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japonicusdb / japonicus-curation

Data files for JaponicusDB
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over riding pombase GO inferences #54

Open ValWood opened 1 year ago

ValWood commented 1 year ago

I thought we had a file that I could add S. j gene names and this would override the inferences from PomBAse. We would use this when the biology diverges. I'm pretty sure it exists because I remember using it for Mid1, but wherever I did it, it doesn't seem to be working. I can;t locate such a file.

kimrutherford commented 1 year ago

Hi Val. I can't remember implementing that.

We can only override gene names and products.

ValWood commented 1 year ago

OK, I think that is what I was remembering.

It would be useful to implement the equivalent to the pombe GO filter

pombe-embl/goa-load-fixes filtered_GO_IDs This would allow me to remove GO annotation by term.

We might not need to do this if the NOT annotation over rides an IEA (I'm not sure if it does so I will test first)

kimrutherford commented 1 year ago

It would be useful to implement the equivalent to the pombe GO filter

That's no problem. It's just a matter of making a file of GO term IDs to filter and then adding an extra flag to the command the loads the pombe annotation into the japonicus Chado.

We might not need to do this if the NOT annotation over rides an IEA (I'm not sure if it does so I will test first)

That's not implemented as far as I remember.

kimrutherford commented 1 year ago

It would be useful to implement the equivalent to the pombe GO filter

I've added that to the load script. So now if you want to filter a term from the pombe annotation as it gets mapped over to japonicus, add it to: https://github.com/japonicusdb/japonicus-curation/blob/main/inferred_from_pombe_filtered_GO_IDs

Currently when loading the GOA GAF, we use the pombe filter file: pombe-embl/goa-load-fixes/filtered_GO_IDs but we could use a different file if we needed.

ValWood commented 1 year ago

Change name inferred_from_pombe_filtered_GO_IDs to japonicus_only_filtered_GO_IDs

and use as a filter for external data from any source (PomBase and GOA)

kimrutherford commented 1 year ago

Change name ... and use as a filter for external data from any source (PomBase and GOA)

Both done for tonight's load.

ValWood commented 1 year ago

I can't find the file. I want to add

https://www.japonicusdb.org/results/from/id/18714f6d-2a72-46c7-8d2e-a0a7958e8c94 GO:0006094 to it.

(will be a good test) After it works I will also add a GO taxoin restriction (belt and braces)

kimrutherford commented 1 year ago

We decided to give it a more accurate name. It's here: https://github.com/japonicusdb/japonicus-curation/blob/main/japonicusdb_only_filtered_GO_IDs currently empty.

ValWood commented 1 year ago

Right I was looking in the git directory- I'm not completely sure how to find this file?

kimrutherford commented 11 months ago

I'm not completely sure how to find this file?

Do you have a check-out of the japonicus-curation repository?

Otherwise you could edit it here: https://github.com/japonicusdb/japonicus-curation/blob/main/japonicusdb_only_filtered_GO_IDs

ValWood commented 10 months ago

I added GO:0006094 to the filter. https://www.pombase.org/results/from/id/77ff00e4-bf1b-4170-9b10-6fe39a1a0de1 should be empty tomorrow.

@snezhkaoliferenko if you see any other GO annotations which do not apply to japonicus , or are incorrect in any way let me know, I can filter them.

Note to self, once this is working, request a taxon filter for this term for S. japonicus. This will fix in UniPRot, GO etc.

snezhkaoliferenko commented 10 months ago

thanks!

From: Val Wood @.> Sent: 17 August 2023 18:05 To: japonicusdb/japonicus-curation @.> Cc: Snezhana Oliferenko @.>; Mention @.> Subject: Re: [japonicusdb/japonicus-curation] over riding pombase GO inferences (Issue #54)

I added GO:0006094 to the filter. https://www.pombase.org/results/from/id/77ff00e4-bf1b-4170-9b10-6fe39a1a0de1 should be empty tomorrow.

@snezhkaoliferenkohttps://github.com/snezhkaoliferenko if you see any other GO annotations which do not apply to japonicus , or are incorrect in any way let me know, I can filter them.

Note to self, once this is working, request a taxon filter for this term for S. japonicus. This will fix in UniPRot, GO etc.

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ValWood commented 10 months ago

That worked. I need to also block

GO:0045721 | negative regulation of gluconeogenesis GO:0045722 | positive regulation of gluconeogenesis