GREG -The Gene Regulation Graph Database

Hello everyone,
I am a bioinformatician at Guangzhou Medical University in China. My group has developed a new graph database to study gene regulation using Neo4j and we would like to let you know.

Our paper: https://doi.org/10.1093/database/baz162
Our website: http://www.moralab.science/GREG/

We are relatively new to Neo4j so any comments are welcome.
Regards,
Antonio

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Welcome antoniocrmora.
Interesting project and graph. I noticed that the relationships are not directed in your graph visualization, is that an intentional modeling decision? I usually think of all relationships as directional, left, right or both.

I'm interesting in your thoughts on this aspect, in general and in terms of how you modeled this data.

Hi Joel,

Most of the interactions in GREG come from high-throughput technologies that can't offer directionality information by design (I think this is better represented by an undirected edge than by a double-arrow, and that is the way is treated in the biological literature). Biochemical directional information (arrows) usually design chains of reactions (so-called "pathways") and, in some cases, you may need the double-arrow to design pathways that go both ways. Such information is stored in a different type of databases, coming from different types of technologies (or predicted by algorithms).

If we decided to mix the two types of information in our database (interactions and pathways, undirected and directed), which we didn't, we may need to distinguish between directed, double-arrow, and undirected edges; and we may need the ability to have one undirected and one directed relationship between the same two nodes. An alternative would be to add pathway/direction information as properties, so the user could see that in some cases there is available information about direction, while in most cases not. That is just what I think now, but we haven't tried any of this yet.

Thanks for your comment.

Hi Antonio,

   我是俞方桦,负责Neo4j在亚太的售前和产品支持。
   很高兴得知你和你们的项目!虽然基因不是我的专业,但是相信GREG可以为相关研究提供新颖和有价值的参考。
   你们在项目开发过程中有遇到什么问题吗?今后考虑进一步扩展数据和功能吗?有什么挑战还未解决吗?希望可以保持联系、并欢迎随时交流。我的邮箱是:joshua.yu@neo4j.com。

    此致
            敬礼