Closed zakandrewking closed 4 years ago
Is the PubMed ID 21811229 that is attached ...
Good catch! added to the list
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I've also followed up with the unpublished model authors: iJN was just accepted and waiting to hear on iIS
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I've also followed up with the unpublished model authors: iJN was just accepted and waiting to hear on iIS
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I can probably map them all to NCBI tags, but then these models won't reflect the versions attached to the publication
For this case, we can change the model files. That's within the scope of what BiGG does.
Okay, I'll see how they map
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
ok, so map iEC1364_W to CP002185.1
expect not to map iEC1344_C, iEC1364_W, and iYS1720
what about iAM_Pk459?
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
closing in favor of specific tickets