log file check for ID prefixes

[ValWood]

Malformed GO ID was not reported in logs....

/GO="aspect=P; term=spermidine acetylation; GOid=O:0032918; evidence=ISS; db_xref=GO_REF:0000024; with=UniProtKB:P21673; date=20140929"

[mah11]

also doesn't report "UniProt" instead of "UniProtKB" (led to problem in pombase/website#410)

[ValWood]

would
pombase/website#665
find
GOid=O:0032918
?

[ValWood]

Hi @kimrutherford was this covered when you made recent additional checks on the artemis data loaded?

[kimrutherford]

GOid=O:0032918

That should give a warning now.

also doesn't report "UniProt" instead of "UniProtKB"

There is no checking of the "with" values except for making sure there is a prefix. It doesn't check that the prefix is sensible. I'll fix that.

[kimrutherford]

Here are is a list of the prefixes in Chado and how often they are used. Could you let me know if this list looks OK? Could you let me know which of these prefixes are valid?

I'll add a query to the chado-checks that warns about any prefix not on your list. The query results will include the publication, session, gene and term of the annotation with the dodgy "with".

    prefix        | count
------------------+-------
AGI_LocusCode     |     5
CBS               |     6
dictyBase         |     1
EC                |   208
ECOGENE           |     7
FB                |     8
GO                |    95
InterPro          |  1598
MGI               |    19
Panther           |     1
PANTHER           |    32
PDB               |     2
Pfam              |   847
PomBase           |  3318
RGD               |     2
SGD               |  5368
SUPERFAMILY       |     1
UniPathway        |    86
UniProtKB         |  1547
UniProtKB-KW      |  1776
UniProtKB-SubCell |    73
UniRule           |     2
WB                |     2

[ValWood]

I think all are correct, except "Panther" case which I will fix now. More than reported, possibly because of redundancy filtering.

chromosome1.contig:FT BDH1 ortholog; db_xref=Panther:PTHR43490; date=20170625"
chromosome1.contig:FT YKL128C; db_xref=Panther:PTHR43387; date=20170627"
chromosome1.contig:FT db_xref=Panther:PTHR43016:SF3; date=20170726"
chromosome1.contig:FT YKL128C; db_xref=Panther:PTHR43387; date=20170627"
chromosome2.contig:FT YBL029C-A; db_xref=Panther:PTHR28139; date=20170618"
chromosome3.contig:FT with=Panther:PTHR23029; date=20170625"
chromosome3.contig:FT db_xref=Panther:PTHR15892; date=20170227"
chromosome3.contig:FT in fungi; db_xref=Panther:PTHR10957; date=20170618"
chromosome3.contig:FT in metazoa; db_xref=Panther:PTHR10957; date=20170618"
chromosome3.contig:FT in vertebrates; db_xref=Panther:PTHR10957; date=20170618"
chromosome3.contig:FT in eukaryotes; db_xref=Panther:PTHR10957; date=20170618"
chromosome3.contig:FT in eukaryoties only; db_xref=Panther:PTHR10957;
chromosome3.contig:FT db_xref=Panther:PTHR10957; date=20170618"
chromosome3.contig:FT YPL161C; db_xref=Panther:PTHR10957; date=20170618"
chromosome3.contig:FT db_xref=Panther:PTHR10957; date=20170618"

[ValWood]

fixed

[kimrutherford]

I've added Chado check to catch illegal "with" prefixes. It will report the problematic ID, the session ID and the PubMed ID.