warnings still showing in logs though they have been fixed

[pombase-admin]

I fixed these yesterday but they are still showing in the logs? http://curation.pombase.org/dumps/latest_build/logs/log.2015-02-09-23-49-04.curation-tool-data-load-output

warning in 67631dafe77debd1: requires_sequence_feature() not allowed for molecular_function warning in cafc26135a141916: requires_sequence_feature() not allowed for molecular_function

warning in 4d5512a5dc8ea4bc: requires_sequence_feature() not allowed for biological_process warning in 4d5512a5dc8ea4bc: requires_sequence_feature() not allowed for molecular_function warning in 4d5512a5dc8ea4bc: requires_sequence_feature() not allowed for biological_process

warning in 1999a5fbfad09eed: requires_substance() not allowed for biological_process warning in 1999a5fbfad09eed: requires_substance() not allowed for biological_process

warning in a6a51043db00c124: requires_modification() not allowed for cellular_component

warning in 7b18cacb1717e352: requires_modification() not allowed for cellular_component warning in 5d9eb85117dc739f: requires_sequence_feature() not allowed for molecular_function

warning in 929e3ae344538c03: requires_sequence_feature() not allowed for molecular_function warning in 929e3ae344538c03: requires_sequence_feature() not allowed for molecular_function warning in 929e3ae344538c03: requires_sequence_feature() not allowed for molecular_function warning in 929e3ae344538c03: requires_sequence_feature() not allowed for molecular_function warning in 929e3ae344538c03: requires_sequence_feature() not allowed for molecular_function warning in 488ebe84ae41b570: requires_modification() not allowed for molecular_function warning in 641e9af49e65dc1e: requires_substance() not allowed for molecular_function warning in 641e9af49e65dc1e: requires_substance() not allowed for molecular_function

Original comment by: Antonialock

[pombase-admin]

I think that was probably just a timing problem. The curation tool data is exported to a file once a day (at 3am) and I set that load off before then. I've been meaning to fix that. I'll do it now.

Another load is running now and should be be done at lunchtime or so. Could you check again then?

Original comment by: kimrutherford

[pombase-admin]

Aha ok. How about this one? this is from the embl files

: failed to add annotation extension to SPAC12B10.07.1 <-> cellular protein localization: localizes() not allowed for biological_process (in the logs here http://curation.pombase.org/dumps/latest_build/logs/qualifier_problems.txt)

the entry for the gene (no localizes extension?): /GO="aspect=C; term=F-actin capping protein complex; GOid=GO:0008290; evidence=IDA; db_xref=PMID:15743909; date=20050517" /GO="aspect=P; term=barbed-end actin filament capping; GOid=GO:0051016; evidence=IDA; db_xref=PMID:15743909; date=20050517" /GO="aspect=F; term=actin filament binding; GOid=GO:0051015; evidence=IDA; db_xref=PMID:15743909; date=20050517" /GO="aspect=P; term=regulation of cell shape; GOid=GO:0008360; evidence=IGI; db_xref=PMID:11694585; with=PomBase:SPBC1778.06c; date=20050912" /GO="aspect=P; term=actin cytoskeleton organization and biogenesis; GOid=GO:0030036; evidence=IGI; db_xref=PMID:11694585; with=PomBase:SPBC1778.06c; date=20050912" /GO="aspect=P; term=negative regulation of actin filament depolymerization; GOid=GO:0030835; evidence=IDA; db_xref=PMID:15743909; date=20050912" /GO="aspect=P; term=cellular protein localization; qualifier=localization_dependency; GOid=GO:0034613; evidence=IGI; db_xref=PMID:15743909; with=PomBase:SPAC631.01c; date=20050912" /GO="aspect=P; term=cellular protein localization; qualifier=localization_dependency; GOid=GO:0034613; evidence=IGI; db_xref=PMID:15743909; with=PomBase:SPCC126.06; date=20050912" /GO="aspect=C; term=actin cortical patch; GOid=GO:0030479; evidence=IDA; db_xref=PMID:15743909; date=20050517" /GO="aspect=C; term=actin filament; GOid=GO:0005884; evidence=IDA; db_xref=PMID:15743909; date=20050517" /GO="aspect=C; term=cell tip; annotation_extension=exists_during(GO:0051329); GOid=GO:0051286; evidence=IDA; db_xref=PMID:15743909; date=20050921" /GO="aspect=P; term=mitotic cytokinesis; qualifier=antagonistic_interaction; GOid=GO:0000281; evidence=IGI; db_xref=PMID:15743909; with=PomBase:SPAC1F5.04c; date=20050921" /colour=2 /fasta_file="fasta/chromosome1.contig.seq.01882.out" /primary_name="acp1" /product="F-actin capping protein alpha subunit" /systematic_id="SPAC12B10.07" /db_xref="SPD:41/41G03" /controlled_curation="term=phenotype, viable; allele=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YKL007W; date=19700101" /controlled_curation="term=phenotype, viable; cv=phenotype; db_xref=PMID:15743909; date=19700101" /controlled_curation="term=species distribution, conserved in eukaryotes; date=20081110" /controlled_curation="term=species distribution, conserved in metazoa; date=20081110" /controlled_curation="term=species distribution, conserved in fungi; date=20081110" /controlled_curation="term=species distribution, conserved in vertebrates; date=20081110" /controlled_curation="term=species distribution, conserved in eukaryotes only; date=20081110" /controlled_curation="term=modification, phosphorylated; db_xref=PMID:18257517; cv=pt_mod; date=20100125" /gene="acp1" /gene="SPAC12B10.07"

Original comment by: Antonialock

[pombase-admin]

If you'd asked me yesterday I would have been very confused by that but I've been looking at that code today. I think the warning is happening because of: https://sourceforge.net/p/pombase/chado/13/

qualifier=localization_dependency + evidence=IGI;

is changed to:

annotation_extension=localizes(...)

during the load.

Does that make sense? If not we can chat at 10:30.

Original comment by: kimrutherford

[pombase-admin]

hmm, I guess these should get changed to has_input now?

Original comment by: Antonialock

[pombase-admin]

yep, has_input

Original comment by: ValWood

[pombase-admin]

yay for getting a butt-load of log-fixes done automagically :p

Original comment by: Antonialock

[pombase-admin]

So, change:

qualifier=localization_dependency + evidence=IGI + with=cdc2;

to:

annotation_extension=has_input(cdc2)

?

Original comment by: kimrutherford

[pombase-admin]

The requires_sequence_feature() warnings have now gone.

Original comment by: kimrutherford

[pombase-admin]

• status: open --> closed-fixed

Original comment by: Antonialock

[pombase-admin]

yes, but keep the Gene ID in the with field too (as at present).

Original comment by: ValWood

[pombase-admin]

I'll reopen just as a check for the localization extension fix

Original comment by: ValWood

[pombase-admin]

• status: closed-fixed --> open

Original comment by: ValWood

[pombase-admin]

• status: open --> closed

Original comment by: ValWood

[pombase-admin]

closing, Antonia opened a new ticket

Original comment by: ValWood