Can we give different attributes to the node?

[Satish]

HI All,

I am new to BEL so getting to know more about it. <eanwhile I would really like to know whether we can provide any attributes to the nodes. As I can see we can give attributes to the edges (like evidences, species etc etc...). In the same way is there any possibility to give the same to the nodes.

My aim is to have some additional information stored on the nodes so that when you click on them we could see those extra information. I would be really thankful if someone can help me out in this.

Thank you.

..

Satish

[William Hayes]

Hi Satish,

It sounds like you are talking about using BEL for network building as opposed to knowledgebase building.  We have started standardizing on the JGF (JSON Graph Format - http://json-graph-format.info) as a way of representing networks.  This child jsonschema - https://github.com/jsongraph/json-graph-specification/blob/master/child-schemas/bel-json-graph.schema.json demonstrates an extension to JGF to capture BEL Evidences as part of the network dataset.  You can add arbitrary metadata at the graph, node and edge level.  There is a sub-schema for BEL evidences as part of that schema. Charlene Fletcher (ADS) with support from Tony Bargnesi (Selventa) has also built a JGF importer/exporter for Cytoscape — http://apps.cytoscape.org/apps/jgfapp

Please let us know if you need any help.  Reading jsonschema can be difficult, but I love the JSON format and jsonschema helps to validate the structure and content of JSON files in a powerful manner.

Best,

William 

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[Satish]

Hi William,

Thanks for the fast response and valuable information. I can explain a little more about what I need to do. I have lot of knowledge stored in the mysql database and need to convert everything into a network. My approach was to  bulid a knowledgebase network from the available knowledge that we have for so many datasets. 

1) Do you think it is possible to make a network using BEL?

2) I understand that the BEL plugins are only for cytoscape 2.8 and so how will the JGF plugin in cytoscape 3 support BEL document file or KAM file.

I am really sorry if I am asking really bad questions. I am trying to get more and more knowledge regarding the BEL language and will improve soon.

Satish