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mazeller / FLUture

Source Code for FLUture website
GNU General Public License v3.0
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Incorporate global nomenclature into FLUture #4

Open mazeller opened 5 years ago

mazeller commented 5 years ago

Currently FLUture is using US clade nomenclature. Global nomenclature should be incorporated into the website. H1 global nomenclature is based on the following paper;

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2408-7

*Additionally, add text with explanation for all nomenclature.

mazeller commented 5 years ago

Current Conversion Table

US Clade | Global Clade

alpha | 1A.1.1 beta | 1A.2 gamma | 1A3.3.3 gamma-like | 1A.3.3-like gamma2 | 1A.3.2 gamma2-beta-like |   gamma-npdm-like |   delta1 | 1B.2.2 delta1a | 1B.2.2.1 delta1b | 1B.2.2.2 delta2 | 1B.2.1 delta-like |   pdmH1 | 1.A.3.3.2 Other | Other

cluster_I | 3.1990.1 cluster_IV | 3.1990.4 cluster_IVA | 3.1990.4.a cluster_IVB | 3.1990.4.b cluster_IVC | 3.1990.4.c cluster_IVD | 3.1990.4.d cluster_IVE | 3.1990.4.e cluster_IVF | 3.1990.4.f 2010.1 | 3.2010.1 2010.2 | 3.2010.2 human-to-swine-2013 | human-to-swine-2013 human-to-swine-2016 | human-to-swine-2016 human-to-swine-2017 | human-to-swine-2017 human-to-swine-2018 | human-to-swine-2018

H4 | H4

tkanderson commented 5 years ago

Cluster I = 3.1990.2

H1 revisions are in progress.

anugrah-saxena commented 5 years ago

@tkanderson thank you for the update.

@mazeller can you please give the complete list of NA clade mapping as well. The paper mentions some N1 and N2 names but me and @SiyingLyu are not sure. Thank you.

mazeller commented 5 years ago

@anugrah-saxena For the time being use the same NA clades. There is no current global naming scheme for NA.

anugrah-saxena commented 5 years ago

@mazeller So, we are planning to use this table:

N1 Classical Classical N1 Pandemic Pandemic N1 Human-Seasonal Human-Seasonal N2 1998 1998 N2 2002 2002 N1 and N2 both also have a common clade N1.Human-seasonal & N2.Human-seasonal. Should those be included as well and how? Also, when you get time later can you please check your email. Me and @SiyingLyu have shared our questions with you :)

mazeller commented 5 years ago

N1 Classical Classical N1 Pandemic Pandemic N2 Human-Seasonal Human-Seasonal N2 1998 1998 N2 2002 2002

See correction. I am half tempted to implement either Slack or Discord.

anugrah-saxena commented 5 years ago

Thank you for the update. Let's have an early meeting next week? @mazeller @SiyingLyu

anugrah-saxena commented 5 years ago

@mazeller The HA Clade table was missing gamma-like clade. Added to your original comment as well as in the database

tkanderson commented 5 years ago

gamma-like = 1A.3.3-like.

I will check on the other openings in the H1 later; for now, just map the US name into the global name.