# Make our Scientific Datasets Accessible and Interoperable on the Web

Franck Michel

► To cite this version:

Franck Michel. Make our Scientific Datasets Accessible and Interoperable on the Web. École thématique. Journées "Conduire et construire un plan de gestion des données: De la base de données à la pérennisation", Sètes, France. 2015, pp.95. cel-01486617

HAL Id: cel-01486617

https://hal.science/cel-01486617

Submitted on 10 Mar 2017

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
Make our
Scientific Datasets
Accessible and
Interoperable
on the Web

<figure><img src="image_2.png" /></figure>

RBDD2015, CNRS Database Network
Oct. 21st 2015

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

Franck MICHEL

I3S - UMR 7271, CNRS - Univ. Nice Sophia
Make our datasets
accessible and
interoperable on the Web...

What
for?

<figure><img src="image_5.png" /></figure>

* Not only because of H2020 requirement

* Linking data increases its value

* Mash up with related data

* Produce new knowledge

* Opportunity for new (unexpected) usage

* Citizenship demand for access to public data (scientific, government...)

* ...

<figure><img src="image_6.png" /></figure>
From a Web of Documents
...to a Web of Data

□ Publication/interlinking of open datasets

• Publish heterogeneous data in a **common format**

• Using **common vocabularies**

□ Driven by major initiatives, e.g.:

• Linking Open Data

• W3C Data Activity

• Open Data hosting services... OpenAIRE, Zenodo...

□ As well as other domain-specific projects

• Bio2RDF, BioPortal
<caption># Linked Open Data Cloud</caption>

<figure><img src="image_7.png" /><figcaption>April 2008</figcaption></figure>

<figure><img src="image_8.png" /><figcaption>Sept. 2008</figcaption></figure>

<figure><img src="image_9.png" /><figcaption>March 2009</figcaption></figure>

<figure><img src="image_10.png" /><figcaption>Sept. 2010</figcaption></figure>

<figure><img src="image_11.png" /><figcaption>Sept. 2011</figcaption></figure>

<figure><img src="image_12.png" /><figcaption>Aug. 2014</figcaption></figure>

<figure><img src="image_13.png" /></figure>
<caption>Linked Open Data Cloud</caption>

<figure><img src="image_14.png" /><figcaption>April 2008</figcaption></figure>

<figure><img src="image_15.png" /><figcaption>Sept. 2008</figcaption></figure>

<figure><img src="image_16.png" /><figcaption>March 2009</figcaption></figure>

<figure><img src="image_17.png" /><figcaption>Aug. 2014</figcaption></figure>

<figure><img src="image_18.png" /></figure>

Publications

<figure><img src="image_19.png" /></figure>

Life Sciences

<figure><img src="image_20.png" /></figure>

Cross-Domain

<figure><img src="image_21.png" /></figure>

Social Networking

<figure><img src="image_22.png" /></figure>

Geographic

<figure><img src="image_23.png" /></figure>

Government

<figure><img src="image_24.png" /></figure>

Media

<figure><img src="image_25.png" /></figure>

User-Generated Content

<figure><img src="image_26.png" /></figure>

Linguistics

<figure><img src="image_27.png" /></figure>

<figure><img src="image_28.png" /><figcaption>Sept. 2011</figcaption></figure>

<figure><img src="image_29.png" /></figure>

As of September 2010

<figure><img src="image_30.png" /></figure>
<figure><img src="image_31.png" /></figure>

Visible Web

Deep Web
## Tabular

<table><thead><tr><td>ID</td><td>NAME</td></tr></thead><tbody><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr></tbody></table>

## Directory

<figure><img src="image_32.png" /></figure>

o=fr

<figure><img src="image_33.png" /></figure>

ou=cnrs

<figure><img src="image_34.png" /></figure>

cn=Franck Michel
objectclass=user
userid=65286

## XML Native DBs, Document stores...

```xml
<Books>
  <Book ISBN="0553212419">
    <title>Sherlock Holmes: Complete Novels...</title>
    <author>Sir Arthur Conan Doyle</author>
  </Book>
  <Book ISBN="0743273567">
    <title>The Great Gatsby</title>
    <author>F. Scott Fitzgerald</author>
  </Book>
  <Book ISBN="0684826976">
    <title>Undaunted Courage</title>
    <author>Stephen E. Ambrose</author>
  </Book>
  <Book ISBN="0743203178">
    <title>Nothing Like It In the World</title>
    <author>Stephen E. Ambrose</author>
  </Book>
</Books>
```

## Graph

<figure><img src="image_35.png" /></figure>

## Object-Oriented

<figure><img src="image_36.png" /></figure>

## Documents

<figure><img src="image_37.png" /></figure>

<figure><img src="image_38.png" /></figure>

<figure><img src="image_39.png" /></figure>

<figure><img src="image_40.png" /></figure>
# Heterogeneous query capabilities

* RDBs, NewSQL => SQL

* XML native DBs => XPath/XQuery

* Graph - Neo4J: Cypher, Allegrograph: SPARQL

* Document - MongoDB, CouchDB: similar JS/JSON-based QL

* Column - Cassandra (CQL), HIVE (HQL)

* Key-value - Riak, DynamoDB: low level API

* ...

<figure><img src="image_41.png" /></figure>
Make our datasets
accessible and
interoperable on the Web...

<figure><img src="image_42.png" /></figure>

Which
data?
<figure><img src="image_43.png" /></figure>

© NeuroLOG project
<figure><img src="image_44.png" /></figure>

© MicroStep-Mis. 3D meteorological modelling.
<figure><img src="image_45.png" /></figure>

© CERN. First proton-lead ion collisions recorded by ALICE
To others,

your data may mean that...
# Finding, understanding, and reusing scientific datasets requires consistent, high-quality metadata

* Context: identification, authors, dates, license, version, reference articles

* Access: format, structure, location (dwld), query method

* Meaning:

* What does it represent? What concepts, entities, semantics?

* Interpretation: units (cm or inches, left/right)...

* Provenance:

* Acquired with what equipment? Parameters, protocols?

* Derived from what dataset? With what processing?

* Dataset-level or entity-level provenance

* Statistics

* Etc.
☐ Help access and understand CSV tabular data available on the web

• Recommendations for **Metadata vocabulary for CSV data**

• **Access methods** for CSV Metadata

• **Mapping mechanism** to transforming CSV into various Formats (e.g., RDF, JSON, or XML)

☐ Annotations on a table or group of tables, columns...
# CSV on the Web*

<figure><img src="image_46.png" /></figure>

GID, Street, Species, Trim Cycle, Inventory Date
1, Addison Av, Celtis australis, 2010/10/18
2, Emerson St, Liquidambar styraciflua, 2010/06/02

<figure><img src="image_47.png" /></figure>

GET tree-ops.csv

Content-Type: text/csv
Link: <http://example.org/tree-ops.json>; rel="..."

```json
{
    "@context": ["http://www.w3.org/ns/csvw", {"@language":"en"}],
    "url": "tree-ops.csv",
    "dc:title": "Tree Operations",
    "dc:license": { "@id":
        "http://opendefinition.org/licenses/cc-by/"},
    "dc:modified": {"@value":"2010-12-31", "@type":"xsd:-date"},
    "tableSchema": {
        "columns": [
            {
                "name":"GID", "titles":["GID", "Generic Identifier"],
                "dc description":"...",
                "datatype": "string", "required":true },
            {
                "name":"< Street", "titles":"On Street",
                "dc description":"The street that the tree is on.",
                "datatype": "string" }, ...
        ],
        "primaryKey": "GID", "aboutUrl": "#gid-{GID}" }
```

Species, Trim Cycle, Inventory Date
Celtis australis, 2010/10/18
Liquidambar styraciflua, 2010/06/02

*https://www.w3.org/standards/techs/csv#w3c_all
- Health Care and the Life Sciences

- Consensus among participating stakeholders on the description of datasets using RDF

- Data description, versioning, provenance, discovery, exchange, query, and retrieval

RDF, RDFS, XSD

Citation Typing Ontology

Data Catalog

Dublin Core Metadata Types, Dublin Core Metadata Terms

Friend-of-a-Friend

Collection Description Frequency Vocabulary

Identifiers.org vocabulary

Lexvo.org - Lexical Vocabulary

Provenance Authoring and Versioning ontology (PAV)

PROV Ontology

Semanticscience Integrated Ontology (SIO)

Vocabulary of Interlinked Datasets (VoID)

Used vocabularies
# Challenges of publishing Metadata and/or Data?

<figure><img src="image_48.png" /></figure>
Make our datasets
accessible and
interoperable on the Web...

How?

<figure><img src="image_49.png" /></figure>

☐ Have a common representation format

⇒ **Structural heterogeneity**

☐ Have common ways to describe the data

• Vocabularies, ontologies, thesaurus...

⇒ **Semantic heterogeneity**

☐ Have common ways to query the data
- The Web of Data and the Semantic Web

- Create, reuse and link vocabularies

- Populate the Web of Data

- Publish Linked Open Data on the Web

<figure><img src="image_50.png" /></figure>
The Web of Data
And
the Semantic Web

<figure><img src="image_51.png" /></figure>

Source: C. Faron Zucker[1], O. Corby[1]. *Introduction au web de données et au web sémantique*. Séminaire INRA Open Data Dec. 2014.
[1] INRIA Sophia Antipolis, CNRS, UNS.
User Interface & Applications

Trust

Proof

Unifying Logic

SPARQL

Ontology:
OWL

RDF-S

RDF

XML

URI/IRI

Rule:
RIF

Crypto
<figure><img src="image_52.png" /></figure>
<figure><img src="image_53.png" /></figure>
<figure><img src="image_54.png" /></figure>
<figure><img src="image_55.png" /></figure>
Web of Data

<figure><img src="image_56.png" /></figure>
RDF is a model based on triples, i.e. any fact consists of 3 components:

( subject, predicate, object )

<figure><img src="image_57.png" /></figure>

<figure><img src="image_58.png" /></figure>
<figure><img src="image_59.png" /></figure>

websem.html is a texte

websem.html has as author Fabien

websem.html has as author Olivier

websem.html has as author Catherine

websem.html has as subject Semantic Web

websem.html was written in 2011
<figure><img src="image_60.png" /></figure>
# The Resource Description Framework

<figure><img src="image_61.png" /></figure>
## N-Triples syntax

<http://inria.fr/ex/websem.html>
<http://purl.org/dc/elements/1.1/author>
<http://ns.inria.fr/catherine.faron> .

<http://inria.fr/ex/websem.html>
<http://purl.org/dc/elements/1.1/theme> "Semantic Web" .

## Turtle syntax

@prefix dc: <http://purl.org/dc/elements/1.1/> .
<http://inria.fr/ex/websem.html>
dc:author <http://ns.inria.fr/catherine.faron> ;
dc:theme "Semantic Web" .
## XML Syntax

```xml
<rdf:RDF
```

```xml
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
```

```xml
xmlns:dc="http://purl.org/dc/elements/1.1/">```

```xml
<rdf:Description rdf:about="http://inria.fr/ex/websem.html">```

```xml
<dc:author
```

```xml
rdf:resource="http://ns.inria.fr/catherine.faron"/>
```

```xml
<dc:theme>Semantic Web</dc:theme>
```

```xml
</rdf:Description>
```

```xml
</rdf:RDF>
```

<figure><img src="image_62.png" /></figure>
<figure><img src="image_63.png" /></figure>
<figure><img src="image_64.png" /></figure>

**RDF Schemas** define **classes** of resources, their **properties**, and organize their **hierarchies**
@prefix igeo: <http://rdf.insee.fr/def/geo#> .

<figure><img src="image_65.png" /></figure>
@prefix igeo: <http://rdf.insee.fr/def/geo#> .

<figure><img src="image_66.png" /></figure>
@prefix igeo: <http://rdf.insee.fr/def/geo#> .

<figure><img src="image_67.png" /></figure>
Query **RDF with SPARQL**

**SPARQL Protocol** and **RDF Query Language**

<figure><img src="image_68.png" /></figure>
* Query Language (using the Turtle syntax)

* SPARQL 1.1 Query Language

* SPARQL 1.1 Update

* Representation of query results

* SPARQL Query Results Format XML, CSV/TCV, JSON

* Protocols

* SPARQL 1.1 Protocol

* SPARQL 1.1 Graph Store HTTP Protocol

* Entailments

* SPARQL 1.1 Entailment Regimes
# SPARQL: triple patterns

Turtle syntax with « ? » to mark **variables**:

`?x rdf:type ex:Person`

Describe patterns of triples that we look for:

SELECT ?subject ?type

WHERE { ?subject rdf:type ?type }

Default pattern: **conjunction** of triple patterns:

SELECT ?x WHERE

{ ?x rdf:type ex:Person .

?x ex:name ?name . }

<figure><img src="image_69.png" /></figure>
# SPARQL: namespace prefixes

Declare prefixes of used vocabularies:

```sparql
PREFIX mit: <http://www.mit.edu#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?student
WHERE {
    ?student mit:registeredAt ?x .
    ?x foaf:homepage <http://www.mit.edu> .
}
```

<figure><img src="image_70.png" /></figure>

Declare a base namespace for relative URIs:

```sparql
BASE <http://www.example.org/people#>
SELECT ?student
WHERE { ?student foaf:knows <Ted> . }
```
SPARQL: language and typed literals

```sparql
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?x ?f WHERE {
    ?x foaf:name "Fabien"@fr ; foaf:knows ?f .
}
```

```sparql
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?x WHERE {
    ?x foaf:name "Fabien"@fr ;
    foaf:age "21"^^ xsd:integer .
}
```

<figure><img src="image_71.png" /></figure>
```sparql
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
```

```sparql
SELECT ?person ?name
```

```sparql
WHERE {
    ?person foaf:homepage <http://fabien.info> .
    OPTIONAL { ?person foaf:name ?name . }
}
```

<figure><img src="image_72.png" /></figure>

Variable ?name is potentially **unbound**.
SPARQL alternative pattern

Merge the results of two graph patterns:

```sparql
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?person ?name
WHERE {
    ?person foaf:name ?name .
    { ?person foaf:homepage <http://fabien.info> . }
    UNION
    { ?person foaf:homepage <http://bafien.org> . }
}
```

<figure><img src="image_73.png" /></figure>
```sparql
PREFIX ex: <http://inria.fr/schema#>
SELECT ?person ?name
WHERE {
    ?person rdf:type ex:Person; ex:name ?name; ex:age ?age .
    FILTER (xsd:integer(?age) >= 18)
}
```

Other examples:

`FILTER(?name IN ("fabien", "olivier", "catherine"))`

`FILTER(if (langMatches(lang(?name), "FR"), ?age>=21))`

`FILTER NOT EXISTS {?x foaf:age -1}`
Subtract results

WHERE { ?x a ex:Person MINUS { ?x a ex:John } }

Bind values

?person foaf:name ?name .

VALUES ?name { "Peter" "Pietro" "Pedro" "Pierre" }

Property paths

?x foaf:knows+ ?friend .

From

FROM <http://www.mit.edu/datalei>

SELECT ?student

WHERE { ?student mit:registeredAt ?x . }
```xml
<?xml version="1.0"?>
<sparql xmlns="http://www.w3.org/2005/sparql-results#">
<head><variable name="student"/></head>
<results>
``

```xml
<result>
<binding name="student">
<uri>http://www.mit.edu/data[rdf#ndieng]</uri>
</binding>
</result>
```

```xml
<result>
<binding name="student">
<uri>http://www.mit.edu/data[rdf#jdoe]</uri>
</binding>
</result>
```

```xml
</results>
</sparql>
```
<figure><img src="image_74.png" /></figure>

DataLift

<figure><img src="image_75.png" /></figure>

Institut national de la statistique
et des études économiques

Mesurer pour comprendre

SPARQL endpoint

Description du nœud <http://id.insee.fr/geo/departement/971>

Rechercher

Texte

dans

Toutes les colonnes

<figure><img src="image_76.png" /></figure>

<table><thead><tr><td>Sujet</td><td>Prédicat</td><td>Objet</td></tr></thead><tbody><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://www.w3.org/1999/02/22-rdf-syntax-ns#type</td><td>http://rdf.insee.fr/def/geo#Departement</td></tr><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://www.w3.org/2002/07/owl#sameAs</td><td>http://data.ign.fr/id/geofla/departement/971</td></tr><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://www.w3.org/2002/07/owl#sameAs</td><td>http://nuts.geovocab.org/id/FRA10</td></tr><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://www.w3.org/2002/07/owl#sameAs</td><td>http://fr.dbpedia.org/resource/Guadeloupe</td></tr><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://rdf.insee.fr/def/demo#population</td><td>http://id.insee.fr/demo/populationLegale/departement/971/2010</td></tr><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://rdf.insee.fr/def/demo#population</td><td>http://id.insee.fr/demo/populationLegale/departement/971/2011</td></tr><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://rdf.insee.fr/def/demo#population</td><td>http://id.insee.fr/demo/populationLegale/departement/971/2012</td></tr><tr><td>http://id.insee.fr/geo/departement/971</td><td>http://rdf.insee.fr/def/geo#subdivisionDe</td><td>http://id.insee.fr/geo/region/01</td></tr></tbody></table>

III
(BnF

Bibliothèque
nationale de France

data.bnf.fr

<figure><img src="image_77.png" /></figure>

Charles Perrault (1628-1703)

<figure><img src="image_78.png" /></figure>

Pays : France

Langue : français

Sexe : masculin

Naissance : Paris, 12-01-1628

Mort : Paris, 16-05-1703

Note :
Homme de lettres, conteur, membre de l'Académie française (1671). - Contrôleur général de la Surintendance des bâtiments du roi. - Les contes ont été publiés en 1697 sous le de son fils : Perrault d'Armancour

Domaine : Littéraire

Outils

<figure><img src="image_79.png" /></figure>

Imprimer la page

<figure><img src="image_80.png" /></figure>

Exporter en PDF

<figure><img src="image_81.png" /></figure>

Signaler un problème sur la page

Citer la page

Permalien: http://data.bnf.fr/ark:/12148/cb119

<figure><img src="image_82.png" /></figure>

Télécharger les données

<figure><img src="image_83.png" /></figure>

<figure><img src="image_84.png" /></figure>

Télécharger en JSON

Le Web sémantique dans data.bnf.fr
<figure><img src="image_85.png" /></figure>

Charles Perrault (1628-1703)

<figure><img src="image_86.png" /></figure>

Pays :

France

<rdf:Description rdf:about="http://data.bnf.fr/ark:/12148/cb119192165#foaf:Person">

<foaf:familyName>Perrault</foaf:familyName>

<bnf-onto:firstYear rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1628</bnf-onto:firstYear>

<foaf:gender>male</foaf:gender>

<rdagroup2elements:dateOfBirth rdf:resource="http://data.bnf.fr/date/1628/"/>

<owl:sameAs rdf:resource="http://dbpedia.org/resource/Charles_Perrault"/>

<bio:death>1703-05-16</bio:death>

<rdagroup2elements:placeOfBirth>Paris</rdagroup2elements:placeOfBirth>

<owl:sameAs rdf:resource="http://viaf.org/viaf/34461426"/>

<foaf:depiction rdf:resource="http://gallica.bnf.fr/ark:/12148/bpt6k1020573 thumbnail"/>

<rdagroup2elements:fieldOfActivityOfThePerson rdf:resource="http://dewey.info/class/80"/>

<rdagroup2elements:dateOfDeath rdf:resource="http://data.bnf.fr/date/1703/"/>

<rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Person"/>

<foaf:birthday>01-12</foaf:birthday>

<foaf:depiction rdf:resource="http://gallica.bnf.fr/ark:/12148/bpt6k6154661t thumbnail"/>
<figure><img src="image_87.png" /></figure>

PREFIX igeo:<http://rdf.insee.fr/def/geo#>

SELECT ?x

WHERE { ?x rdf:type igeo:TerritoireAdministratif }
<figure><img src="image_88.png" /></figure>

PREFIX igeo:<http://rdf.insee.fr/def/geo#>

SELECT ?x ?code

WHERE { ?x igeo:codeINSEE ?code}
<figure><img src="image_89.png" /></figure>

SELECT ?x WHERE { ?x rdf:type igeo:Commune }

SELECT ?x WHERE { ?x rdf:type igeo:PaysOuTerritoire }
<figure><img src="image_90.png" /></figure>
<figure><img src="image_91.png" /></figure>

symmetric prop.

<figure><img src="image_92.png" /></figure>

<figure><img src="image_93.png" /></figure>

<figure><img src="image_94.png" /></figure>

<figure><img src="image_95.png" /></figure>

<figure><img src="image_96.png" /></figure>

prop. disjunction

<figure><img src="image_97.png" /></figure>

cardinality

<figure><img src="image_98.png" /></figure>

indiv. prop. negation

<figure><img src="image_99.png" /></figure>

chained prop.

<figure><img src="image_100.png" /></figure>

class disjunction

<figure><img src="image_101.png" /></figure>

def. by union

<figure><img src="image_102.png" /></figure>

def. by intersection

<figure><img src="image_103.png" /></figure>

def. by complement

<figure><img src="image_104.png" /></figure>

def. by restriction

<figure><img src="image_105.png" /></figure>

def. by cardinality

<figure><img src="image_106.png" /></figure>

def. by equivalence

<figure><img src="image_107.png" /></figure>

def. by enumeration

<figure><img src="image_108.png" /></figure>

def. by value restrict.

...
**Web of Data:** first step
in the deployment of
the **Semantic Web**

<figure><img src="image_109.png" /></figure>
Make our datasets
accessible and
interoperable on the Web...

<figure><img src="image_110.png" /></figure>

What
languages
can you
speak?
<figure><img src="image_111.png" /></figure>

Taxonomy:

* Practice and science of classification

• Hierarchical categorization of controlled classes/terms

• Nested classes under broader categories

<figure><img src="image_112.png" /></figure>

Thesaurus

* Networked collection of controlled vocabulary terms, grouped according to various types of relationship, e.g. similarity of meaning (synonyms, antonyms),

<figure><img src="image_113.png" /></figure>

Ontology

* Formal semantic description for the taxonomy terms, properties and interrelationships between categories in a domain of discourse, to facilitate conceptual search and natural language queries.

<figure><img src="image_114.png" /></figure>

Folksonomy

• Collaborative/social tagging, social classification...

• Tag category schemes

• No (not necessarily) hierarchical categorization
Create my own vocabulary

□ May seem easier: “I do whatever I want”

□ Can be derived from an existing schema, e.g.:

* RDB: table -> class, column -> property,
primary key -> resource URI

• Thesaurus -> list of classes or SKOS Concepts

But modeling implies choosing a point of view...

* E.g. biologist vs. geneticist, surgeon vs. anatomist, history...

• Domain experts must be involved

Risk: create an island of data

□ How to link my vocabulary/dataset
with other related ones?

<figure><img src="image_115.png" /></figure>

LOST ISLAND
ENTERTAINMENT
## Reuse existing vocabularies

* Where to look for: vocab./ontologies catalogs (see later)

* Difficulty to find the appropriate description

* Partial coverage of the domain I'm dealing with

* E.g. geographical area

* Granularity: level of details

* Too many (cumbersome), not enough (useless)

* Different points of view

## Frequently, a mixed approach is used

* Reuse + create

* Need for interlinking => alignment
Link ontologies (very basic)

<figure><img src="image_116.png" /></figure>
## Classes

- owl:equivalentClass, owl:disjointWith, rdfs:subClassOf,

## Properties

- owl:equivalentProperty, owl:inverseOf, rdfs:subPropertyOf

## Individuals

- owl:sameAs, owl:differentFrom, owl:allDifferent

## rdfs:seeAlso

- Indicate a resource that might provide additional information about the subject resource

## SKOS concepts

- skos:exactMatch: transitive

- skos:closeMatch, skos:relatedMatch

- skos:narrowMatch, skos:broaderMatch
Ontology matching: “representing declaratively relations
between heterogeneous models”

☐ Discovery of matching between classes, properties

- Discovery of matching between
individuals

- Named Entity Recognition,
Entity matching, text-mining...

<figure><img src="image_117.png" /></figure>
RDF-based standard to represent controlled vocabularies:
**glossary, dictionary, taxonomy, thesaurus...**

Bridge the gap between existing KOSs and the SW and LD

## Definition and documentation of classification systems

* SKOS concepts

* skos:Concept

* Labels and classification codes

* skos:prefLabel, skos:altLabel, skos:notation...

* Documentation

* skos:definition, skos:changeNote, skos:editorialNote, skos:example, etc.

* SKOS schemas

* skos:ConceptScheme, skos:hasTopConcept, skos:isTopConceptOf
Semantic relations between concepts

☐ Hierarchy of collections of concepts

• skos:Collection, skos:OrderedCollection, skos:member...

☐ Semantic network and Hierarchies of concepts

• skos:related

• skos:broader, skos:narrower

☐ Alignment of schemas

• skos:closeMatch, skos:exactMatch

• skos:relatedMatch, skos:broadMatch, skos:narrowMatch
<figure><img src="image_118.png" /></figure>

522 curated vocabularies

<figure><img src="image_119.png" /></figure>

Quality requirements

* URI stability and availability,

* Quality metadata and documentation,

* Identifiable and trustable publication body,

* Proper versioning policy,

* ...

http://lov.okfn.org/dataset/lov/

<figure><img src="image_120.png" /></figure>

"Vocabularies provide the semantic glue enabling Data to become meaningful Data."
<figure><img src="image_121.png" /></figure>

UniProt: protein sequence and
functional information.
Linked Open Vocabularies

<figure><img src="image_122.png" /></figure>

functional information.
Other catalogs of vocabularies

☐ Schemapedia (?) http://schemapedia.org

☐ schema.org
"Create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond".
Controlled set of curated vocabularies: cars, TV series, arts, administrations, diseases...

☐ DERI Vocabularies http://vocab.deri.ie/
URI space for RDFS vocabularies and OWL ontologies maintained at DERI.
No search interface.

General

☐ NCBO BioPortal http://bioportal.bioontology.org/ontologies/

☐ TDWG - Biodiversity Information Standards
http://www.tdwg.org/standards/
TDWG - Taxonomic Databases Working Group

And your favorite web search engine...

Domain specific
CD_NOM : Unique identifier of the scientific name

CD Sup : Identifier of the upper taxon in the classification

CD_REF : Identifier of the reference taxon

RANG : taxonomical rank

<table><thead><tr><th>1</th><th>REGNE</th><th>PHYLUM</th><th>CLASSE</th><th>ORDRE</th><th>FAMILLE</th><th>GROUP1</th><th>GROUP2</th><th>INP</th><th>CD_NOM</th><th>CD_TAXS</th><th>CD_REF</th><th>RANG</th><th>LB_NOM</th><th>LB_AUTEUR</th><th>NOM_COMPLET</th><th>NOM_COMP</th><th>NOM_</th></tr></thead><tbody><tr><td>189650</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>186227</td><td>186227</td><td>186227 FM</td><td></td><td></td><td>Delphinidae</td><td>Gray, 1821</td><td>Delphinidae</td><td>Gray</td><td>Delphinidae</td></tr><tr><td>189651</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>53642</td><td>186227</td><td>535142 GN</td><td></td><td></td><td>Cephalorhynchus</td><td>Gray, 1846</td><td>Cephalorhynchus</td><td>Gray</td><td>Cephalorhynchus</td></tr><tr><td>189652</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>535143</td><td>535142</td><td>535143 ES</td><td></td><td></td><td>Cephalorhynchus commersonii</td><td>(Lacépède, 1804)</td><td>Cephalorhynchus</td><td>(Lacépède, 1804)</td><td>Cephalorhynchus</td></tr><tr><td>189653</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589250</td><td>535142</td><td>535143 ES</td><td></td><td></td><td>Cephalorhynchus commersonii</td><td>Yanez, 1948</td><td>Cephalorhynchus</td><td>(Lacépède, 1804)</td><td>Cephalorhynchus</td></tr><tr><td>189654</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>586998</td><td>535142</td><td>535143 ES</td><td></td><td></td><td>Delphinus commersonii</td><td>Lacépède, 1804</td><td>Delphinus commersonii</td><td>(Lacépède, 1804)</td><td>Delphinus commersonii</td></tr><tr><td>189655</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>577923</td><td>535142</td><td>535143 ES</td><td></td><td></td><td>Lagenorhynchus burmeisteri</td><td>Moreno, 1892</td><td>Lagenorhynchus</td><td>(Lacépède, 1804)</td><td>Lagenorhynchus</td></tr><tr><td>189656</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>586999</td><td>535142</td><td>535143 ES</td><td></td><td></td><td>Lagenorhynchus floweri</td><td>Moreno, 1892</td><td>Lagenorhynchus</td><td>(Lacépède, 1804)</td><td>Lagenorhynchus</td></tr><tr><td>189657</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>577966</td><td>535142</td><td>535143 ES</td><td></td><td></td><td>Phocoena commersonii</td><td>Lesson, 1827</td><td>Phocoena commersonii</td><td>(Lacépède, 1804)</td><td>Phocoena commersonii</td></tr><tr><td>189658</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>191591</td><td>186227</td><td>191591 GN</td><td></td><td></td><td>Delphinus</td><td>Linnaeus, 1758</td><td>Delphinus Linnaeus</td><td>(Lacépède, 1804)</td><td>Delphinus Linnaeus</td></tr><tr><td>189659</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>361079</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus capensis</td><td>Gray, 1828</td><td>Delphinus capensis</td><td>(Lacépède, 1804)</td><td>Delphinus capensis</td></tr><tr><td>189660</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589323</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus bairdi</td><td>Norris &amp; Prescott</td><td>Delphinus bairdi</td><td>(Lacépède, 1804)</td><td>Delphinus bairdi</td></tr><tr><td>189661</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>60880</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus bairdi</td><td>Dall, 1873</td><td>Delphinus bairdi</td><td>(Lacépède, 1804)</td><td>Delphinus bairdi</td></tr><tr><td>189662</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589339</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus dussumieri</td><td>Blanford, 1891</td><td>Delphinus dussumieri</td><td>(Lacépède, 1804)</td><td>Delphinus dussumieri</td></tr><tr><td>189663</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589370</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus frithii</td><td>Blyth, 1859</td><td>Delphinus frithii</td><td>(Lacépède, 1804)</td><td>Delphinus frithii</td></tr><tr><td>189664</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589383</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus longirostris</td><td>G. Cuvier, 1829</td><td>Delphinus longirostris</td><td>(Lacépède, 1804)</td><td>Delphinus longirostris</td></tr><tr><td>189665</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589385</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus major</td><td>Gray, 1866</td><td>Delphinus major</td><td>(Lacépède, 1804)</td><td>Delphinus major</td></tr><tr><td>189666</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589394</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus microps</td><td>Burmeister, 1866</td><td>Delphinus microps</td><td>(Lacépède, 1804)</td><td>Delphinus microps</td></tr><tr><td>189667</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589395</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus moorei</td><td>Gray, 1866</td><td>Delphinus moorei</td><td>(Lacépède, 1804)</td><td>Delphinus moorei</td></tr><tr><td>189668</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589415</td><td>191591</td><td>361079 ES</td><td></td><td></td><td>Delphinus sao</td><td>Gray, 1850</td><td>Delphinus sao</td><td>(Lacépède, 1804)</td><td>Delphinus sao</td></tr><tr><td>189669</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>669537</td><td>361079</td><td>669537 SSES</td><td></td><td></td><td>Delphinus capensis tropicalis</td><td>Jefferson &amp; Van</td><td>Delphinus capensis</td><td>(Lacépède, 1804)</td><td>Delphinus capensis</td></tr><tr><td>189670</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>60878</td><td>191591</td><td>60878 ES</td><td></td><td></td><td>Delphinus delphis</td><td>Linnaeus, 1758</td><td>Delphinus delphis</td><td>(Lacépède, 1804)</td><td>Delphinus delphis</td></tr><tr><td>189671</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589316</td><td>191591</td><td>60878 ES</td><td></td><td></td><td>Delphinus albimanus</td><td>Peale, 1848</td><td>Delphinus albimanus</td><td>(Lacépède, 1804)</td><td>Delphinus albimanus</td></tr><tr><td>189672</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589319</td><td>191591</td><td>60878 ES</td><td></td><td></td><td>Delphinus algeriensis</td><td>Loche, 1860</td><td>Delphinus algeriensis</td><td>(Lacépède, 1804)</td><td>Delphinus algeriensis</td></tr><tr><td>189673</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>551374</td><td>191591</td><td>60878 ES</td><td></td><td></td><td>Delphinus delphus</td><td>Linnaeus, 1758</td><td>Delphinus delphus</td><td>(Lacépède, 1804)</td><td>Delphinus delphus</td></tr><tr><td>189674</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589344</td><td>191591</td><td>60878 ES</td><td></td><td></td><td>Delphinus forsteri</td><td>Gray, 1846</td><td>Delphinus forsteri</td><td>(Lacépède, 1804)</td><td>Delphinus forsteri</td></tr><tr><td>189675</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589368</td><td>191591</td><td>60878 ES</td><td></td><td></td><td>Delphinus fulvifasciatus</td><td>Wagner, 1846</td><td>Delphinus fulvifasciatus</td><td>(Lacépède, 1804)</td><td>Delphinus fulvifasciatus</td></tr><tr><td>189676</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589369</td><td>191591</td><td>60878 ES</td><td></td><td></td><td>Delphinus fulvofasciatus</td><td>True, 1889</td><td>Delphinus fulvofasciatus</td><td>(Lacépède, 1804)</td><td>Delphinus fulvofasciatus</td></tr></tbody></table>
CD_NOM : Unique identifier of the scientific name

CD Sup : Identifier of the upper taxon in the classification

CD_REF : Identifier of the reference taxon

RANG : taxonomical rank

<table><thead><tr><th></th><th>REGNE</th><th>PHYLUM</th><th>CLASSE</th><th>ORDRE</th><th>FAMILLE</th><th>GROUP1</th><th>GROUP2</th><th>INP</th><th>CD_NOM</th><th>CD_TAXS</th><th>CD_REF</th><th>RANG</th><th>LB_NOM</th><th>LB_AUTEUR</th><th>NOM_COMPLET</th><th>NOM_COMP</th><th>NOM_</th></tr></thead><tbody><tr><td>189650</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>186227</td><td></td><td></td><td></td><td></td><td></td><td></td><td>Gray, 1821</td><td>Delphinidae</td><td>Gray</td><td>Delphinidae</td></tr><tr><td>189651</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>535142</td><td>186227</td><td>535142</td><td>GN</td><td></td><td></td><td></td><td>Gray, 1846</td><td>Cephalorhynchus</td><td>Lacépède, 1804</td><td>Cephalorhynchus</td></tr><tr><td>189652</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>535143</td><td>535142</td><td>535143</td><td>ES</td><td></td><td></td><td></td><td>Cephalorhynchus commersonii</td><td></td><td>Cephalorhynchus</td></tr><tr><td>189653</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589259</td><td>535142</td><td>535143</td><td>ES</td><td></td><td></td><td></td><td>Yanez, 1948</td><td>Cephalorhynchus commersonii</td><td></td><td>Cephalorhynchus</td></tr><tr><td>189654</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>586998</td><td>535142</td><td>535143</td><td>ES</td><td></td><td></td><td></td><td>Lacépède, 1804</td><td>Delphinus commersonii</td><td></td><td>Delphinus</td></tr><tr><td>189655</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>1892</td><td>Lagenorhynchus</td><td>Lagenorhynchus</td><td>Cepha</td></tr><tr><td>189656</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>1892</td><td>Lagenorhynchus</td><td>Lagenorhynchus</td><td>Cepha</td></tr><tr><td>189657</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>1892</td><td>Phocoena commersonii</td><td>Phocoena</td><td>Cepha</td></tr><tr><td>189658</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>1758</td><td>Delphinus Linnaeus</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189659</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>Delphinus capensis</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189660</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>Delphinus bairdi</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189661</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>Delphinus bairdi</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189662</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>Delphinus dousso</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189663</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589370</td><td>191591</td><td>361079</td><td>ES</td><td></td><td></td><td></td><td></td><td>1891</td><td>Delphinus</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189664</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589383</td><td>191591</td><td>361079</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Delphinus frithii</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189665</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589385</td><td>191591</td><td>361079</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Delphinus major</td><td>Delphinus</td><td>Delphi</td></tr><tr><td>189666</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589394</td><td>191591</td><td>361079</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Burmeister, 1866</td><td>Delphinus micro</td><td>Delphinus</td></tr><tr><td>189667</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589395</td><td>191591</td><td>361079</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Gray, 1866</td><td>Delphinus moorei</td><td>Delphinus</td></tr><tr><td>189668</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589415</td><td>191591</td><td>361079</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Gray, 1850</td><td>Delphinus sao</td><td>Delphinus</td></tr><tr><td>189669</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>669537</td><td>361079</td><td>669537</td><td>SSES</td><td></td><td></td><td></td><td></td><td></td><td>Jefferson &amp; Van</td><td>Delphinus capensis</td><td>Delphinus</td></tr><tr><td>189670</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>60878</td><td>191591</td><td>60878</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Linnaeus, 1758</td><td>Delphinus capensis</td><td>Delphinus</td></tr><tr><td>189671</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589316</td><td>191591</td><td>60878</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Peale, 1848</td><td>Delphinus albimanus</td><td>Delphinus</td></tr><tr><td>189672</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589319</td><td>191591</td><td>60878</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Loche, 1860</td><td>Delphinus algeriensis</td><td>Delphinus</td></tr><tr><td>189673</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>551374</td><td>191591</td><td>60878</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Linnaeus, 1758</td><td>Delphinus delphus</td><td>Delphinus</td></tr><tr><td>189674</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589344</td><td>191591</td><td>60878</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Gray, 1846</td><td>Delphinus forsteri</td><td>Delphinus</td></tr><tr><td>189675</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589368</td><td>191591</td><td>60878</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>Wagner, 1846</td><td>Delphinus fulvifasciatus</td><td>Delphinus</td></tr><tr><td>189676</td><td>Animalia</td><td>Chordata</td><td>Mammalia</td><td>Cetacea</td><td>Delphinidae</td><td>Chordés</td><td>Mammifères</td><td>589369</td><td>191591</td><td>60878</td><td>ES</td><td></td><td></td><td></td><td></td><td></td><td>True, 1889</td><td>Delphinus fulvofasciatus</td><td>Delphinus</td></tr></tbody></table>

How to translate this table into a thesaurus exploitable as a semantic reference using semantic web technologies?
# TAXREF SKOS Modelling

<figure><img src="image_123.png" /></figure>

ZOOMATHIA

aurotropos huii

<figure><img src="image_124.png" /></figure>

<figure><img src="image_125.png" /></figure>
## "Static" (hand-made) alignments:

predicates, reference values (habitats, taxonomical ranks)

* **TaxonConcept Ontology:** properties habitat and authority, taxonomic ranks

* **NCBI Organismal Classification:** property has_rank, taxonomic ranks

* **GeoSpecies Knowledge Base:** taxonomic ranks

* **ENVO Environment Ontology:** habitats

* **Geonames:** mainland France and overseas territories

* **Darwin Core Terms:** properties occurrenceStatus, locationID

* **TDWG Occurence Status Terms:** biogeographical statuses

* **World Geographical Scheme for Recording Plant Distributions**
## Alignment of taxa and names done in a second step

<figure><img src="image_126.png" /></figure>

- Automate search of matches within other taxonomical references

- DBpedia

- NCBI Organismal Classification

- Agrovoc

- BnF

- Encyclopedia of Life

- Vertebrate Taxonomy Ontology

<figure><img src="image_127.png" /></figure>

- Difficulties

- Spelling differences

- Disagreements: reference vs. synonym, taxonomical rank

- owl:sameAs (individuals), owl:equivalentClass (classes), rdfs:seeAlso, skos:exactMatch, skos:closeMatch, skos:relatedMatch (concepts)...
Populate
the
Web of Data

<figure><img src="image_128.png" /></figure>

RDF
Many methods for many data sources

☐ HTML: RDFa, Microformats

☐ XML, XHTML

• XPath: RML

• XQuery: XSPARQL, SPARQL2XQuery

• XSLT: Gleaning Resource Descriptions from Dialects of Languages (GRDDL), Scissor-Lift

☐ CSV/TSV/Spreadsheets: CSV on the web (W3C WG)

☐ RDBs (next slides)

☐ NoSQL stores (MongoDB...): xR2RML (next slides)

☐ Integration frameworks

• DataLift, Asio Tool Suite, Talend (with Semantic Web plugin?)

<figure><img src="image_129.png" /></figure>
<figure><img src="image_130.png" /></figure>

: http://rbdd.cnrs.fr

<figure><img src="image_131.png" /></figure>

<body vocab="http://schema.org/">
<div resource="/jrbdd2015" typeof="Event">
<h2 property="title">RBDD 2015</h2>
<p>Date: <span property=" STARTE dATe">2015-10-20</span></p>
...
<p>Conduire et construire un plan de gestion des données.
<a property="url" href="http://rbdd.cnrs.fr/spip.php?article179">More...</a>
</p>
</div>
</body>
</html>

<figure><img src="image_132.png" /></figure>

prefix sch: <http://schema.org/>
<http://rbdd.cnrs.fr/jrbdd2015>
rdf:type sch:Event ;
sch: title "RBDD 2015";
sch:startDate "2015-10-20" ;
sch:uri <http://rbdd.cnrs.fr/spip.php?article179> .
# Translation of RDBs to RDF (RDB2RDF)

## ☐ Various initial motivations

* Web of Data, Linked Data

* OBDA

* Ontology learning

* Schema mapping...

## ☐ Historical products: D2RQ, Virtuoso...

## ☐ R2RML

* 2012 W3C recommendation, mapping language, several implementations

## ☐ Several methods: direct mapping vs. domain-specific
Direct Mapping of RDB to RDF

<table><thead><tr><th colspan="3">Table: PEOPLE</th></tr><tr><th>ID</th><th>FNAME</th><th>ADDR (FK ADDRESS/ID)</th></tr></thead><tbody><tr><td>7</td><td>Catherine</td><td>18</td></tr><tr><td>8</td><td>Olivier</td><td>22</td></tr><tr><td>...</td><td>...</td><td>...</td></tr></tbody></table>

<PEOPLE>ID=7> rdf:type <PEOPLE> .
<PEOPLE>ID=7> <PEOPLE#FNAME> "Catherine" .
<PEOPLE>ID=7> <PEOPLE#ADDR> <ADDRESS>ID=18> .

<PEOPLE>ID=8> rdf:type <People> .
<PEOPLE>ID=8> <PEOPLE#FNAME> "Olivier" .
<PEOPLE>ID=8> <PEOPLE#ADDR> <ADDRESS>ID=22> .
Customized Mapping of RDB to RDF

<#TriplesMap1>

rr:logicalTable [ rr:tableName "PEOPLE" ];

rr:subjectMap [
  rr:template "http://i3s.wimmics.org/staff/{ID}";
  rr:class ex:Teacher;
];

rr:predicateObjectMap [
  rr:predicate foaf:name;
  rr:objectMap [ rr:column "FNAME" ];
].

<figure><img src="image_133.png" /></figure>

<figure><img src="image_134.png" /></figure>

<http://i3s.wimmics.org/staff/7> rdf:type ex:Teacher.

<http://i3s.wimmics.org/staff/7> foaf:name "Catherine".

<http://i3s.wimmics.org/staff/8> rdf:type ex:Teacher.

<http://i3s.wimmics.org/staff/8> foaf:name "Olivier".
# xR2RML: Mapping of heterogeneous DBs to RDF

* Uniform language to describe mappings from most common types of DB to RDF

* Extends R2RML and RML

* Features:

* Allow any declarative query language

* Allow any syntax to reference data elements from query results (column name, attribute name, JSONPath, XPath...)

* Generate RDF lists and containers (bag, sequence, alternate)

* Support mixed content, e.g. XML value in relational column

* Implementation for MongoDB

* Data Materialization

* Query rewriting

<figure><img src="image_135.png" /></figure>
xR2RML mapping example

```xml
<#TriplesMap>
  xrr:logicalSource [
    xrr:query "db.studies.find({ studyid: { $exists:true } })";
  ];

  rr:subjectMap [
    rr:template "http://example.org/study#{$.studyid}";
    rr:class ex:Study
  ];

  rr:predicateObjectMap [
    rr:predicate ex:involves;
    rr:objectMap [
      xrr:reference "$.centres.*.name" ];
  ];
```

<figure><img src="image_136.png" /></figure>
# xR2RML in practice: data materialization

<figure><img src="image_137.png" /></figure>
# xR2RML in practice: query rewriting

<figure><img src="image_138.png" /></figure>
# Publish Linked Open Data on the Web

<figure><img src="image_139.png" /></figure>
1. Use URIs as names for things

2. Use HTTP URIs so that people can look up those names

3. When someone looks up a URI, provide useful information, using the standards (RDF*, SPARQL)

4. Include links to other URIs, so that they can discover more things

<figure><img src="image_140.png" /></figure>
□ Dereferencing the URI returns a representation of the document

* Either a direct link to the representation: the URI is a URL

* Or content negotiation links to an appropriate representation

<figure><img src="image_141.png" /></figure>

Source: http://www.w3.org/TR/cooluris/
HTTP content negotiation

<figure><img src="image_142.png" /></figure>
HTTP content negotiation

<figure><img src="image_143.png" /></figure>
One option: use Hash URIs for non-document resources

http://www.example.com/about#alice

<figure><img src="image_144.png" /></figure>

Thing

Automatic truncation of fragment

<figure><img src="image_145.png" /></figure>

http://www.example.com/about

<figure><img src="image_146.png" /></figure>

application/rdf+xml wins

content
negotiation

text/html wins

<figure><img src="image_147.png" /></figure>

RDF

<figure><img src="image_148.png" /></figure>

HTML

Content-Location:

Content-Location:

http://www.example.com/about.html

http://www.example.com/about.pdf

Source: http://www.w3.org/TR/cooluris/
* Use HTTP 303 forwarding to an information resource

* 303 See Other: the requested resource is not a regular Web doc. There is no suitable representation for the resource, but we can provide information about the resource

http://www.example.com/id/alice

<figure><img src="image_149.png" /></figure>

http://www.example.com/data/alice

http://www.example.com/people/alice

Source: http://www.w3.org/TR/cooluris/
* Cool URIs for the Semantic Web.
  W3C Interest Group Note 03 December 2008
  http://www.w3.org/TR/cooluris/

<figure><img src="image_150.png" /></figure>

* Dereferencing HTTP URIs
  Draft Tag Finding 04 October 2007
  http://www.w3.org/2001/tag/doc/httpRange-14/HttpRange-14.html
<figure><img src="image_151.png" /></figure>

Main idea: better publish less
data but publish useful data

* Choose an appropriate modeling

- Choose appropriate vocabularies

* Include high quality metadata, provenance information

- Deal with privacy issues

* Interlink

<figure><img src="image_152.png" /></figure>

Time consuming activity => significant cost

<figure><img src="image_153.png" /></figure>

Need skilled scientists who know the data, the software...

* Under-valued, no reward: data must become citable like any scientific publication => **Data Paper**

<figure><img src="image_154.png" /></figure>

BioMedBridges

<figure><img src="image_155.png" /></figure>

ENVRI

CRISP

<figure><img src="image_156.png" /></figure>

<figure><img src="image_157.png" /></figure>

DASISH

Realising the full potential of research
data: common challenges in data
management, sharing and integration
across scientific disciplines

Version: 3

Date: 20 December 2013

Authors: L. Field (CERN), S. Suhr (EMBL-EBI), J. Ison (EMBL-EBI), W. Los (UVA), P. Wittenburg (MPI), D. Broeder (MPI), A. Hardisty (Cardiff University), S. Repo (ELIXIR), A. Jenkinson (EMBL-EBI)
<figure><img src="image_158.png" /></figure>

Thank
you!