import extra info for ortholog table and write out at update time

pombase-admin commented 11 years ago

New ortholog (version 19 is made) https://sourceforge.net/p/pombase/curation-tasks/208/

All of the genes which are tandem fusions, or map to a tandem fusion are annotated thus:

/controlled_curation="term=orthologous to S. cerevisiae YDR267C; qualifier=SPAC806.02c,C_term; date=19700101" /controlled_curation="term=orthologous to S. cerevisiae YIL003W; qualifier=SPAC806.02c,N_term; date=19700101"

OR tandem fusion in S. cerevisia his7 /controlled_curation="term=orthologous to S. cerevisiae YCL030C; qualifier=YCL030C(N-term); date=19700101" his2 /controlled_curation="term=orthologous to S. cerevisiae YCL030C; qualifier=YCL030C(C-term); date=19700101"

So next you need to

Make sure "qualifier= is parsed and stored (this might happen already)
Make sure db_xref is parsed and stored Let us know if this is happening as we can open a jira ticket to display these
Write out an equivalent version (V.19) from Chado (I will compare this to my existing V 19 to amke sure nothing has gon awry, because the table is currently maintained independently from the data in Artemis). Once I have checked it, this will become the official release.

Original comment by: ValWood

pombase-admin commented 11 years ago

There is now also one example for human: ade5 /controlled_curation="term=human GART ortholog; qualifier=HGMP:GART,C-term; date=20130815" ade1 /controlled_curation="term=human GART ortholog; qualifier=HGMP:GART,N-term; date=20130815"

Original comment by: ValWood

pombase-admin commented 11 years ago

Also when these table sare written out, they should exclude "dubious genes" (currently included in both the human table, and in my manual pombe table)

Original comment by: ValWood

pombase-admin commented 11 years ago

When a cluster occurs , make sure it has the same gene combination each time it occurs like this

SPAC1002.17c | UCK1 UCK2 UCKL1 SPAC1399.04c | UCK1 UCK2 UCKL1

not like this:

SPAC1002.17c | UCK1 UCK2 UCKL1 SPAC1399.04c | UCK1 UCK2

Original comment by: ValWood

pombase-admin commented 10 years ago

pasting this ole e-mail exchange in here so I don't forget... but it may well be on the tracker somewhere. don't worry about this one...I will go through all of the ortholog table related tickets soon and figure out what still needs to be done and write a sensible ticket.

Val

Hi Kim, I wonder if when you write out the human ortholog table, the Human Id lists could be alphabetised. I have a list of cut and grep command I can use on the cerevisiae ortholog table to generate a table of 1:1, 1:many many:1 many:many.

It doesn't work on the human table becasue it depends on sorting similar, so these currently sort individually even though they have the same orthologs:

1 ATAD2B|ATAD2 1 ATAD2|ATAD2B

1 RPL10L|RPL10 1 RPL10|RPL10L

Original comment by: ValWood

ValWood commented 2 years ago

Closing. Will open a new ticket for the outstanding task.

pombase / pombase-chado

import extra info for ortholog table and write out at update time #202