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BgeeDB / bgee_apps

Source code of the Java Bgee applications
https://www.bgee.org/
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Remap automatically some anatomical terms #208

Open fbastian opened 4 years ago

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 12, 2019, 13:20

Some terms need to be automatically remapped

"UBERON:0002097, UBERON:0000014"        "skin of body, zone of skin"
"UBERON:0006566, UBERON:0003382"        "left ventricle myocardium, cardiac muscle of left ventricle"
"UBERON:0006567, UBERON:0003381"        "right ventricle myocardium, cardiac muscle of right ventricle"
"UBERON:0007798, UBERON:0002049"        "vascular system, vasculature [Uberon:comment: see also: vascular system. Consider merging?]"

@ANiknejad can you please tell us what is the main term to conserve in each case, and what term should be remapped?

@smoretti I think we have a pipeline step to remap terms automatically already, right? Can you please add them after reply from Anne?

fbastian commented 4 years ago

In GitLab by @ANiknejad on Feb 12, 2019, 13:27

| the main term to conserve in each case, and what term should be remapped?

I guess, we should conserve the one we used in expression data annotations (if any), right? Otherwise, we just have to let these multiple entities commented

fbastian commented 4 years ago

In GitLab by @smoretti on Feb 12, 2019, 14:17

assigned to @smoretti

fbastian commented 4 years ago

In GitLab by @smoretti on Mar 6, 2019, 09:16

So @ANiknejad which one to we keep? The left or the right term?

Also have you already done this remapping on annotation files?

fbastian commented 4 years ago

In GitLab by @smoretti on Apr 30, 2019, 16:04

@ANiknejad should those terms be added to Bgee14.1_mapToUberon_6.xlsx?

I didn't get them as warnings currently

fbastian commented 4 years ago

In GitLab by @ANiknejad on Apr 30, 2019, 18:26

no, I do not think so, this is a different problem here.

Bgee14.1_mapToUberon_6.xlsx is to currently bypass the problem of non-synchronisation between Bgee ontologies files and annotation files.

Here I do not know from where @fbastian is getting this list...but as said, we just have to select the UberonID/name that has the most expression annotation, for example UBERON:0000014 zone of skin, I know this is the term we use to report expression data from any 'skin' samples.

fbastian commented 4 years ago

In GitLab by @ANiknejad on May 1, 2019, 15:48

assigned to @fbastian and unassigned @smoretti

fbastian commented 4 years ago

In GitLab by @fbastian on May 1, 2019, 17:47

I guess the list simply comes from annotations that we identified as being inconsistent.