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Legacy PATRIC Website (JBoss Portal Version)
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Mycobacterium PLFam has Gordonia member #1498

Closed ARWattam closed 7 years ago

ARWattam commented 7 years ago

PLF_1763_00147431 should be restricted to Mycobacterium, but it contains Gordonia.

https://www.patricbrc.org/view/FeatureList/?eq(plfam_id,PLF_1763_00147431)#view_tab=features

olsonanl commented 7 years ago

My guess is at the time we generated families last time that taxonomy ID was under genus Mycobacterium in the taxonomy data in PATRIC (that's how it appears in the underlying data).

The new families have it in the right place in the Gordonia genus.

ARWattam commented 7 years ago

When will we see the new families?

On Wed, May 3, 2017 at 4:40 PM, olsonanl notifications@github.com wrote:

My guess is at the time we generated families last time that taxonomy ID was under genus Mycobacterium in the taxonomy data in PATRIC (that's how it appears in the underlying data).

The new families have it in the right place in the Gordonia genus.

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olsonanl commented 7 years ago

Later than it would be if I hadn't gotten dragged into some talk or another :-)

Next week hopefully.

ARWattam commented 7 years ago

Blame Senior Shukla for that one!

On Wed, May 3, 2017 at 5:03 PM, olsonanl notifications@github.com wrote:

Later than it would be if I hadn't gotten dragged into some talk or another :-)

Next week hopefully.

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mshukla1 commented 7 years ago

The genome was labeled as Gordonia when we got it from genbank, it later got reclassified/renamed as Mycobacterium for the sam taxonomy id.

Ideally, we should mark the genomes whose names do not match the taxonomy as obsolete and reload them.

On May 3, 2017, at 4:12 PM, ARWattam notifications@github.com wrote:

Blame Senior Shukla for that one!

On Wed, May 3, 2017 at 5:03 PM, olsonanl notifications@github.com wrote:

Later than it would be if I hadn't gotten dragged into some talk or another :-)

Next week hopefully.

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mshukla1 commented 7 years ago

With the recent taxonomy and protein family updates, gordonia genomes are no longer displayed under mycobacteriam and corresponding local families.