Difference between revisions of "TransgeneOme import"

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==Image name convention==
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==Data we want to import==
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What we want to have for each gene that has <Explore localization>  data, is a table with Gene Strain image_name life_stage Annotations_by Anatomy_annotations Subcellular_annotations Construct
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Ideally a tab delimited file with pipe separated entries for multiple entries, for example: WBGene00000095\tOP124\tL4larva\tMihail Sarov\tintestine|gonadal
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primordium|head\tnucleus\t7842083679062579 H01
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JSON format is also good
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 +
 
 +
==Image format==
 +
 
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We would like to have the images in JPG format
 +
 
 +
==Image naming convention==
  
 
*Daniela: Do the images have permanent IDs?  If you replace the  image with a higher resolution version, does that get a new ID that  gets assigned to the gene while the previous image ID association gets removed?
 
*Daniela: Do the images have permanent IDs?  If you replace the  image with a higher resolution version, does that get a new ID that  gets assigned to the gene while the previous image ID association gets removed?
  
Stephan: The imaging works in our DB like this. We have imaging data. It has some metadata (created, creator, width, height) and a list of imaging data
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*Stephan: The imaging works in our DB like this. We have imaging data. It has some metadata (created, creator, width, height) and a list of imaging data
 
channels (can be one of ZVI, DIC, GREEN, RED, BLUE, OTHER). The channel need to have same resolutions. Generally all entities in our DB get unique IDs. So if you replace a low resolution version of a DIC image in a imaging data (set), the imaging data ID stays the same, but the single imaging data ID changes.
 
channels (can be one of ZVI, DIC, GREEN, RED, BLUE, OTHER). The channel need to have same resolutions. Generally all entities in our DB get unique IDs. So if you replace a low resolution version of a DIC image in a imaging data (set), the imaging data ID stays the same, but the single imaging data ID changes.
  
*Daniela:
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*Daniela: We also don't know how to see the file name of the image. For example 'strain-OP124-aha-1.png' for  https://transgeneome.mpi-cbg.de/transgeneomics/user/downloadWidOverlay.html?id=31873093
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*Stephan: The filenames for the overlays are not the real ones. These are generated on the fly. A real imaging data channel filename looks like
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that: imagingdata-59891682-DIC-1.tiff
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So we store the original uploaded file renamed having the imaging data ID in it. The ID for that image would be 59891683.

Revision as of 18:40, 14 March 2016

Data we want to import

What we want to have for each gene that has <Explore localization> data, is a table with Gene Strain image_name life_stage Annotations_by Anatomy_annotations Subcellular_annotations Construct

Ideally a tab delimited file with pipe separated entries for multiple entries, for example: WBGene00000095\tOP124\tL4larva\tMihail Sarov\tintestine|gonadal primordium|head\tnucleus\t7842083679062579 H01

JSON format is also good


Image format

We would like to have the images in JPG format

Image naming convention

  • Daniela: Do the images have permanent IDs? If you replace the image with a higher resolution version, does that get a new ID that gets assigned to the gene while the previous image ID association gets removed?
  • Stephan: The imaging works in our DB like this. We have imaging data. It has some metadata (created, creator, width, height) and a list of imaging data

channels (can be one of ZVI, DIC, GREEN, RED, BLUE, OTHER). The channel need to have same resolutions. Generally all entities in our DB get unique IDs. So if you replace a low resolution version of a DIC image in a imaging data (set), the imaging data ID stays the same, but the single imaging data ID changes.

  • Stephan: The filenames for the overlays are not the real ones. These are generated on the fly. A real imaging data channel filename looks like

that: imagingdata-59891682-DIC-1.tiff So we store the original uploaded file renamed having the imaging data ID in it. The ID for that image would be 59891683.