Requirements

Before diving into this slide deck, we recommend you to have a look at:

• Introduction to Galaxy Analyses

• Sequence analysis
  • Quality Control: slides slides - tutorial hands-on
  • Mapping: slides slides - tutorial hands-on

question Questions

• What is the Semantic Web and how can it help integrating and querying data?

• How can AskOmics help benefiting from Semantic Web technologies without having to write RDF or SPARQL code?

objectives Objectives

• Understand the basics of RDF and SPARQL

• Learn how input data must be structured to be integrated with AskOmics

• Learn how to connect distant SPARQL endpoints to local data with AskOmics

How to explore data

Requirements

Study of biological mechanisms requires to:

• integrate multiple data sources (differential expression results, genome annotation, remote protein database)
• query them to answer a biological question (which genes are over-expressed in a condition, and what are the proteins coded by these genes)

What is the Semantic Web?

Semantic Web

Set of recommendations to integrate data, to integrate domain knowledge and to perform query and reasoning.

• Resource Description Framework (RDF): annotate data
• RDFS + OWL: represent knowledge (data description)
• SPARQL Protocol and RDF Query Language (SPARQL): query data

RDF

• RDF is for describing resources (the R in RDF)

  • resources are identified by URIs (nextprot:P01137, taxon:9606)

• describing (D in RDF) a resource is representing it explicitly

  • its attributes (nextprot:P01137 :hasSequence "MPPSGLRLLL...")
  • its relations to other entities (nextprot:P01137 :hasTaxon taxon:9606)
  • its descriptions (aka classes) (nextprot:P01137 :is nextprot:Protein)

RDF: Set of triples

• RDF is represented by triples (subject, predicate, object)
  • Subject: the resource being described
  • Predicate: the relation (from subject to object)
  • Object: a value of the predicate for the subject

 Copy
nextprot:P01137 :hasTaxon taxon:9606 .
nextprot:P01137 :hasSequence "MPPSGLRLLL" .

RDF: triples form a labeled directed graph

 Copy
# Description
nextprot:P01137 rdf:type nextprot:Protein .
taxon:9606 rdf:type nextprot:Organism .
# Data
nextprot:P01137 :hasTaxon taxon:9606 .
nextprot:P01137 :hasSequence "MPPSGLRLLL" .

SPARQL

• The SPARQL language is a set of triple patterns with variables (?variable_name)

 Copy
SELECT ?gene
WHERE {
    ?gene rdf:type :Gene .
    ?gene :hasTaxon taxon:9606 .
}

• All ?gene with rdf:type :Gene and with :hasTaxon taxon:9606
• In other words, the query returns all the human genes

SPARQL: entity matching allow federated queries

What is AskOmics?

AskOmics

Web software for data integration and query using Semantic Web. The main functionalities are:

• Convert of multiple data formats into RDF triples and store them in a local triplestore
• Generate complex SPARQL queries using a user-friendly interface
• Support external SPARQL endpoint to cross-reference integrated data with remote data

AskOmics can be used as a standalone software, or with Galaxy

Data integration with AskOmics

Local data integration

• RDF and SPARQL are good infrastructures to describe and query biological datasets, but most of them are still stored on flat files like CSV/TSV and GFF.

• AskOmics converts multiple structured data formats into RDF triples

  • CSV/TSV
  • GFF
  • BED

AskOmics generates the graph of data and the abstraction

AskOmics uses the file structure (e.g. header of TSV files) to generate the graph of data description: the abstraction

The rest of the files is converted to RDF triples that correspond to the data.

Distant RDF data integration

• Some public databases (e.g. neXtProt) provide RDF data through a SPARQL endpoint (public access for RDF data)

• To connect with a remote SPARQL endpoint, AskOmics needs its RDF abstraction
• The abstraction can be generated with abstractor

 Copy
pip3 install abstractor
abstractor -s https://sparql.nextprot.org/sparql -o nextprot_abstraction.ttl -f turtle

• This abstraction can then be uploaded into AskOmics as a standard file

Query multiple data sources with AskOmics

Query composition

• Users navigate through the abstraction of local and remote data and create a path that represents a query

• The query is converted to SPARQL code that is executed on the local and remote RDF data
• Results are returned and can be downloaded

keypoints Key points

• RDF and SPARQL are Semantic Web technologies that come useful for data integration and querying but the technical aspects may deter end-users

• AskOmics is a web platform for data integration and query using Semantic Web in a user-friendly way

Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Author(s)	Xavier Garnier Anthony Bretaudeau Anne Siegel Olivier Dameron Mateo Boudet
Reviewers

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.