I have an interesting problem that I don't know how to solve.
I have collected a large dataset of 80 million graphs (they are CFG as in Control Flow Graph produced by programs I have analysed from Github) which I need to be able to search efficiently.
I looked into existing solutions like Neo4j but they are all designed to store a global single graph.
In my case this is the opposite all graphs are independent -like rows in a table - but I need to search through all of them efficiently.
For example I want to find all CFGs that has a particular IF condition or a WHILE loop with a particular condition.
What's the best database for this use case?
I don't think that there's a reason not to simply store all those graphs in a single graph, whether it's Neo4j or a different graph database. It's not a problem to have many disparate graphs in a single graph where the disparate graphs are disconnected from one another.
As for searching them efficiently, you would either (1) identify properties in your CFGs that you want to search on and convert them to some indexed value of the graph or (2) introduce some graph structure (additional vertices/edges) between the CFGs that will allow you to do the searches you want via graph traversal.
Depending on what you need to search on approach 1 may not be flexible enough for you especially, if what you intend to search on is not completely known at the time of loading the data. Also, it is important to note that with approach 2 you do not really lose the fact that you have 80 million distinct graphs just because you provided some connection between them. Those physical connections don't change that basic logical fact. You just need to consider those additional connections when you write traversals that you expect to occur only within a single CFG.
I'm not sure what Neo4j supports in this area, but with Apache TinkerPop (an open source graph processing framework that lets you write vendor agnostic code over different graph databases, including Neo4j), you might consider doing some form of graph partitioning to help with approach 2. Or you might subgraph() the larger graph to only contain the CFG and then operate with that purely in memory when querying. Both of these approaches will help you to blind your query to just the individual CFG you want to traverse.
Ultimately, however, I see this issue as a modelling problem. You will just need to make some choices on how to best establish the schema for your use case and virtually any graph database should be able to support that.
Related
With a normal 'graph database' the data is broken up into nodes and edges, and there isn't much of a restriction/schema between the connections. With this, it seems great for modeling straightforward graphs where the relationships are relatively consistent -- Movies with cast and crew; Computer networks with IPs and devices; Social networks with users and connections; etc.
Are there any graph-like databases that can be more specialized? For example to be able to model something like an electrical circuit where each component has a sort of 'schema' or well defined input and output -- i.e., a Resistor has two connections and has various properties:
a Transistor takes has three connections and has various properties, etc.
I'm not asking about particular circuit simulators, such as https://www.falstad.com/circuit/circuitjs.html, but more about whether it's possible in any graph (or pseudo-graph) databases to model and enforce very specific, well-defined relationships in a network, such as circuit design.
Definitely possible.
I've been working on this problem with Neo4j, and Restagraph is the result. It provides a REST API that enforces a schema on any updates to the database, and I've packaged it as a Docker image.
I haven't really promoted it so far, because it's only recently been mature enough for my own use, and I really need to improve the documentation. If you try it out, though, I'd love to hear any feedback you have.
TLDR: in general yes, but it depends.
This is a really broad question, so let me break it down.
While it's a little exaggerating to talk about all graph databases (which are not as standardized as SQL databases - which in turn are not very standardized as well), so take this answer with a grain of salt: Yes, that is possible.
As in SQL databases, you usually can set up constraints to be checked before any changes in data is persisted.
Most graph databases incorporate something along the lines of a "type", similarly to what a table represents in SQL databases. Some allow to constrain relationships to only target specific types, so you could restrict relationships e.g. between a node using a CAN bus and an I2C-bus to the specific types.
If a database does not provide these mechanisms, it's usually possible to constrain relationships to the existence of specific keys and values in the model. To have another example than your circuit one: Imagine a node-based system, which has typed inputs and outputs - an int-based output can only be connected to an int based input, a float based output only to a float based input, etc. Then you could add a field output_type and input_type to the nodes and constrain relationships between the values.
As soon as you add the ability to write (the SQL-similar stored) procedures, you can write very complex data integrity constraints.
So, while it is possible, the question is, if you should.
How much logic you actually want to put into your database is a decades-long heated argument. At some point in your application architecture, you will have to check the validity of the data that you are handling. Handling the data consistency in the database itself solves a lot of problems with race conditions or performance issues through multiple round trips between the application and the database, which would occur if the consistency checks are done in the application layer.
Putting a lot of your logic into the database severely limits your ability to switch databases ("vendor lock-in"), might lead to code duplication between your application layer and your database, and sprays your logic between two (or more) layers of your architecture (which makes it harder to find bugs, introduces temporal coupling, and might re-introduce race conditions and performance problems where you have to use transactions again).
My personal take is along the lines of Steve Wozniak - see your database as another service. If that service can provide you with everything you need to ensure data integrity, it might be a good idea to just use the database directly. But if this increases the problems I mentioned before, you might be better off putting a layer between your database and your business logic.
Objectivity/DB is object/graph database that uses schema. You can absolutely do what you are proposing. It supports complex object definitions including type inheritance and it has a full graph/navigational query language similar to Cypher. www.objectivity.com
Most of the reasons for using a graph database seem to be that relational databases are slow when making graph like queries.
However, if I am using GraphQL with a data loader, all my queries are flattened and combined using the data loader, so you end up making simpler SELECT * FROM X type queries instead of doing any heavy joins. I might even be using a No-SQL database which is usually pretty fast at these kinds of flat queries.
If this is the case, is there a use case for Graph databases anymore when combined with GraphQL? Neo4j seems to be promoting GraphQL. I'd like to understand the advantages if any.
GraphQL doesn't negate the need for graph databases at all, the connection is very powerful and makes GraphQL more performant and powerful.
You mentioned:
However, if I am using GraphQL with a data loader, all my queries are flattened and combined using the data loader, so you end up making simpler SELECT * FROM X type queries instead of doing any heavy joins.
This is a curious point, because if you do a lot of SELECT * FROM X and the data is connected by a graph loader, you're still doing the joins, you're just doing them in software outside of the database, at another layer, by another means. If even that software layer isn't joining anything, then what you gain by not doing joins in the database you're losing by executing many queries against the database, plus the overhead of the additional layer. Look into the performance profile of sequencing a series of those individual "easy selects". By not doing those joins, you may have lost 30 years value of computer science research...rather than letting the RDMBS optimize the query execution path, the software layer above it is forcing a particular path by choosing which selects to execute in which order, at which time.
It stands to reason that if you don't have to go through any layer of formalism transformation (relational -> graph) you're going to be in a better position. Because that formalism translation is a cost you must pay every time, every query, no exceptions. This is sort of equivalent to the obvious observation that XML databases are going to be better at executing XPath expressions than relational databases that have some XPath abstraction on top. The computer science of this is straightforward; purpose-built data structures for the task typically outperform generic data structures adapted to a new task.
I recommend Jim Webber's article on the motivations for a native graph database if you want to go deeper on why the storage format and query processing approach matters.
What if it's not a native graph database? If you have a graph abstraction on top of an RDBMS, and then you use GraphQL to do graph queries against that, then you've shifted where and how the graph traversal happens, but you still can't get around the fact that the underlying data structure (tables) isn't optimized for that, and you're incurring extra overhead in translation.
So for all of these reasons, a native graph database + GraphQL is going to be the most performant option, and as a result I'd conclude that GraphQL doesn't make graph databases unnecessary, it's the opposite, it shows where they shine.
They're like chocolate and peanut butter. Both great, but really fantastic together. :)
Yes GraphQL allows you to make some kind of graph queries, you can start from one entity, and then explore its neighborhood, and so on.
But, if you need performances in graph queries, you need to have a native graph database.
With GraphQL you give a lot of power to the end-user. He can make a deep GraphQL query.
If you have an SQL database, you will have two choices:
to compute a big SQL query with a lot of joins (really bad idea)
make a lot of SQL queries to retrieve the neighborhood of the neighborhood, ...
If you have a native graph database, it will be just one query with good performance! It's a graph traversal, and native graph database are made for this.
Moreover, if you use GraphQL, you consider your data model as a graph. So to store it as graph seems obvious and gives you less headache :)
I recommend you to read this post: The Motivation for Native Graph Databases
Answer for Graph Loader
With Graph loader you will do a lot of small queries (it's the second choice on my above answer) but wait no, ... there is a cache record.
Graph loaders just do batch and cache.
For comparaison:
you need to add another library and implement the logic (more code)
you need to manage the cache. There is a lot of documentation about this topic. (more memory and complexity)
due to SELECT * in loaders, you will always get more data than needed Example: I only want the id and name of a user not his email, birthday, ... (less performant)
...
The answer from FrobberOfBits is very good. There are many reasons to add (or avoid) using GraphQL, whether or not a graph database is involved. I wanted to add a small consideration against putting GraphQL in front of a graph. Of course, this is just one of what ought to be many other considerations involved with making a decision.
If the starting point is a relational database, then GraphQL (in front of that datbase) can provide a lot of flexibility to the caller – great for apps, clients, etc. to interact with data. But in order to do that, GraphQL needs to be aligned closely with the database behind it, and specifically the database schema. The database schema is sort of "projected out" to apps, clients, etc. in GraphQL.
However, if the starting point is a native graph database (Neo4j, etc.) there's a world of schema flexibility available to you because it's a graph. No more database migrations, schema updates, etc. If you have new things to model in the data, just go ahead and do it. This is a really, really powerful aspect of graphs. If you were to put GraphQL in front of a graph database, you also introduce the schema concept – GraphQL needs to be shown what is / isn't allowed in the data. While your graph database would allow you to continue evolving your data model as product needs change and evolve, your GraphQL interactions would need to be updated along the way to "know" about what new things are possible. So there's a cost of less flexibility, and something else to maintain over time.
It might be great to use a graph + GraphQL, or it might be great to just use a graph by itself. Of course, like all things, this is a question of trade-offs.
Neo4j is a great tool for mapping relational data, but I am curious what under what conditions it would not be a good tool to use.
In which use cases would using neo4j be a bad idea?
You might want to check out this slide deck and in particular slides 18-22.
Your question could have a lot of details to it, but let me try to focus on the big pieces. Graph databases are naturally indexed by relationships. So graph databases will be good when you need to traverse a lot of relationships. Graphs themselves are very flexible, so they'll be good when the inter-connections between your data need to change from time to time, or when the data about your core objects that's important to store needs to change. Graphs are a very natural method of modeling some (but not all) data sources, things like peer to peer networks, road maps, organizational structures, etc.
Graphs tend to not be good at managing huge lists of things. For example, if you were going to build a customer transaction database with analytics (where you need 1 million customers, 50 million transactions, and all you do is post transactions all day long) then it's probably not a good fit. RDBMS is great at that, notice how that use case doesn't exploit relationships really.
Make sure to read those two links I provided, they have much more discussion.
For maintenance reasons, any service aggregating data feeds has until now been well advised to keep their sources independent.
If I want to explore relationships between different feeds, this can be done at application level, using data tracking (for example) user preferences amongst the other feeds.
Graph databases are about managing relationship complexity, but this complexity is in many cases a design choice. Putting all your kids in one bathtub is fine until you drop the soap..
I´ve been looking for a triple store for my project. In this project i want to store my data according to certain ontologies (OWL).
From my research i ended up with two tecnologies Neo4J and BigData that seems to fit well in this case.
I want to know if any of this two is more apropriated to use with RDF, RDFS, OWL and SPARQL Queries.
Neo4j can be used to store as entity-relationship-entity form. In case of Bigdata, you should not be upload your whole data into Neo4j because it will become very heavy and process will be very much slow. You should use complimentary db for storing actual data and store ids and some params into Neo4j for Graph traversal to perform sort of Graph Analytics. Neo4j is mainly build up for Graph Analytics that its power or you have to use Graph engine e.g GraphX (Spark).
Thanks,
You might want to try out the SparQL plugin for Neo4j, see here for a HTTP based test, and this Berlin Dataset Test for embedded usage.
Neo4J is a specific technology, while big data is more a generic term. I think what you're asking about OLAP and OLTP. As data gets bigger, there are differences between use cases for RDF style graph databases, which are often used for OLAP (On-line Analytical Processing) style analytics. In short, OLAP is designed for analytics that look across an big data set, while OLTP is more aimed at INSERT/DELETEs (on potentially big data).
OLAP-based traversals tend to process the entire graph, while OLTP based traversals tend to process smaller data sets by starting with one or a handful of vertices and traversing from there.
For example, let’s say you wanted to calculate the average age of friends of one particular user. Great use case for OLTP, since the query data set is small. However, if you wanted to calculate the average age of everyone on the database, OLAP is the preferred technology.
OLAP is optimal for deep analysis of a lot of data, while OLTP is better suited for fast running queries and a lot of INSERTs. If you’re trying to achieve a SLA where the analytics must complete within a certain timeframe, consider the type of analytics and which one is better suited. Or maybe you need both.
I am developing a web-based application using Rails. I am debating between using a Graph Database, such as InfoGrid, or a Document Database, such as MongoDB.
My application will need to store both small sets of data, such as a URL, and very large sets of data, such as Virtual Machines. This data will be tied to a single user.
I am interested in learning about peoples experiences with either Graph or Document databases and why they would use either of the options.
Thank you
I don't feel enough experienced with both worlds to properly and fully answer your question, however I'm using a document database for some time and here are some personal hints.
The document databases are based on a concept of key,value, and static views and are pretty cool for finding a set of documents that have a particular value.
They don't conceptualize the relations between documents.
So if your software have to provide advanced "queries" where selection criteria act on several 'types of document' or if you simply need to perform a selection using several elements, the [key,value] concept is not appropriate.
There are also a number of other cases where document databases are inappropriate : presenting large datasets in "paged" tables, sortable on several columns is one of the cases where the performances are low and disk space usage is huge.
So in many cases you'll have to perform "server side" processing in order to pick up the pieces, and with rails, or any other ruby based framework, you might run into performance issues.
The graph database are based on the concept of tripplestore, meaning that they also conceptualize the relations between the entities.
The graph can be traversed using the relations (and entity roles), and might be more convenient when performing searches across relation-structured data.
As I have no experience with graph database, I'm not aware if the graph database can be easily queried/traversed with several criterias, however if an advised reader has such an information I'd really appreciate any examples of such queries/traversals.
I'm currently reading about InfoGrid and trying to figure if such databases could by handy in order to perform complex requests on a very large set of data, relations included ....
From what I can read, the InfoGrah should be considered as a "data federator" able to search/mine the data from several sources (Stores) wich can also be a NoSQL database such as Mongo.
Wich means that you could use a mongo store for updates and InfoGraph for data searching, and maybe spare a lot of cpu and disk when it comes to complex searches inside a nosql database.
Of course it might seem a little "overkill" if your app simply stores a large set of huge binary files in a database and all you need is to perform simple key queries and to retrieve the result. In that cas a nosql database such as mongo or couch would probably be handy.
Hope some of this helps ;)
When connecting related documents by edges, will you get a shallow or a deep graph? I think the answer to that question is important when deciding between graphdbs and documentdbs. See Square Pegs and Round Holes in the NOSQL World by Jim Webber for thoughts along these lines.