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Known issues in BiGG 1.6 Beta #355

Closed zakandrewking closed 4 years ago

zakandrewking commented 4 years ago
draeger commented 4 years ago

Is the PubMed ID 21811229 that is attached to the model iYS854 of Staphylococcus aureus subsp. aureus USA300_TCH1516 correct? It seems to be a paper from 2011 describing a model of Chlamydomonas.

Was there a specific problem in ModelPolisher that prevented this model from being loaded?

zakandrewking commented 4 years ago

Is the PubMed ID 21811229 that is attached ...

Good catch! added to the list

cnorsig commented 4 years ago

For the genes not mapping iEC1368_DH5a, iEC1344_C, and iEC1364_W I believe that is because these were re-annotated and have tags like "locus_XXXX" so they don't match NCBI

iYS1720 I would expect to need to make an exception because of the pan-reactome content

I've also followed up with the unpublished model authors: iJN was just accepted and waiting to hear on iIS

zakandrewking commented 4 years ago

iEC1368_DH5a, iEC1344_C, and iEC1364_W

Can these be easily updated to map then?

On Fri, Oct 25, 2019 at 2:52 PM cnorsig notifications@github.com wrote:

For the genes not mapping iEC1368_DH5a, iEC1344_C, and iEC1364_W I believe that is because these were re-annotated and have tags like "locus_XXXX" so they don't match NCBI

iYS1720 I would expect to need to make an exception because of the pan-reactome content

I've also followed up with the unpublished model authors: iJN was just accepted and waiting to hear on iIS

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cnorsig commented 4 years ago

I can probably map them all to NCBI tags, but then these models won't reflect the versions attached to the publication

zakandrewking commented 4 years ago

For this case, we can change the model files. That's within the scope of what BiGG does.

cnorsig commented 4 years ago

Okay, I'll see how they map

cnorsig commented 4 years ago

Upon further inspection I think we can fix iEC1364_W by having it map to CP002185.1 instead of what it is currently. Those IDs match the model file.

The other 2 strains are more problematic as in each case there isn't a unified way to go from the "locus_" tag right now to the annotation locus tags. I looked into creating a translation based on the "gene names" as they each seem to have that information, but those don't match up with any other content to rename the GPRs

zakandrewking commented 4 years ago

ok, so map iEC1364_W to CP002185.1

expect not to map iEC1344_C, iEC1364_W, and iYS1720

what about iAM_Pk459?

cnorsig commented 4 years ago

For iAM_Pk459 it looks like locus tags within the annotation are of the form "PKH_XXXXXX" but within the model are "PKNH_XXXXXXX" but the annotations do not have any "old_locus_tag" fields

zakandrewking commented 4 years ago

closing in favor of specific tickets