Old data settings value

[doctormo]

These items are in the settings column and need translating.

• Endemic beijing
• highly transmitted in NYC
• FZB Lineage6
• FZB Lineage5
• patient-1 RFLP w1 1/5 cases from contam b-scope
• mine
• FZB Lineage1
• Endemic strain(s) from identical spoligocluster with progressive resistance
• RIVM Lineage2
• derived from lung extracts of patient with original H37 strain
• Lab generated mutant with isolated low level kanamycin resistance
• isolated in SF Lineage4B
• Community outbreak with identical spoligotype
• isolated from a single host during the course of a chronic infection
• RIVM Lineage4C
• RIVM Lineage4B
• Endemic Beijing
• Outbreak Northern BC
• Multiple countries, first isolated in Haarlem, The Netherlands
• Endemic strain(s) from identical spoligocluster with variable levels of resistance
• |N
• Endemic beijing family strain(s) with relatively low transmission
• isolated in SF from patient born in China Hirsh et al 2004 Lineage3C
• Philip Hopewell
• Virulent reference beijing
• None
• isolated from patient in Gambia 2002 previously analyzed by genomic deletion analysis Gagneux et al 2006 Lineage1
• Single IV-Drug User with non-compliance
• russian clin isolate w high level cap resistance
• highly drug resistant
• isolated in SF Lineage3C
• isolated in SF Lineage3B
• clin isolate w unknown mech pza resistance
• RIVM LineageM_canettii
• Community outbreak with progressive resistance with similar but non identical spoligotype
• isolated in SF from patient born in Philipines Hirsh et al 2004 Lineage4A
• RIVM Lineage3A
• RIVM Lineage1
• Endemic beijing-low-copy-clade family strain(s) with relatively low transmission
• 2177-N / clin isolate in college student travel to india com to another pt
• isolated in SF Lineage6
• Mine outbreak
• isolated in SF Lineage2 Philip Hopewell
• russian clin isolate w low level kan resistance

[mahafarhat]

Ok can you please send me the name, source and setting field info for each of these.

I think we will need to rename the "Source" field to a field called "LaboratorySource", and move all the RIVM/MSLI/CDC etc "setting" data from gtbdr to this laboratory field.

For the wgsmtb data, erase the source data as it is (current a researcher's name) and replace with the following info for each line of data:

Name: LaboratorySource borowski\d: UCSF CDC-\d+: CDC \d\d-R\d+: MSLI
H37Ra: NCBI K-\d: FZB X122: Stellenbosch R1207: Stellenbosch R\d[3]\w?: Stellenbosch w-148: PHRI/NCBI c: PHRI/NCBI M\d{2-3}\w?: Stellenbosch haarlem: PHRI/NCBI MT00\d\d: BCCDC HN878: NCBI MTB210: NCBI K\d{2}\d?: RIVM \d{4-5}_\d{2}: FZB T\d{2}: UCSF GM0981: UCSF \d{2}\d{4}: UCSF M4100: UCSF

If not listed above leave LaboratorySource blank

Please also make the following corrections to the data: M4100 country is: South Korea, setting is: isolated in SF lineage 3A, city is NULL

If there is a reference eg. agerton 1997 JAMA; Maus, AAC; Sacchettini, Ioerger BMC Genomics 2010 etc in the current course field please add this to the setting field using comma as a separator between the current info and this new info, and then replace source with laboratorysource data as I detail above.

thank you!