TransgeneOme import

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WormBase will import expression data (Images, constructs, and annotations) from the TransgeneOme project -Sarov et al., Cell, 2012. WBPaper00041419. The original data is always present on the Max Planck Institute (MPI) website. WormBase will fetch the data periodically (Release-basis) to have the collection up-to-date. WormBase does not provide means of annotating the patterns, hence community curation will happen on the TransgeneOme MPI site.

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.

Transgeneome DB API

The goal is an API for the Transgeneome DB in order to provide information about

  • constructs
  • strains
  • images
  • image annotations.

Export format will be JSON by default. For images it will be JPEG.

Things to consider:

  • different species in TRG DB (request parameter)
 * c.ele and d.mel
  • genome (assembly versions)
  • export image format, jpeg by default
  • only provide public data

Transgeneome DB Data model

Here is a part of our class diagram without attributes. Excluded is the relation strain - well - feature - tag, which connects a strain to a gene.

TRG Imaging ClassDiagram.png

Showing also the attributes helps to decode the json below immensely. Excluded is the relation strain - well - feature - tag, which connects a strain to a gene.

TRG imaging extended class diagram.png

ImagingData

https://transgeneome.mpi-cbg.de/transgeneomics/api/imagingData.json

Example: Json explaination.png

Example: 

[
  {
    "lifeStageTerm": {
      "termId": "WBls:0000057",
      "name": "adult hermaphrodite",
      "id": 7160
    },
    "strain": {
      "well": {
        "wellRow": "D",
        "wellColumn": 6,
        "selectedFeature": {
          "tags": [
            {
              "field": "identifier",
              "value": "WBGene00006375",
              "id": 49490539
            },
            {
              "field": "name",
              "value": "syp-1",
              "id": 49490541
            },
            {
              "field": "id",
              "value": "830756",
              "id": 49490538
            },
            {
              "field": "alias",
              "value": "F26D2.2",
              "id": 49490540
            }
          ],
          "name": null,
          "id": 830756
        },
        "geneUnchangedFor": null,
        "externalDbId": null,
        "id": 13985414
      },
      "creator": {
        "firstName": "Mihail",
        "lastName": "Sarov",
        "wormbaseID": "WBPerson3853",
        "name": "sarov",
        "id": 15
      },
      "dateCreated": "Mar 2, 2011",
      "integrated": true,
      "distroCenterId": null,
      "allele": "ddIs226",
      "alleleBackground": "unc-119(ed3)",
      "genoType": null,
      "url": null,
      "name": "TH379",
      "id": 32736214
    },
    "annotations": [
      {
        "dateCreated": "Jul 14, 2011",
        "person": {
          "firstName": "Mihail",
          "lastName": "Sarov",
          "wormbaseID": "WBPerson3853",
          "name": "sarov",
          "id": 15
        },
        "anatomyTerms": [
          {
            "termId": "WBbt:0005175",
            "name": "gonad",
            "id": 6191
          }
        ],
        "subcellularLocalizationTerms": [
          {
            "termId": "GO:0000795",
            "name": "synaptonemal complex",
            "id": 7677
          }
        ],
        "id": 46650021
      }
    ],
    "width": null,
    "height": null,
    "creator": {
      "firstName": "TransgeneOmics Facility",
      "lastName": "",
      "wormbaseID": null,
      "name": "schloissnig@mpi-cbg.de",
      "id": 45762821
    },
    "dateCreated": "Mar 2, 2011",
    "imagingDataChannels": [
      {
        "channelType": "GREEN",
        "filename": "imagingdata-32736227-GREEN-1.jpg",
        "id": 32736228
      },
      {
        "channelType": "DIC",
        "filename": "imagingdata-32736227-DIC-1.jpg",
        "id": 32736229
      }
    ],
    "id": 32736227
  },
  {
    "lifeStageTerm": {
      "termId": "WBls:0000057",
      "name": "adult hermaphrodite",
      "id": 7160
    },
    "strain": {
      "well": {
        "wellRow": "D",
        "wellColumn": 6,
        "selectedFeature": {
          "tags": [
            {
              "field": "identifier",
              "value": "WBGene00006375",
              "id": 49490539
            },
            {
              "field": "name",
              "value": "syp-1",
              "id": 49490541
            },
            {
              "field": "id",
              "value": "830756",
              "id": 49490538
            },
            {
              "field": "alias",
              "value": "F26D2.2",
              "id": 49490540
            }
          ],
          "name": null,
          "id": 830756
        },
        "geneUnchangedFor": null,
        "externalDbId": null,
        "id": 13985414
      },
      "creator": {
        "firstName": "Mihail",
        "lastName": "Sarov",
        "wormbaseID": "WBPerson3853",
        "name": "sarov",
        "id": 15
      },
      "dateCreated": "Mar 2, 2011",
      "integrated": true,
      "distroCenterId": null,
      "allele": "ddIs226",
      "alleleBackground": "unc-119(ed3)",
      "genoType": null,
      "url": null,
      "name": "TH379",
      "id": 32736214
    },
    "annotations": [],
    "width": null,
    "height": null,
    "creator": {
      "firstName": "TransgeneOmics Facility",
      "lastName": "",
      "wormbaseID": null,
      "name": "schloissnig@mpi-cbg.de",
      "id": 45762821
    },
    "dateCreated": "Mar 2, 2011",
    "imagingDataChannels": [
      {
        "channelType": "GREEN",
        "filename": "imagingdata-32736230-GREEN-1.jpg",
        "id": 32736231
      },
      {
        "channelType": "DIC",
        "filename": "imagingdata-32736230-DIC-1.jpg",
        "id": 32736232
      }
    ],
    "id": 32736230
  }
]

Imaging Data Gallery

https://transgeneome.mpi-cbg.de/transgeneomics/api/gallery.jpg?id=[ID]

e.g.: 

https://transgeneome.mpi-cbg.de/transgeneomics/api/gallery.jpg?id=32736230

Trg export gallery.jpg

  • the script that downloads the images is here:

/home/daniela/OICR/TransgeneOme/downloadPicturesTransgeneome.pl

  • The images will be downloaded from the transgeneome site as above and will be saved on Canopus in this directory:

/home/daniela/OICR/TransgeneOme/WBPerson3853

  • Every time the script downloads a fresh batch of pictures and delete what is already in the WBPerson3853 folder
  • Once it finished downloading copy the WBPerson3853 folder in /home/daniela/OICR/Pictures (that happens after rsyncing files from Lario to Canopus):

cp -r WBPerson3853 /home/daniela/OICR/Pictures

  • run the make thumbs script as usual

ImagingDataChannel

Having the imaging data channel id from the json, would allow a call like 

https://transgeneome.mpi-cbg.de/transgeneomics/api/imagingDataChannel.jpg?id=46472095

which would result in a file like

Imagingdata-46472093-DIC-1.tif.jpg


Linking back to The Transgeneome DB

This will be relevant once the objects are on the site. Ask Sybil or Todd to implement the same mechanism is in place for Wormviz to link back to TransgeneOme

That URL will lead all images/annotations for that particular gene. Use the WBGeneId 

https://transgeneome.mpi-cbg.de/transgeneomics/public/geneLocalization.html?geneDbId=WBGene00001689

Generating a .ace file

  • note that on 09/26/2019 we have added an error message to notify us for BAD transgenes and BAD strains. This will alert us in case the transgeneome project added new transgenes or strains that are not in WB. Daniela will need to contact Karen for transgenes and Paul D for STRAINS in order to create new objects.


Tazendra directory /home/azurebrd/work/parsings/daniela/20160324_transgeneome/

The parsing of the JSON to just get data is here : /home/azurebrd/work/parsings/daniela/20160324_transgeneome/all_data

the json output is here: https://transgeneome.mpi-cbg.de/transgeneomics/api/imagingData.json

Parsing output example for gene WBGene00023497 /home/azurebrd/work/parsings/daniela/20160324_transgeneome/WBGene00023497 

 Expr_pattern : "someID"
 WBGene : "WBGene00023497" // 31872735
 Strain        "OP184"
 Transgene     "wgIs184"
 Remark        "Annotated by TransgeneOmics Facility"
 Anatomy_term  "WBbt:0003681" "WBls:0000024"
 Anatomy_term  "WBbt:0005135" "WBls:0000024"
 Anatomy_term  "WBbt:0005741" "WBls:0000024"
 Anatomy_term  "WBbt:0005742" "WBls:0000024"
 Anatomy_term  "WBbt:0006751" "WBls:0000024"
 Anatomy_term  "WBbt:0006761" "WBls:0000024"
 Anatomy_term  "WBbt:0006919" "WBls:0000024"
 GO_term       "GO:0005634"

Request strain IDs that comply to standard WB nomenclature

During the process of generating WBStrain IDs (September 2019), we noticed that many of the TransgeneOme strain names did not comply with standard nomenclature. Daniela will contact Stephan Janosch and will ask to assign proper strain names

WS258

on 10_10_2016:

  • 381 expression patterns
  • 2548 pictures

WS259

on 01_09_2017:

  • 381 expression patterns
  • 2560 pictures

WS260

on 04_24_2017:

  • 381 expression patterns
  • 2559 pictures


WS261

on 06_19_2017:

  • 381 expression patterns
  • 2559 pictures


WS262

  • 381 expression patterns
  • 2559 pictures


WS263

  • 381 expression patterns
  • 2559 pictures

WS264

  • 381 expression patterns
  • 2559 pictures
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