Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies

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# Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies

<div class="contributors-line">
		Authors: 
<a href="/training-material/hall-of-fame/xgaia/" class="contributor-badge contributor-xgaia"><img src="https://avatars.githubusercontent.com/xgaia?s=27" alt="Avatar">Xavier Garnier</a>

<a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/abretaud?s=27" alt="Avatar">Anthony Bretaudeau</a>

<a href="/training-material/hall-of-fame/annesiegel/" class="contributor-badge contributor-annesiegel"><img src="https://avatars.githubusercontent.com/annesiegel?s=27" alt="Avatar">Anne Siegel</a>

<a href="/training-material/hall-of-fame/odameron/" class="contributor-badge contributor-odameron"><img src="https://avatars.githubusercontent.com/odameron?s=27" alt="Avatar">Olivier Dameron</a>

<a href="/training-material/hall-of-fame/mboudet/" class="contributor-badge contributor-mboudet"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/mboudet?s=27" alt="Avatar">Mateo Boudet</a>

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<div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Jul 26, 2021</div>

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## Requirements

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

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

- [Sequence analysis](/training-material/topics/sequence-analysis)
    - Quality Control: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html)
    - Mapping: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/mapping/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html)

---

### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> 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?

---

### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> 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)

.image-00[ ![Local data tables and remote data with gene and proteins is combined in data integration. Now a graph is produced with differential expression pointing to a gene which points to a protein. Next the data is queried and results produced.](images/from_data_to_result.png)]

---

# 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

.image-01[ ![a small graph, subject points to object with an arrow labelled predicate.](images/rdf_schema_1.png)]

```turtle
nextprot:P01137 :hasTaxon taxon:9606 .
nextprot:P01137 :hasSequence "MPPSGLRLLL" .
```

---

## RDF: triples form a labeled directed graph

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

.image-02[ ![A graphic with two regions, data description and data. In the data is a circle labelled nextprot:P01137 which points to a sequence via a hasSequence arrow. The nextprot points to a taxon:9606 with a hasTaxon arrow. The taxon points to a nextprot:Organism in the data description region. The nextprot protein points to nextprot:Protein in the data description region via an rdf:type arrow.](images/rdf_schema_2.png)]

---

## SPARQL

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

```
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

.pull-left[
- Using the same identifier for the same entity (**entity matching**) across multiple datasets allows federated queries

- Federated SPARQL queries provide unified querying capabilities over multiple datasets as if they were a single virtual graph

]

.pull-right[
.image-03[ ![Dataset 1 and 2 are shown as two silos, each with different small graphs. Each has a red node. Those nodes are connected via a dashed line. A picture of a cloud points at the two datasets, and their individual graphs collapsed into one larger graph. A query is sent to this cloud which comes out as a result table.](images/rdf_schema_3.png)]
]

---

# 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**

.image-04[ ![Two tables are provided, pointing to RDF abstraction with a small graph of DE, Gene, and their attributes. And RDF data which has the same graph as abstraction, but with real identifiers.](images/askomics_convertion.png)]

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](https://sparql.nextprot.org)) 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](https://github.com/askomics/abstractor)

```bash
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

.image-06[ ![A picture of an RDF graph with many nodes. On the right is a query interface of some sort.](images/askomics_query_builder.png)]

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

---
### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> 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](https://training.galaxyproject.org) and all the contributors!

<a href="/training-material/hall-of-fame/annesiegel/" class="contributor-badge contributor-annesiegel"><img src="https://avatars.githubusercontent.com/annesiegel?s=27" alt="Avatar">Anne Siegel</a>

<a href="/training-material/hall-of-fame/odameron/" class="contributor-badge contributor-odameron"><img src="https://avatars.githubusercontent.com/odameron?s=27" alt="Avatar">Olivier Dameron</a>

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This material is licensed under the Creative Commons Attribution 4.0 International License</a>.