Submission Interface

About The Submission Interface

This document is also available for download Here


Overview

The page briefly describes the submission interface for candidate data intended to populate the Chick Atlas Gene Expression Database (Coming Soon!!!)

In this project, 4 laboratories are performing a large number of ISH experiments on Gallus gallus embryos, in order to detect the expression within the resulting embryos, for a selected range genes. For each experiment, the data produced is typically a series of OPT image scans, which are described by metadata submitted via this submission interface. The image data is submitted via FTP, and is processed out with this submission interface.

The metadata and data will be processed by the HGU, MRC and ultimately presented via a single gene expression database.


What is an Assay?

(as defined by the Edinburgh Mouse Atlas Project (EMAP - http://www.emouseatlas.org/ ) at the HGU, MRC)

An Assay is equivalent to a single description of a single gene expression pattern in a single specimen (with any accompanying images and metadata).

Therefore:

Nota Bene:
There is no need to link data via gene, probe, protocol, lab, breed, etc. The link is inherent in the data itself.

(Jeff Christiansen & Mike Wicks, Tuesday, 30th March 2010)


Metadata

This submission interface is designed to capture all the experimental details used in each ISH experiment. Such data about experiments is called Metadata.

For each ISH experiment:

  1. An Assay is produced;
  2. Each assay uses a Probe;
  3. Each experiment is performed using a particular Protocol;
  4. Each Submitter of metadata (You, the User of this system) has specific User Attributes.

In order to submit an Assay to the Chick Atlas, you must ensure that you have followed these Steps:


Step 1 - Define your User Preferences

Go to http://www.echickatlas.org/submission/users Click on your User Id, and then click onEdit

Here, you can define, for all your experiments, the following attributes:

Also, you can specify System Preferences, being the number of Assays, Probes and Protocols that will be displayed per page:


Step 2 - Specify your experimental Protocols

Go to http://www.echickatlas.org/submission/protocols/new

You may have a number of Protocols that are used in your Lab to produce your Assays, and you can specify each of them here:

For each Protocol you can specify the following attributes:

You are free to call each protocol any name you desire, but the names used MUST be unique.

Protocols can be deleted at any time, provided you OWN it, however, any assay you submit MUST have a Protocol, so any protocol that has been used on an existing assay can NOT be deleted.


Step 3 - Create the Probe used with your Assay

Go to http://www.echickatlas.org/submission/probes/new

You will be using probes in each of your ISH experiments, and these contain the following attributes:

Further fields will be presented depending on the options chosen for fields 6 (Was the probe fragment PCR Amplified or Cloned?) and 7 (Was the probe sequence verified?).

You may give each probe a Local Name, used to help you find your probes, but the local name MUST be unique.

Each new probe is allocated a name by the system, consisting of:

Each Probe is numbered within each gene for each Laboratory, so you can have more than 1 probe for the same gene and still be able to distinguish them.

Laboratory Identifiers have been allocated thus:

Probes can be deleted at any time, provided you OWN it, but if a probe has been used with an assay, then deletion is forbidden.


Step 4 - Submit the Assay

Go to http://www.echickatlas.org/submission/assays/new

Once you have created a probe, you can create assays.

Assays contain the following information:

User Preferences that are previously defined, can be overwritten when creating an assay, however, this overwriting does NOT overwrite the User Preferences themselves.

Selecting a Protocol automatically populates 12 fields on the assay. These fields can be overwritten when creating an assay, however, this overwriting does NOT overwrite the Protocol Details. This flexibility allows for variations to the Protocol used to be recorded. It is strongly advised that you note any such variation in the assay Notes for Interpretation field.

Each new assay is allocated a Public Id. Number thus:

Assays may be deleted at any time provided you OWN them, however, the missing identifier number will NOT be reallocated.


Annotations

Annotations can be added for each assay for as many components in the anatomy as you have identified or wish to comment on.

An Annotation consists of:


Data (Images)

Data must be sent to the HGU, MRC via the Chick Atlas FTP Server:

Go to ftp://www.echickatlas.org/

You will need to request a User Id and password to access the FTP Server

  1. For Output from a Bioptonics OPT machine

    2. Your Zipfile MUST have the same name as the assay to which it relates. Eg.20020.zip

    Your Zipfile must contain the following artefacts:

    • An Original Wholemount TIF Image
    • Reconstructed Images Folder 1
    • Reconstructed Images Folder 2
    • Raw Images Folder 1
    • Raw Images Folder 2

    Naming Conventions:

    • The name of Original Wholemount TIF Image follows this format: submssion number +.tif. Eg. 20020.tif
    • The name of the Reconstructed Images Folder 1 is ReconC1
    • The name of the Reconstructed Images Folder 2 is ReconC2
    • The name of the Raw Images Folder 1 is RawC1
    • The name of the Raw Images Folder 2 is RawC2

    Nota Bene:
    For this type of data, please ensure that the flag on the assay, Image Folder? is set to bioptonics


  2. For Output from a Prototype OPT machine:

    3. Your Data will consist of several stacks of images, zipped into a single Zipfile, to placed on the Chick Atlas FTP Server.

    Zipfiles of data from Prototype OPT machines must be placed in the prototype sub-folder on the FTP Server only.

    Your Zipfile MUST have the same name as the assay to which it relates.

    eg. 20020.zip

    Your Zipfile must contain the following artefacts:

    To Be Continued!!!

    Nota Bene:
    For this type of data, please ensure that the flag on the assay, Image Folder? is set to prototype_bath or prototype_dublin


  3. For Photographic-Only Output:

    4. Your Data will consist of at least 1 image.

    Zipfiles of wholemount images (photographs) must be placed in the photography sub-folder on the FTP Server only.

    If you have more than 1 image, these must be zipped into a single Zipfile.

    Your Zipfile MUST have the same name as the Assay to which it relates.

    eg. 20020.zip

    The names of your images must be prefixed with the Assay number, followed by an underscore, a 2 digit number and the suffix, thus:

    eg. 20020_08.tif

    Photographs, typically of Wholemount images, can be supplied in JPEG format too, however, there are no space constraints on the Chick Atlas servers. Therefore the original TIFF images, which by definition are uncompressed and hence unprocessed, can be sent without any worries.

    Nota Bene:
    For this type of data, please ensure that the flag on the assay, Image Folder? is set to photography


  4. For Historical Data:

    5. To Be Continued!!!

    Nota Bene:
    For this type of data, please ensure that the flag on the assay, Image Folder? is set to historical


Processing

The HGU will process any image submissions placed in the FTP folder daily overnight.

The HGU will process all image submissions placed in the FTP folders overnight each day.

For the output from the Bioptonics OPT machines, 2 Woolz objects are generated, together with 5 movies: consisting of 3 planar and 2 rotational movies. All supplied photographs, resulting movies and woolz objects are stored locally on the Chick Atlas server.

At the present, output from the Prototype OPT machines and Historical Data are not processed.

Photographic submissions are unpacked and stored locally on the server.


Comments

Any comments on the Submission Interface should be directed via email to:

Mike Wicks: mwicks at hgu dot mrc dot ac dot uk

Or,

during working hours: 0(+44)131 332 2471 x4021


Mike Wicks
24th May, 2010