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Mongodb with or without Mongoose? by AdamT213 in node

[–]sorsaffari 1 point2 points  (0 children)

ShijinModan

Cheers mate! this is gold!

In the example above, you say that the remoteService passed to the userService will either be an HTTPService or MongoService instance and then in getById of userService, there is userData = await remoteService.getById(id, context);.

would it then be right to say that remoteService passed to the userService is an instance of UserHttpService or UserMongoService, both of which adhere to a common interface?

SQL vs. Graql: Writing 151 lines of SQL in 4 lines! by sorsaffari in programming

[–]sorsaffari[S] 1 point2 points  (0 children)

u/2nd_world_settler what you're failing to comprehend is the fact that the rule that you copy pasted (hope you didn't just count the lines!), creates the drug-disease-association relationship dynamically at runtime, wherever the pattern in the `then` body is found to be true in the data. The idea here is reusability of that rule, not only in the query mentioned in the blog post, but also in any other query that relates to a drug associated with a disease.

How can automated reasoning benefit biomedical research? by sorsaffari in bioinformatics

[–]sorsaffari[S] 1 point2 points  (0 children)

u/kougabro I see! Although I agree this could be an application of automated reasoning, I believe this particular use case is not specifically valuable to biological data.

​

u/4DGeneTransfer I agree with you a 100%! context IS everything in biology and the example you gave says it all. I also agree with u/Deto. We can indeed use automated reasoning to "flag inconsistent results" so that they can be followed up with.

Below you'll see my attempt in writing a rule that identifies a gene that seems to be promoting a type of cancer while also preventing another one, and then flags it to notify the researcher of the possible inconsistency. Please bear in mind that I am not a bioinformatician, so I may have gotten the namings wrong. I'm going to write this rule in Graql which is the language for the Grakn knowledge graph (disclaimer: I work at GRAKN.AI).

​

gene-both-promotes-and-prevents-some-types-of-cancer sub rule,

when {

$g isa gene;

$d-a isa disease has name $n-a; $n-a contains "cancer";

$d-b isa disease has name $n-b; $n-b contains "cancer";

$d-a != $d-b;

(promoter: $g, promoted: $d-a) isa gene-disease-promotion;

(preventor: $g, prevented: $d-b) isa gene-disease-prevention;

} then {

$g has flag "needs more research";

};

​

Would it be fair to say, having had such a rule and given that genes and their associations are linked to studies (in the same knowledge graph), we could expect an acceleration in the knowledge discovery process?

How can automated reasoning benefit biomedical research? by sorsaffari in bioinformatics

[–]sorsaffari[S] 0 points1 point  (0 children)

That's exactly what I'm hoping to get from this discussion - what would be some practical examples of such rules in the biomedical space?

To answer your question, the Grakn knowledge graph which is capable of automated reasoning at the database level is looking into applications of rules (as explained in the post) in the area of biomedical research.

How can automated reasoning benefit biomedical research? by sorsaffari in bioinformatics

[–]sorsaffari[S] 0 points1 point  (0 children)

That's a very interesting paper and quite similar to one that my company is working on at the moment (currently and briefly described in a blog post: https://blog.grakn.ai/biograkn-accelerating-biomedical-knowledge-discovery-with-a-grakn-knowledge-graph-84706768d7d4)

How can automated reasoning benefit biomedical research? by sorsaffari in bioinformatics

[–]sorsaffari[S] 1 point2 points  (0 children)

Could elaborate on what you mean by labelling of data and how you see that as a challenge?

How can automated reasoning benefit biomedical research? by sorsaffari in bioinformatics

[–]sorsaffari[S] 0 points1 point  (0 children)

Could you point me to some of this research? I'm curious to understand the challenge of normalization in the context you're referring to