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We have a very complex form describing a genetically modified lab animal. One animal can have multiple mutations.

A genetically engineered mutation occurs when a researcher inserts a foreign gene into the animal's DNA. The gene then starts producing new proteins (for example, it can start producing antibodies against some pathogen). But the gene only does so in organs and cells where it is activated. Different genes get activated in a different way:

  1. Organ specific: The new gene is expressed in all celltypes of a given organ (e.g. the liver)
  2. Cell specific: The new gene is expressed in all cells of a given type (e.g. fibroblasts, which are cells found in skin, meninges, bones and other organs).
  3. Organ-and-cell-combination specific: The new gene is expressed in different celltypes in different organs. For example, it can be expressed in the fibroblasts of the bones, but not in the fibroblasts of the skin.

Our application has to allow researchers to describe where the gene is expressed in an animal. Our interface is currently something like:

mockup

download bmml source – Wireframes created with Balsamiq Mockups

In reality, the part above the "expressed in" is much busier, and the whole thing is a part of a more complicated form.

I am unhappy with the design, because it does not support any of the cases mentioned above especially well:

  • if a gene is expressed in all cells of a specific organ, the researcher would have to type lots of cell types for each organ (or will enter something nonsensical like "all" - we accept the creation of new cell types by users)

  • if a gene is expressed in all organs which have a given celltype, the user will have to select multiple organs, and type in the same cell type for each

  • if a gene is expressed in some organ-and-cell combinations, the researcher still has to enter all needed organs, and to repeat the cells for each organ combination.

There is a constraint here. Our system does not know which celltypes are available in which organ. It does not even have a list of all possible organs. Both types of data are impossible to be created within our project scope, so we have to rely on user-entered data. So, while I would love to offer the user who has just selected Skin to have a checkbox "all celltypes in skin", I can't do that.

Do you have any idea how this can be managed, despite the constraint? I would welcome any suggestions which - reduce user effort - reduce visual clutter - reduce the chance of the user entering something which is not an organ or cell, but is descriptive in the context of this one model. For example, I saw a user enter "ubiquitous" in the organ field, to communicate the fact that the gene is expressed in all organs of the animal.

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By curiosity and even if it's off topic, can you please explain why you can't know the organs in your organism? –  A.L Feb 26 at 22:05
    
@n.1 Because the term "organ" has no precise definition. A researcher specializing in the eye can have the view that the lens and retina are two separate organs, while a molecular biologist can stick to the sixth-grade-idea of the eye being an organ. As for cell types, there are new subtypes discovered all the time, and our application has to record the difference between them :( It can easily happen that there are only 3 labs in the world working with a celltype, and they all use mice, so nobody in the world actually knows if that type is also present in a drosophila proboscis too. –  Rumi P. Feb 27 at 14:56
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1 Answer 1

Here are my suggestions:

if a gene is expressed in all cells of a specific organ, the researcher would have to type lots of cell types for each organ (or will enter something nonsensical like "all" - we accept the creation of new cell types by users)

You can use:

  • a Select all button to select all the cell types (but it may display lots of checkboxes in complex organs)
  • a checkbox In all cells of this organ which will hide the Cells box
  • duplicate organs in order to add In all cells of this organ, for example:
    • Skin
    • Skin (all cells)

if a gene is expressed in all organs which have a given celltype, the user will have to select multiple organs, and type in the same cell type for each *if a gene is expressed in some organ-and-cell combinations, the researcher still has to enter all needed organs, and to repeat the cells for each organ combination*

Add a button to add an expression type cell, then add all the organs containing this cell type.

These solutions will require that you already associated organs with cells type. I'm pretty sure you can find this list in popular biology database, but you'll have to post the question on another StackExchange website. Once an user has added an organ with its cells, you can use this data when adding a gene, display the list of previously typed genes in this organ.

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Sorry, but I already wrote in the question that it is not possible to associate organs with cell types. " I'm pretty sure you can find this list in popular biology database" - this is not true, as confirmed by the biologists I work for. I cannot find such data. I have to let users enter completely new organs and cell types too. –  Rumi P. Feb 26 at 15:44
    
That's interesting and in the same time disappointing, I managed to find data about genes expression but data about cells types in organs seems to be hard to find. Anyway, you can still use the data you already have to fill your form. Once an user have added an organ with its cells, you can use it when adding a gene, display the list of previously typed genes in this organ. –  A.L Feb 26 at 22:00
    
While I am not yet sure if I can use the already-entered data in a meaningful way, it is indeed a new idea not hurting the constraint from the question. Can you please edit it into the main answer? THen I can remove the downvote too. –  Rumi P. Feb 27 at 14:58
    
I added it to my answer, thanks! –  A.L Feb 27 at 17:51
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