tutorial.md

layout	title	zenodo_link	questions	objectives	time_estimation	contributors	subtopic
tutorial_hands_on	InterMine integration with Galaxy	https://zenodo.org/record/3407174	How to export your query results from your InterMine of choice to Galaxy? How to export a list of identifiers from Galaxy to your InterMine of choice?	Learn how to import/export data from/to InterMine instances Understand the InterMine Interchange Dataset	1h	danielabutano yochannah	analyse

Introduction

{:.no_toc}

InterMine ({% cite Smith2012 %}) is a well-establish platform to integrate and access life sciences data. It provides the integrated data via a web interface and RESTful web services.

Other organizations download and deploy InterMine on their servers: there are more than 30 instances over the world (registered at registry.intermine.org), covering many organism, including human data, model animals, plants and drug targets.

InterMine has been integrated with Galaxy: the InterMine tool server in Galaxy allows to import the data returned by any InterMine search and viceversa, using the InterMine Interchange format it's possible to export a list of identifiers from Galaxy into any InterMine instance of your choice.

Learn more in this tutorial.

Agenda

In this tutorial, we will cover:

1. TOC {:toc}

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Import data from InterMine

{% icon hands_on %} Hands-on: Import

Search Galaxy for InterMine (not case sensitive; intermine is fine too), and click on InterMine Server under Get Data.

1. {% tool InterMine Server %}

2. This will redirect you to the InterMine registry, which shows a full list of InterMines and the various organisms they support. Find an InterMine that has the organism type you’re working with, and click on it to redirect to that InterMine.

3. Once you arrive at your InterMine of choice, you can run a query as normal - this could be a search, a list results page, a template, or a query in the query builder. Eventually you’ll be presented with an InterMine results table.

4. Click on Export (top right). This will bring up a modal window.

5. Select Send to Galaxy and double-check the "Galaxy Location" is correct.

6. Click on the Send to Galaxy button on the bottom right of the pop-up window.

   {% icon tip %} Enable popups

   If you get an error when you click on the Send to Galaxy button, please make sure to allow popups and try again. {: .tip}

{: .hands_on} You have now exported your query results from InterMine to Galaxy.

Export identifiers into InterMine

Get data

{% icon hands_on %} Hands-on: Data upload

1. Import some fly data from Zenodo or from the data library

   https://zenodo.org/record/3407174/files/GenesLocatedOnChromosome4.tsv
   

   {% include snippets/import_via_link.md %} {% include snippets/import_from_data_library.md %}

2. Rename the dataset to GenesLocatedOnChromosome4

   {% include snippets/rename_dataset.md %}

3. Inspect the data

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The dataset contains the secondary identifier and the symbol of the Drosophila melanogaster genes and their location on the chromosome 4

{% icon question %} Questions

Do the data contain the type, e.g Protein or Gene?

{% icon solution %} Solution

No, they don't. So we have to specify it, when we create the InterMine Interchange file

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Create InterMine Interchange dataset

We will use Create InterMine Interchange Dataset {% icon tool %} in order to generate an intermediate file which will be used to send the identifiers (e.g. gene identifiers) to InterMine. This file requires the identifier's type (e.g. Gene), the identifier (e.g WBGene00007063) and, optionally, the organims's name.

{% icon hands_on %} Hands-on: Generate InterMine file

1. {% tool Create InterMine Interchange dateset %} with the following parameters:

   • {% icon param-file %} "Tabular file": select the GenesLocatedOnChromosome4 dataset which contains some fly's genes
   • "Feature Type Column": Column: 1
   • "Feature Type": Gene
   • "Feature Identifier column": Column: 2

   {% icon comment %} Comment

   • In this example, because the GenesLocatedOnChromosome4 dataset does not contain the type we have to specify it, in the "Feature Type"
   • "Feature Type": this is type of the identifiers you are exporting to InterMine, in this example Gene. It must be a class in the InterMine data model.
   • "Feature Identifier column": select a column from the input file which contains the identifier. We have selected Column 2, which contains the gene symbol.
   • "Feature Identifier": This could be, as an example, a gene symbol like GATA1 or another other identifier, e.g. FBGN0000099 or perhaps a protein accession. In our example we do not have to edit anything because the values for this field are contained in the GenesLocatedOnChromosome4 dataset, in Column 2.
   • "Organism Name column": select a column from the input file which contains the organism's name, if you have multiple organisms in the same dataset.
   • "Organism Name": alternatively you can directly provide the organism's name. The organims' name is not mandatory, but is good to provide if it is known. It does not have to be precise {: .comment}

2. Click on Execute

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Send identifiers to InterMine

Once the generation of the interchange dataset has been completed, open the green box related to Create InterMine Interchange on data.

{% icon hands_on %} Hands-on: Send data

1. Click on view intermine at Registry to be redirected to the InterMine registry, which shows a full list of InterMines and the various organisms they support.
2. Find an InterMine that has the organism type you’re working with, in our case FlyMine, and click on the Send to green button to export the identifiers to. 3. You are redirected to FlyMine, in the List Analysis page showing the identifiers you have just exported from Galaxy.

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Conclusion

You have now exported your identifiers from Galaxy to InterMine.