we might have this order:

D. discoideum Genome
D. purpupureum Genome
D. fasciculatum Genome
P. pallidum Genome
AX2 Phosphoproteome
Anatomy ontology
dictyBase

[erichartline]

Some updates based on the original post:

1. I have shortened the citations to first author et. al
2. I will change this in the next frontpage release
3. I added the file formats to that section
4. I have removed that reference for now