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PomBase website v2
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Remap the DO slim to Mondo #1108

Closed ValWood closed 4 years ago

ValWood commented 5 years ago

from https://github.com/pombase/website/issues/989

similar to https://www.pombase.org/browse-curation/fission-yeast-go-slim-terms

kimrutherford commented 5 years ago

I've added the code to make the table, but there's no text on the page yet and there is no link to it: https://www.pombase.org/browse-curation/disease-slim

Let me know what text you'd like or you can directly edit the text directly here: https://github.com/pombase/website/blob/master/frontend/src/docs/browse-curation/disease-slim.md

ValWood commented 5 years ago

Looks great!

ValWood commented 5 years ago

For approval by @Antonialock @mah11

A "slim" is a high-level subset of an Ontology terms and their annotations. The table below shows disease grouping terms from the we have selected for a "disease slim-set", and the number of annotations to each term. DO IDs link to PomBase ontology term pages. The annotation totals link to pages with information about the term and a list of annotated genes. A gene may be included in more than one slim set.

If you would like to see additional grouping terms in the slim, please contact the

ValWood commented 5 years ago

We should add a link to

Genes with a DO: term which do not map to a broad classifier XXX

ValWood commented 5 years ago

see https://github.com/pombase/website/issues/1514

Because it is quick to do, if we provide a flat file like this:

https://curation.pombase.org/dumps/latest_build/pombe-embl/supporting_files/slimTab.txt

For DO slim, we could get an automated disease networks in EsyN

GOID TERM NUM_LIST_ANNOTATIONS LIST_SIZE CLUSTER_FREQUENCY TOTAL_NUM_ANNOTATIONS POPULATION_SIZE GENOME_FREQUENCY ANNOTATED_GENES GO:0006355 regulation of transcription, DNA-templated 447 5065 8.83% 448 5398 8.30% SPAC1002.05c, SPAC1002.08c, SPAC1002.10c, SPAC1002.15c, SPAC1039.05c, SPAC105.03c, SPAC1071.06, SPAC1142.08, SPAC11D3.07c, SPAC11D3.11c,

(the only info Dan useds from this file is the GO ID, term name and gene list I think....but so he doesnt need to change anything we could use the same format)

mah11 commented 5 years ago

edited blurb:

A "slim" is a high-level subset of terms from an ontology, used to analyze sets of annotated genes. The table below shows a slim set of grouping terms that we have selected from the Disease Ontology, and the number of annotations to each term. DO IDs link to PomBase ontology term pages. The annotation totals link to pages with information about the term and a list of annotated genes. A gene may be included in the annotation sets for more than one slim term.

ValWood commented 5 years ago

No hurry for the DO esyN... the networks will look rather fragmented,

cancer: cancer

neurological

neurilogical

(I expected a lot of DNA repair in here but maybe they aren't linked up yet)

mah11 commented 5 years ago

I added the blurb to the page in the git repo.

ValWood commented 5 years ago

@kimrutherford you can make this live and @Antonialock can announce.

@Antonialock also need the ~"resource spotlight"~ "explore PomBase" entry

kimrutherford commented 5 years ago

Thanks for the text. It's on the main site now: https://www.pombase.org/browse-curation/disease-slim

kimrutherford commented 5 years ago

Should I add the Disease Ontology slim page to one of the menus?

ValWood commented 5 years ago

Yes please, and a front page "Disease slim" link.

kimrutherford commented 5 years ago

and a front page "Disease slim" link.

Where should the new link go? Should we start a new row under:

"Advanced search ● GO process overview ● Genome browser"

ValWood commented 5 years ago

I would go: Advanced search Disease slim ● GO process overview ● Genome browser

kimrutherford commented 5 years ago

So Advanced search on its own line?

ValWood commented 5 years ago

Or Advanced search ● Genome browser Disease slim ● GO process overview

I was putting the "browse" things together, but it's a bit odd ;)

kimrutherford commented 5 years ago

Disease slim

Would it be better to label it "Disease association overview"?

ValWood commented 5 years ago

Yeah probably, I considered that, but thought it was quite long...but yes that's better.

kimrutherford commented 5 years ago

I've added a front page link to the disease association table and added a link in the Genome Status menu.

kimrutherford commented 5 years ago

Is there anything else to do here?

ValWood commented 5 years ago

https://github.com/pombase/website/issues/1513

Yep, we want the "drop out"

Genes with a DO: term which do not map to a broad classifier XXX

(although not critical because Antonia can get this by making a query for all - slim diseases). so we can close, and open a now low priority ticket for that task.

ValWood commented 5 years ago

@Antonialock you an announce the slim. ....And tell people there will be improvements that you are still waiting for new ontology terms and relationships to be added.

Then you can post an update once all the changes are through...

ValWood commented 5 years ago

@Antonialock Also nee to update the "explore PomBase" text with a link to the slim.

ValWood commented 5 years ago

The disease slim wasn't announced yet? Needs: i) PomBase spotlight ii) pombelist post iii) tweet iv) news item.

(You can provide updates as they happen but we should announce the slim because it's there on the front page).

ValWood commented 5 years ago

Once done open a new ticket for outstanding tasks. (one is to have a list of genes with disease associations which do not map to the slim)

ValWood commented 5 years ago

@Antonialock

Antonialock commented 5 years ago

The disease slim needs fixing. I just want to get the poster out of the way. It needs to be printed ASAP.

ValWood commented 5 years ago

What needs fixing? If it isn't correct it shouldn't have gone live?

Antonialock commented 5 years ago

well I kinda said I didn’t want it to. There’s some parent terms that need creating, I never tweaked it etc. It is really not in my head right now. I’d prefer to wait to fix it. I need to sort posters and get on with everyday tasks.

ValWood commented 5 years ago

Yes but these things are due to DO so they are out of our hands. It is good, and useful as it is, and because it is already there, it should be announced.

You can announce updates as you go along.

If we waited until GO was this good we wouldn't be using it yet. 80%

kimrutherford commented 4 years ago

I think the last big thing to do for switching to MONDO is to create a MONDO slim.

ValWood commented 4 years ago

I think we can begin with a direct mapping of the DO-> Mondo slim.

@Antonialock is that OK?

Antonialock commented 4 years ago

moved to https://github.com/pombase/website/issues/1512

Not sure it will be very useful. It was very constrained on what's in DO.

malacards have an anatomical slim + 'global categories' https://www.malacards.org/categories

  1. Take their anatomical slim.

  2. Have two (or more "global" categories: Rare diseases

    • subset: predisposition (Id like to see what we have in this category)

And add second slim more 'process focused': Mitochondrial disorders Lysosomal storage disorders Cancer Metabolic disorders Infectious diseases (weird, but I took out malaria from pombe, aven though it looked ok when I looked it up...I got unsure)

ValWood commented 4 years ago

Not sure it will be very useful. It was very constrained on what's in DO.

You are not sure that 'what' will be useful? I don't understand what you are proposing? This is our starting point https://www.pombase.org/browse-curation/disease-slim so we should map to this, and then consider which extensions are required. Let's not try to do everything at the same time.

Right now, we are just trying to get up and running replacing DO with MONDO in our current set up.

Then we can add the new grouping terms to the slim. It's too complicated to do this during the migration.

ValWood commented 4 years ago

I changed this ticket to "remap DO slim to Mondo"

Once that is done this can close. I will move the pending things to new tasks

kimrutherford commented 4 years ago

Great. Once you have the MONDO slim terms ready I'll deploy it on my desktop so you can have a look.

ValWood commented 4 years ago

They are all above, but I don't know what I need to do with them from here?

ValWood commented 4 years ago

in here https://github.com/pombase/pombase-chado/issues/751

ValWood commented 4 years ago

Do I need to put them somewhere?

kimrutherford commented 4 years ago

Do I need to put them somewhere?

Could you either paste or attach them to an issue. Here's good.

ValWood commented 4 years ago

can't find: DOID:0050013 (carbohydrate metabolism disease) -> MONDO:0037792 can't find: DOID:870 (neuropathy) -> MONDO:0005244 can't find: DOID:1289 (neurodegenerative disease) -> MONDO:0005559 can't find: DOID:607 (paraplegia) -> MONDO:0003757 can't find: DOID:1443 (cerebral degeneration) -> MONDO:0024238 can't find: DOID:1561 (cognitive disorder) -> MONDO:0002039 can't find: DOID:0080006 (bone development disease) -> MONDO:0005497 can't find: DOID:2355 (anemia) -> MONDO:0002280 can't find: DOID:557 (kidney disease) -> MONDO:0005240 can't find: DOID:3118 (hepatobiliary disease) -> MONDO:0002515 can't find: DOID:9120 (amyloidosis) ->MONDO:0019065 can't find: DOID:2914 (immune system disease) ->MONDO:0005046 can't find: DOID:0050177 (monogenic disease) ->MONDO:0000275 can't find: DOID:0050736 (autosomal dominant disease) -> MONDO_0000426 can't find: DOID:0050737 (autosomal recessive disease) -> MONDO:0006025

ValWood commented 4 years ago

closing this as the remapping is done, essentially