Single or Single-End

[HLWeil]

Type of Issue

• [ ] Report a Bug
• [ ] Report a Typo or Error
• [ ] Feature Request
• [X] Help or Question

Comments

Hey, I noticed a small inconsistency in this section of the DPBO:

[Term]
id: DPBO:1000086
name: single
def: "placeholder def of single" []
comment: To be transformed to an instance. DB
is_a: DPBO:0000015 ! library layout
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "RAW FILES_single or paired-end" xsd:string

[Term]
id: DPBO:1000087
name: paired-end
def: "placeholder def of paired-end" []
comment: To be transformed to an instance. DB
is_a: DPBO:0000015 ! library layout
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "RAW FILES_single or paired-end" xsd:string

I think single should be renamed to single-end.

[kdumschott]

Hi Lukas, thanks for adding this as an issue. I downloaded the seq_template.xlsx from https://www.ncbi.nlm.nih.gov/geo/info/seq.html#metadata and I believe the term was originally added this way as it's listed like this in the metadata sheet:

While I agree single-end is more consistent, the term 'single' exactly matches what the GEO metadata sheet expects or asks for. What're your thoughts on this @Brilator?

[Brilator]

Jip, this was the reason. GEO curators were usually easy; so they'd probably allow both unless automated. In any case I would suggest not to modify the term but add a new + deprecate and link to the old.

[kdumschott]

Done and done.