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Localization data: additional dataset, external links and image hosting #2295

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ValWood opened this issue Dec 9, 2024 · 7 comments
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@ValWood
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ValWood commented Dec 9, 2024

RELABEL EXTERNAL LINKS TO ORFEOME LOCALIZATION DATA

Strain and reagents SPD / RIKEN 50/50D08 Orfeome Localization Data

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Localization SPD / RIKEN 50/50D08 Riken Orfeome Localization Data
@ValWood
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ValWood commented Dec 9, 2024

ADDITIONAL DATASET
We can't add gene-specific links to
https://www2.nict.go.jp/bio/seibutsu/DATA/GFP-lib-New/indexGFP.html
because the data is in tables rather than individual entries

the authors would need to provide a mapping file of
https://www2.nict.go.jp/bio/seibutsu/DATA/GFP-lib-New/IMAGE/H01_C08.jpg
to the PomBAse systematic identifiers.

unless it's buried:
https://www.pombase.org/reference/PMID:19170768

@ValWood ValWood changed the title Localization data Localization data external links and image hosting Dec 9, 2024
@kimrutherford
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We can't add gene specific links to
https://www2.nict.go.jp/bio/seibutsu/DATA/GFP-lib-New/indexGFP.html
because the data is in tables rather than individual entries

We could capture the genes from each table and add links to them if necessary. I agree that it's a better long term plan to get the images into an archive.

kimrutherford added a commit to pombase/pombase-config that referenced this issue Dec 10, 2024
kimrutherford added a commit to pombase/pombase-config that referenced this issue Dec 10, 2024
@kimrutherford
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change to
Localization SPD / RIKEN 50/50D08 Riken Orfeome Localization Data

Done for tomorrow morning.

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@ValWood ValWood changed the title Localization data external links and image hosting Localization data additional dataset, external links and image hosting Jan 14, 2025
@ValWood
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ValWood commented Jan 14, 2025

IMAGE HOSTING

We aren't really able to store images, the best solution to this data would be for the authors to submit to one of the image repositories and we would link to it there:
https://www.ebi.ac.uk/bioimage-archive/
https://idr.openmicroscopy.org/

@ValWood ValWood changed the title Localization data additional dataset, external links and image hosting Localization data: additional dataset, external links and image hosting Jan 14, 2025
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