search

pombase / website

PomBase website v2
MIT License
6 stars 1 forks source link

Add disease associations to annotation datasets #2197

Closed ValWood closed 2 weeks ago

ValWood commented 3 months ago

Add disease associations to annotation datasets here: https://www.pombase.org/datasets

kimrutherford commented 3 months ago

Which file should we link to?

ValWood commented 3 months ago

Good point, we don't export this file.

We only have: vw253$ more pombase_disease_associations_mondo_ids.tsv SPAC27F1.06c MONDO:0016002 PB_REF:0000003 2024-04-04 SPBC83.01 MONDO:0016576 PB_REF:0000003 2023-12-12 SPBC800.10c MONDO:0016576 PB_REF:0000003 2023-12-12 SPAC1687.09 MONDO:0016576 PB_REF:0000003 2023-12-12 SPBC11G11.02c MONDO:0016576 PB_REF:0000003 2023-12-12 SPAC1420.04c MONDO:0016387 PMID:38068960 2023-12-12 SPAC19B12.13 MONDO:0016387 PMID:38068960 2023-12-12 SPBC16D10.08c MONDO:0859237 PB_REF:0000003 2023-09-14 SPBC16D10.08c MONDO:0014561 PB_REF:0000003 2023-09-14 SPBC16D10.08c MONDO:0030726 PB_REF:0000003 2023-09-14 SPAC977.17 MONDO:0859237 PB_REF:0000003 2023-09-14 SPAC977.17 MONDO:0014561 PB_REF:0000003 2023-09-14

as one input file and the rest generated from Ortholog table and Monarch data.

So could we write out a file of all disease associations in this format?

kimrutherford commented 3 months ago

Looks like we already write a file:

Maybe done for PombeMine?

We need to decide where to put in the data directory: https://www.pombase.org/data/

Looks like we already have a good place in the new release directory structure: https://www.pombase.org/public_releases/pombase-2024-06-01/human_disease_annotation/

ValWood commented 3 months ago

We need to decide where to put in the data directory: [https://www.pombase.org/data/](https://eur03.safelinks.protection.outlook.com/?

We could put in "annotations" or give it its own directory.

We also need to link from here: https://www.pombase.org/datasets under "annotation datasets" so maybe "annotation" is the best place?

kimrutherford commented 3 months ago

We could put in "annotations" or give it its own directory.

I've put it in "annotations" to keep things tidy. I've changed the load script to update the files each night.

I'll make sure everything is in place after Wednesday night's load, then update the datasets docs page.

kimrutherford commented 3 months ago

We need a description to put in the table. Can you improve this for me?:

"Fission yeast orthologs of human disease associated genes with disease descriptions and Mondo ontology terms"

(Mostly copied from: https://www.pombase.org/documentation/disease-association) ("Mondo" could be a link to https://mondo.monarchinitiative.org/)

Thanks.

kimrutherford commented 3 months ago

I think this is done now.

ValWood commented 2 months ago

We have the disease association file in the annotation datasets, but it isn't linked to from the annotations section of the annotation datasets downloads https://www.pombase.org/datasets

ValWood commented 2 months ago

Also orthologs doesn't have a page, although it does have a menu item.

We could combine the orthlogs and disease datasets and change the menu tab to "orthologs and disease)? Thoughts?

kimrutherford commented 2 months ago

We have the disease association file in the annotation datasets, but it isn't linked to from the annotations section of the annotation datasets downloads

There's a "Human disease associations" link in the "Annotation datasets" table?

ValWood commented 2 months ago

Of course. I was looking at the l.h. menu. Should we have all the dataset types mentioned in the menu?