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 (daily? 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

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

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"