Slides summarizing best practices for generating Bio2RDF Linked Data

1. Best practices for generating
linked data
Tutorial @ ICBO 2013

2. Tutorial Roadmap

3. Bio2RDF Best Practices
1. Assign a URI for all things
2. Assign labels and identifiers
3. Declare and assign types
4. Provide dataset provenance

4. 1. Assign URIs for all things
● The base Bio2RDF URI pattern:
http://bio2rdf.org/namespace:identifier
● Data provider record identifiers are
maintained from source
● Linked Data = no blank nodes!

5. 1. Assign URIs for all things
● Data provider records are maintained from
source
○ e.g. DrugBank’s resource IRI for
Leucovorin
http://bio2rdf.org/drugbank:DB00650

6. 1. Assign URIs for all things
● Vocabulary namespaces are used for
dataset specific types and predicates
http://bio2rdf.org/drugbank_vocabulary:Drug
● Resource namespaces are used to assign
an identifier when one isn't a provided by the
source
- unique identifier with UUID, hash, counter, concatenated
strings, etc
http://bio2rdf.org/drugbank_resource:DB00440_DB00650

7. 1. Assign URIs for all things
● All valid namespaces are listed in the
Bio2RDF Life Sciences Registry
○ ensures that URIs are consistent across all Bio2RDF
datasets
○ registry is publicly available at http://tinyurl.
com/dataregistry

8. 2. Assign labels and identifiers
● Use rdfs:label to assign a language-specified
label for all resources
○ can be a source provided title, a script generated
phrase, or a phrase provided in a third party dataset
○ Pattern: rdfs:label "label [ns:id]"@lang
● Use Dublin Core predicates for source-
provided label and identifiers
○ Pattern: dc:title "label"@lang (assign language tag
only when one is provided)
○ Pattern: dc:identifier "ns:id"^^xsd:string

9. 2. Assign labels and identifiers
● Use Bio2RDF predicates to assign Bio2RDF
namespace and Bio2RDF identifiers:
○ Pattern: bio2rdf_vocabulary:namespace "ns"^^xsd:
string
○ Pattern: bio2rdf_vocabulary:identifier "id"^^xsd:
string

10. 2. Assign labels and identifiers
Example: DrugBank entry for Nitrazepam
drugbank:DB0159
rdfs:label "Nitrazepam [drugbank:DB0159]"@en ;
dc:title “Nitrazepam”@en ;
dc:identifier “drugbank:DB0159”^^xsd:string ;
bio2rdf_vocabulary:namespace “drugbank”^^xsd:string ;
bio2rdf_vocabulary:identifier “DB0159”^^xsd:string .

11. 3. Declare and assign types
● All resources should be typed as being
resources of the dataset
○ Pattern: rdf:type namespace_vocabulary:Resource
● Instances of a dataset vocabulary type
should also be typed as owl:
NamedIndividual
○ Pattern: rdf:type namespace_vocabulary:Type
○ Pattern: rdf:type owl:NamedIndividual
● Classes should be typed as owl:Class
○ Pattern: rdf:type owl:Class
○ If superclass has been described using
namespace_vocabulary pattern, then link class
using rdfs:subClassOf

12. 3. Declare and assign types
● Object properties and datatype properties
should also be typed
○ Pattern: rdf:type owl:ObjectProperty
○ Pattern: rdf:type owl:DatatypeProperty
● Examples:
drugbank:DB0159
rdf:type drugbank_vocabulary:Resource ;
rdf:type owl:Class ;
rdfs:subClassOf drugbank_vocabulary:Drug .
drugbank_vocabulary:ddi-interactor-in
rdf:type owl:ObjectProperty .

13. 4. Provide dataset provenance
data item
Bio2RDF dataset
Features
-Entity-dataset link
-Creator
-Publisher
-Date created
-License & rights
-Source
-Availability
- SPARQL endpoint
- Data dump
Vocabularies
VoID
Dublin Core
W3C Provenance
Bio2RDF vocabulary
Source dataset
prov:wasDerivedFrom
void:inDataset

14. 4. Provide dataset provenance
● link every resource to the versioned/dated
Bio2RDF dataset in which it is described
○ Pattern: void:inDataset <http://bio2rdf.org/dataset:
namespace-dd-mm-yyyy.rdf>
○ Example:
drugbank:DB0159 void:inDataset <http://bio2rdf.
org/dataset:drugbank-03-07-2013> .

15. A crash course in PHP

16. PHP : Hypertext Preprocessor
● A general-purpose open source scripting
language
○ homepage : http://php.net
● PHP scripts can be executed from the
command line or embedded in HTML
documents
● Syntactically similar to C/C++/Java but it is
not strongly typed

17. A hello world PHP script
● All PHP scripts are surrounded by the <?php
and ?> tags

18. Declaring and instantiating classes

19. Using the Bio2RDF PHP API to create an
RDFizer
● Basic structure of a Bio2RDFizer script:
○ Initialize script parameters - input file(s), default
dataset namespace, etc.
○ Define a Run() function that handles downloading
and iterating over input files, as well as function calls
to parse and convert input data to RDF
○ Define function(s) to convert input data to RDF using
Bio2RDF API helper functions

20. Using the Bio2RDF PHP API to create an
RDFizer
● Bio2RDF PHP API defines helper functions
that implement Bio2RDF best practices:
○ getNamespace()
○ getVoc()
○ getRes()
○ triplify($subject, $predicate, $object) //object is an rdf resource
○ triplifyString($subject, $predicate, "string")// object is a literal
○ describeIndividual($uri, $label, $type, $title, $description, $language)
○ describeClass( ... )
○ describeProperty ( ... )

21. Example: The Comparative
Toxicogenomics Database
CTD Bio2RDFizer
script is available
on GitHub

22. Using and contributing to the
Bio2RDF project on GitHub

23. Using and contributing to the
Bio2RDF project on GitHub
1. Fork the bio2rdf-scripts and php-lib
repositories on Github
https://help.github.com/articles/fork-a-repo
2. Write some code!
3. Commit code to your fork
4. Make a pull request to the bio2rdf-scripts
repo