Closed beamilon closed 2 months ago
OK, and what user were you logged in as when you made these curations?
Curator
@jorvis: some datasets seem to have escaped the transfer of owner for multigene display. If it is just because you are still implementing them, SORRY.
@jorvis, I added multigene display to these additional datasets.
I haven't done anything here yet. Are these datasets all within the same profiles as mentioned initially?
The first list yes. The second list are datasets in NIHL, cell type-specific transcriptomics, mouse cochlea (Hertzano 2021) and in Noise/Damage/Protection.
More curations done today:
OK. I'll tackle these tonight.
Here are more. I will try to finish tomorrow
Last datasets for now:
This is ready and has run on the Adult profile as a test. When I added your expanded list of datasets though there was at least one instance where there were more than one dataset title with the exact same title. Example:
mysql> select id, date_added, marked_for_removal from dataset where title = 'Spiral Ganglion Neurons (SGN) Response to PTS
-inducing noise (scRNA-seq), violin plot display';
+--------------------------------------+---------------------+--------------------+
| id | date_added | marked_for_removal |
+--------------------------------------+---------------------+--------------------+
| 11f16f75-bfdd-0397-c9c1-e4cf35db5287 | 2021-01-31 22:58:37 | 0 |
| 482cb81f-4816-e4e3-a3fe-514707b847d8 | 2021-01-28 03:54:28 | 0 |
+--------------------------------------+---------------------+--------------------+
We can talk and resolve this tomorrow.
Some datasets have several windows with different displays in the single gene search. The dataset is the same but the title is slightly different like the one below. Is this the problem? I took advantage of the multiple windows to create different multigene displays. Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), UMAP display Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), violin plot display
No, it's totally fine to have the display variations in the title as you've shown just there. The ones which are causing an error are those where the titles are absolutely identical. Here are those datasets owned by curator and how many times that title is found. There is even one which is loaded 9 times.
mysql> select title, count(title) from dataset where marked_for_removal = 0 and owner_id = 499 group by title having count(title) > 1;
+-----------------------------------------------------------------------------------------------+--------------+
| title | count(title) |
+-----------------------------------------------------------------------------------------------+--------------+
| scRNAseq, Atoh1+Ikzf2 overexpression in adult supporting cells, published UMAP (Liu, 2021) | 2 |
| P2, mouse, scATAC-seq, organ of Corti apex and base (Waldhaus) | 2 |
| P1, mouse, scRNA-seq, cochlear epithelium,subset50,demo1 (Kelley) | 9 |
| Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), violin plot display | 2 |
| Elena upload test | 2 |
| CD45+ Cochlear Immune Cells Response to PTS-inducing noise, scRNA-seq, violin plot display | 2 |
| Lateral Wall Response to PTS-inducing noise (scRNA-seq), violin plot display | 2 |
| Lateral Wall Immune Cells Response to PTS-inducing noise, scRNA-seq, violin plot display | 2 |
+-----------------------------------------------------------------------------------------------+--------------+
I see. I will check with Ronna because I am sure that some of the duplicates can be removed but we need to make sure that even though the title is the same, the data within them are exactly the same.
All of the datasets within the profiles initially posted in this ticket have been updated.
Can do the rest when we work out the duplication issue.
I started looking at the duplicates.
All the needed datasets have multiple displays now. So I think this ticket can be closed.
I added a display for P0, mouse, RNA-seq, hair cells vs epithelial non-hair cells (Hertzano) So ticket not ready to be closed I guess.
I think that these 2 datasets were not transferred as default. They are in curator but not in my account 4dpf, zebrafish, microarray, hair cell, mantle cell and skin (Hudspeth) 5dpf, zebrafish, RNA-seq, hair cell (IP) and whole larvae input (IN) (Hertzano)
Now that the following dataset has been fixed, I created a multigene display 4dpf, zebrafish, RNA-seq, TU-tagged hair cells mRNA and whole larvae input (Nicolson)
Closing due to inactivity
I have curated multi-gene displays for all datasets in the following profiles (very few have issues and I am keeping track of them and will create tickets later):