Updates needed for GCID version of gEAR

[jorvis]

Transforming a list of issues e-mailed from Julie into tasks/questions:

• [x] https://github.com/IGS/gEAR/issues/128
• [x] #147
• [x] Restore functionality with aliases
• [x] Wants bar charts for graphs vs. life cycle SVGs
• [x] Want red -> blue color coding for these
• [x] Wants Z-scores to be included
• [x] #440
• [x] Need publications and GEO added for datasets
• [x] Want nematode specific example genes on the home page
• [x] Correct grant number in page footer
• [ ] Put links out to Wormbase, Vectorbase, for appropriate organisms (NEED standard IDs first)
• [x] https://github.com/IGS/gEAR/issues/249
• [x] Make gene carts for each of the primary profiles
• [x] Make multi-gene curations for each of the primary profiles
• [x] Migrate Joana's datasets from gEAR to GCID?
• [x] Create a lab group for "Hotopp lab" (Julie doesn't have an account)
• [ ] Verify Julie's Wolbachia dataset is using the correct IDs (IDs in manuscript are desired)
• [ ] #257
• [ ] Verify that all datasets have been migrated from old to new GCID (work has already been done here)
• [x] https://github.com/jorvis/gEAR/issues/1030
• [x] https://github.com/jorvis/gEAR/issues/1159
• [x] https://github.com/jorvis/gEAR/issues/1155

[songeric1107]

I think only these two are left.

https://github.com/jorvis/gEAR/issues/1030

Rhizopus delemar (taxon: 246409)

Aspergillus fumigatus (taxon: 330879)

[adkinsrs]

Added red/blue barcharts for the two Brugia Malayi datasets that did not have them. Left one as the SVG default and changed the other to use the barchart as default

[songeric1107]

upload two Rhizopus delemar datasets and create a profile. all the others are in the gcid already

https://gcid.umgear.org/p?l=a20d57ee

[jorvis]

@songeric1107 @adkinsrs

What's the status of Aspergillus dataset migration? I don't see any in the system still

[songeric1107]

I am working on it now

[songeric1107]

load the Aspergillus to gcid. https://gcid.umgear.org/p?l=7be3a9d6

however, the curated image could not display in the front page.

[songeric1107]

similar for Rhizopus profile. my curation could not display in the front page.

https://gcid.umgear.org/dataset_curator.html#/dataset/7e0184d0-2d30-6faa-0f38-34b89cef477d/displays

[adkinsrs]

I'm loading Aspergillus and Rhizopus genes into the mysql database. List provided by @songeric1107 and I am keeping track of "gene" table row indexes in case we get better annotations and want to reupload

[adkinsrs]

Use cases for mapping

• synonym search (2-way, 3-way, etc) - i.e. Wolbachia - No matter what synonym is searched, show relevant panel result.
• Host-Pathogen-Vector - Show panels of host and pathogen and vector in separate panelsof gen
  • Currently we can do this by having a list of genes from all panels, and search through this.
  • Worth noting that in single-gene situations, we still have to click result-by-result.
• Ensure multigene displays support both of the above scenarios as well. Supports viewing genes across multi-species
  • This works if the user has a gene cart with a mix of IDs across species, and dataset panels representing different species will show heatmaps for those respective species.
• Can we deal with one-to-many gene mapping with respect to showing panels? Suggestions were to preferably show a tree selection for the user to select from, or a tabbed selection. We are really liking the idea of showing a tree to let a user select which mappings to display.

[jorvis]

Wolbachia paper with ID mapping needs examples:

https://journals.asm.org/doi/full/10.1128/mSystems.00596-19#fig9

[adkinsrs]

so… i don’t think i have an actual wolbachia gene mapping file. Pretty sure I created something by extracting the entries from the database on the old GCID server. But we can recreate it using the mySQL gene.ensembl_id to gene.gene_symbol fields where the gene_symbol would be the aliases.

One concerning thing is that the ensembl IDs were just listed as “gene####” (generated by a grad student), and they map to wBM#### or WBM_RS####, but not WBGene#### (which was never given to me nor in the old database

[adkinsrs]

So for Julie’s data: WBGene - Brugia accession wBm & WBM_RS - Wolbachia wBm strain

All are loaded in the GCID database, and we can map aliases for wBm to WBM_RS (though I need to ensure the script I have does what I think it does). I asked him if there is an host-pathogen ortholog mapping between Brugia and Wolbachia and waiting for a response. I’m guessing we may want that, as she may have asked for the ability to search for that at one point.

UPDATE - Julie says no ortholog mapping between Brugia & Wolbachia wBm

[adkinsrs]

Wolbachia - http://bacteria.ensembl.org/Wolbachia_endosymbiont_strain_trs_of_brugia_malayi_gca_000008385/Info/Index Brugia - https://wormbase.org/species/b_malayi#03--10