bio4j: a pioneer graph based database for the integration of biological big data
DESCRIPTION
canceled talk about bio4j, at lest you have their slides here, xD!TRANSCRIPT
Bio4j: A pioneer graph based
database for the integration of
biological Big Data
www.ohnosequences.com www.bio4j.com
What’s Bio4j?
Bio4j is a bioinformatics graph based DB including most data available in :
Uniprot (SwissProt + Trembl)
Gene Ontology (GO)
UniRef (50,90,100)
NCBI Taxonomy
RefSeq
Enzyme DB
www.ohnosequences.com www.bio4j.com
It provides a completely new and powerful framework
for protein related information querying and
management.
Since it relies on a high-performance graph engine, data
is stored in a way that semantically represents its own
structure
www.ohnosequences.com www.bio4j.com
What’s Bio4j?
Bio4j uses Neo4j technology, a "high-performance graph
engine with all the features of a mature and robust
database".
Thanks to both being based on Neo4j DB and the API
provided, Bio4j is also very scalable, allowing anyone
to easily incorporate his own data making the best
out of it.
www.ohnosequences.com www.bio4j.com
What’s Bio4j?
Everything in Bio4j is open source !
released under AGPLv3
www.ohnosequences.com www.bio4j.com
What’s Bio4j?
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Highly interconnected overlapping knowledge spread throughout different DBs
www.ohnosequences.com www.bio4j.com
However all this data is in most cases modeled in relational databases.Sometimes even just as plain CSV files
As the amount and diversity of data grows, domain models become crazily complicated!
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
With a relational paradigm, the double implication
Entity Table
does not go both ways.
You get „auxiliary‟ tables that have no relationship with the smallpiece of reality you are modeling.
You need ‘artificial’ IDs only for connecting entities, (and these are mixed with IDs that somehow live in reality)
Entity-relationship models are cool but in the end you always have to deal with ‘raw’ tables plus SQL.
Integrating/incorporating new knowledge into already existing databases is hard and sometimes even not possible without changing the domain model
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Life in general and biology in particular are probably not 100% like a graph…
but one thing’s sure, they are not a set of tables!
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
NoSQL (not only SQL)
“NoSQL is a broad class of database management systems
that differ from the classic model of the relational database
management system (RDBMS) in some significant ways.
These data stores may not require fixed table schemas,
usually avoid join operations and typically scale
horizontally.”
NoSQ… what !??
Let’s see what Wikipedia says…
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
NoSQL data modelsBioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Cassandra is a highly scalable, eventually consistent, distributed, structured key-value store. Cassandra brings together the distributed systems technologies from Dynamo and the data model from Google's BigTable.
MongoDB (from "humongous") is an open source document-oriented NoSQL database system written in the C++ programming language.
www.ohnosequences.com www.bio4j.com
Neo4j is a high-performance, NOSQL graph database with all the features of a mature and robust database.
The programmer works with an object-oriented, flexible network structure rather than with strict and static tables
All the benefits of a fully transactional, enterprise-strengthdatabase.
For many applications, Neo4j offers performance improvements on the order of 1000x or more compared to relational DBs.
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Ok, but why starting all this? Were you so bored…?!
It all started somehow around our need for massive access to protein GO (Gene Ontology) annotations.
At that point I had to develop my own MySQL DB based on the official GO SQL database, and problems started from the beginning:
I got crazy ‘deciphering’ how to extract Uniprot protein annotations from GO official tables schema
Uniprot and GO official protein annotations were not always consistent
Populating my own DB took really long due to all the joins and subqueries needed in order to get and store the protein annotations.
Soon enough we also had the need of having massive access to basic protein information.
www.ohnosequences.com www.bio4j.com
These processes had to be automated for our (specifically
designed for NGS data) bacterial genome annotation system
BG7
Uniprot web services available were too limited:
- Slow
- Number of queries limitation
- Too little information available
So I downloaded the whole Uniprot DB in XML format (Swiss-Prot + Trembl)
and started to have some fun with it !
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
We got used to having massive direct access to all this proteinrelated information…
So why not adding other resources we needed quite often in most projects and which now were becoming a sort of bottleneck compared to all those already included in Bio4j ?
Then came:
- Isoform sequences
- Protein interactions and features
- Uniref 50, 90, and 100
- RefSeq
- NCBI Taxonomy
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features- Enzyme Expasy DB
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Let’s dig a bit about Bio4j structure:
Data sources and their relationships:
www.ohnosequences.com www.bio4j.com
The Graph DB model: representation
Core abstractions:
Properties on both
Relationships between nodes
Nodes
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Let’s dig a bit about Bio4j structure:
How are things modeled?
Couldn’t be simpler!
Entities
Nodes
Associations / Relationships
Edges
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Some examples of nodes would be:
Protein
GO term
Genome Element
and relationships:
Protein
GO term
PROTEIN_GO_ANNOTATION
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
We have developed a tool aimed to be used both as a reference manual and initial contact for Bio4j domain model: Bio4jExplorer
Bio4jExplorer allows you to:
• Navigate through all nodes and relationships
• Access the javadocs of any node or relationship
• Graphically explore the neighborhood of a node/relationship
• Look up for the indexes that may serve as an entry point for a node
• Check incoming/outgoing relationships of a specific node
• Check start/end nodes of a specific relationship
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Entry points and indexing
There are two kinds of entry points for the graph:
Auxiliary relationships going from the reference node, e.g.
Node indexing
- MAIN_DATASET: leads to both main datasets: Swiss-Prot and Trembl
There are two types of node indexes:
- CELLULAR_COMPONENT: leads to the root of GO cellular component sub-ontology
- Exact: Only exact values are considered hits
- Fulltext: Regular expressions can be used
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Retrieving protein info (Bio4jModel Java API)
//--creating manager and node retriever----
Bio4jManager manager = new Bio4jManager(“/mybio4jdb”);
NodeRetriever nR= new NodeRetriever(manager);
ProteinNode protein = nR.getProteinNodeByAccession(“P12345”);
Getting more related info...
List<InterproNode> interpros = protein.getInterpro();
OrganismNode organism = protein.getOrganism();
List<GoTermNode> goAnnotations = protein.getGOAnnotations();
List<ArticleNode> articles = protein.getArticleCitations();
for (ArticleNode article : articles) {
System.out.println(article.getPubmedId());
}
//And don’t forget to close the Bio4jManager
manager.shutDown();
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Proteins with Interpro motif ‘IPR000847’ (Bio4jModel Java API)
//--creating manager and node retriever----
Bio4jManager manager = new Bio4jManager(“/mybio4jdb”);
NodeRetriever nR= new NodeRetriever(manager);
InterproNode interpro = nR.getInterproById(“IPR000847”);
ProteinInterproRel rel = ProteinInterproRel(null);
Iterator<Relationship> iterator =
interpro.getNode().getRelationships(rel, Direction.INCOMING);
while(relIterator.hasNext()){
ProteinNode p = new ProteinNode(iterator.next().getStartNode());
System.out.println(p.getAccession());
}
//And don’t forget to close the Bio4jManager
manager.shutDown();
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
www.ohnosequences.com www.bio4j.com
Querying Bio4j with Cypher
START k=node:keyword_id_index(keyword_id_index = "KW-0181")
return k.name, k.id
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Getting a keyword by its ID
START d=node:dataset_name_index(dataset_name_index = "Swiss-Prot")
MATCH d <-[r:PROTEIN_DATASET]- p,
circuit = (p) -[:PROTEIN_PROTEIN_INTERACTION]-> (p2) -
[:PROTEIN_PROTEIN_INTERACTION]-> (p3) -
[:PROTEIN_PROTEIN_INTERACTION]-> (p)
return p.accession, p2.accession, p3.accession
Finding circuits/simple cycles of length 3 where at least one protein is from Swiss-Prot dataset:
Check this blog post for more info and our Bio4j Cypher cheetsheet
www.ohnosequences.com www.bio4j.com
gremlin> g.idx('protein_accession_index')[['protein_accession_index':'P12345']].full_name ==> Aspartate aminotransferase, mitochondrial
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Get protein by its accession number and return its full name
Get proteins (accessions) associated to an interpro motif (limited to 4 results)
gremlin>
g.idx('interpro_id_index')[['interpro_id_index':'IPR023306']].inE('PROTEIN_INTERPRO').outV
.accession[0..3]
==> E2GK26
==> G3PMS4
==> G3Q865==> G3PIL8
Check our Bio4j Gremlin cheetsheet
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
You can also query/navigate through Bio4j with the REST API !
The default representation is json, both for responses and or data sent with
POST/PUT requests
http://server_url:7474/db/data/index/node/protein_acc
ession_index/protein_accession_index/Q9UR66
REST Server
Get protein by its accession number: (Q9UR66)
http://server_url:7474/db/data/node/Q9UR66_node_id/re
lationships/out
Get outgoing relationships for protein Q9UR66
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Visualizations (1) REST Server Data Browser
Navigate through Bio4j data in real time !
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Visualizations (2) Bio4j + Gephi
Get really cool graph visualizations using Bio4j and Gephi visualization and exploration platform
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Visualizations (3) Bio4j GO Tools
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Why would I use Bio4j ?
Massive access to protein/genome/taxonomy… related information
Networks analysis
Integration of your own DBs/resources around common information
Development of services tailored to your needs built around Bio4j
Besides many others I cannot think of myself… If you have something in mind for which Bio4j might be useful, please let us know so we can all see how it could help you meet your needs! ;)
Visualizations
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Bio4j + Cloud (1)
Interoperability and data distribution
We use AWS (Amazon Web Services) everywhere we can around Bio4j, giving us the following benefits:
Releases are available as public EBS Snapshots, giving AWS users the opportunity of creating and attaching to their instances Bio4j DB 100% ready volumes in just a few seconds.
CloudFormation templates:
- Basic Bio4j DB Instance
- Bio4j REST Server Instance
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Bio4j + Cloud (2)
Backup and Storage using S3 (Simple Storage Service)
We use S3 both for backup (indirectly through the EBS snapshots) and storage (directly storing RefSeq sequences as independent S3 files)
What kind of benefits do we get from this?
• Easy to use
• Flexible
• Cost-Effective
• Reliable
• Scalable and high-performance
• Secure
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Bio4j + Cloud (3)
Web servers and service providers in the cloud
Deploying your own web server in AWS using Bio4j as back-end is really simple.
A good example of this would be Bio4jTestServer, a continuously developed server showcasing Web Services based on Bio4j.
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Upcoming features
- Relationship indexing for relationships going and coming from supernodes
No one’s perfect, and Bio4j is not the exception. Relationship fetching can become a bottleneck whenever you have to deal with supernodes (unless you index these relationships). Fortunately this is something that Neo4j is going to fix in the next version(s).
- More resources available (Reactome…)
- Improvements in the importing process
- A more complete version of Bio4jModel
Allowing users to perform almost all sorts of queries without having to worry about Neo4j core API.
- New tools, services and visualizations built around Bio4j
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
Community
Bio4j has a fast growing internet presence:
- Twitter: check @bio4j for updates
- Blog: go to http://blog.bio4j.com
- Mail-list: ask any question you may have in our list.
- LinkedIn: check the Bio4j group
- Github issues: don’t be shy! open a new issue if you thinksomething’s going wrong.
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
and... Who’s behind all this?
- Pablo Pareja Tobes: Main developer (that’s me!)
- Eduardo Pareja Tobes: Technology and architecture main advisor
- Raquel Tobes: Bioinformatics main advisor
- Marina Manrique: Bioinformatics support
- Eduardo Pareja: Scientific advisor
Bio4j is being developed by Oh no sequences! Team and Era7 Bioinformatics members:
www.ohnosequences.com www.bio4j.com
Bioinformatics DBs and Graphs
Initial motivation
Bio4j structure
Some samples
Why Bio4j?
Bio4j and the Cloud
Upcoming features
That’s it !
Thanks for your time ;)