Example 1: Proteins linked to a given set of GO terms and NCBI taxonomy nodes

[marina-manrique]

For a given set of GO terms and Taxonomy nodes show the proteins linked to their GO term and their Taxon node.

For this I suggest something simple to start with, something based on this https://github.com/mbostock/d3/wiki/Force-Layout

where the protein nodes have a color, the taxon nodes another color and the go terms another one.

On roll-over basic info from the nodes is displayed and the nodes linked will be highlighted

[pablopareja]

Could you please detail me the data (I mean the properties) you want to see from the three different entities that would be shown? that's to say:

• GO terms
• Proteins
• NCBI taxonomic units

Since we won't be performing any request to the server at this point of development all the data that would be shown through interaction should already be included in the JSON file generated for the whole visualization.

@marina-manrique @rtobes

[pablopareja]

I would also need a sample file for both GO and NCBI taxon Ids so that I can start performing tests with real data :wink:

[rtobes]

GO term (biological_process)

GO:0046677 Name:response to antibiotic

TAXA

Streptococcus pneumoniae

PROPERTIES with labels in the graph visualization

The properties could be:

• protein name
• GO term name
• taxon name

[pablopareja]

Could you provide the NCBI taxon ID ? (the names are redundant many times...)

[rtobes]

Streptococcus pneumoniae Taxonomy ID: 1313

[pablopareja]

thanks!

[rtobes]

If you are trying a Force Layout representation, What is the type of Force Layout that yo are trying to do?

[pablopareja]

The tests I was performing were with this example:

http://bl.ocks.org/mbostock/4062045

[pablopareja]

You can check a very preliminary version here:

http://ec2-54-170-192-6.eu-west-1.compute.amazonaws.com/testD3.html

Please let me know things you would like to add/change (I know that'd be virtually changing everything but we already have something we can work on very quickly! )

[pablopareja]

By the way, I forgot to mention that you have to click on the Start button :wink:

[pablopareja]

I already changed the visualization so that node names are displayed instead of IDs (please clear the cache or just open the link in an incognito tab so that you can access the last version of the html file)

[rtobes]

With name is better but we need to have a more specific taxa (could you try with Staphylococcus Taxonomy ID: 1279)

[rtobes]

Modifications:

• Two alternative options (setting by the user): Selected GO terms visible or not
• Optional: Adding to the network the name property of the GeneLocation node (linked to each protein)

[pablopareja]

OK you can already check the visualization with the taxa you just mentioned (1279) I'm gonna get to work on the suggested improvements :wink:

[rtobes]

The protein name that I would like to have is the large name not the short name that appears now