1.
BioSamples Database Linked Data
(2014 edition)
Marco Brandizi,
Functional Genomics Team
SWAT4LS Tutorial, Dec 9th, 2014
Find this presentation on
http://www.slideshare.net/mbrandizi

2.
Why a BioSamples Database (aka BioSD)?
• A reference system, where to search/browse information about biological
samples, used/useable for biomedical experiments
• Focused on the sample context (i.e., independent on the specific assay
type/technology)
• Supports heterogeneous experiments
– Single place that assay repositories can link (reference samples,
authoritative source for repositories like
Metagenomics/ENA/ArrayExpress)
– Single place for searches and related-to or same-as relationships
(e.g., see the 'myEquivalents' project)
• Common interfaces to access sample information and links to specific
data/repositories (e.g., web, XML/REST, RDF)

3.
Why Linked Data for BioSD?
• Potentially useful to application developers and Linked Data tools
• Integration with similar/related data-sets
• Exploitation of ontologies
– Standardisation
– A little semantics goes a long way
– Improved searching
• As usually, open to unexpected uses
– e.g., http://www.phyloviz.net/NGSonto

4.
The BioSD Model
Sample Groups
Submission
External links
Samples
http://www.ebi.ac.uk/biosamples

5.
The BioSD Model
Group's (or Submission's) samples
Sample's (or Groups') attribute types
and values
External links

6.
Changes to Linked Data Model
• • Main Main Entities: Entities: http://http://tinyurl.tinyurl.com/com/lo33ncc
lo33ncc
• • Details Details about about Sample Sample Attributes: Attributes: http://http://tinyurl.tinyurl.com/com/n5oyvyd
n5oyvyd
Several improvements to the conversion software, Several improvements to the conversion software, A Aimiminingg aatt mmoorree ffrreeqquueenntt aauuttoo--uuppddaatteess

7.
SPARQL Queries

8.
Find Samples and attributes
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX sio: <http://semanticscience.org/resource/>
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel
WHERE
{
?smp
a biosd-terms:Sample;
biosd-terms:has-bio-characteristic | sio:SIO_000332 ?pv. # is about
?pv
rdfs:label ?pvLabel;
biosd-terms:has-bio-characteristic-type ?pvType.
?pvType
rdfs:label ?propTypeLabel.
}
• Exercise: use FILTER()/REGEX() to find organism=homo sapiens
• Exercise: Find sample' repositories of provenance and their links
– Hint: explore the sample's links (?smp) and see how RepositoryWebRecord
looks like
Try it at: http://www.ebi.ac.uk/rdf/services/biosamples/sparql
Excercise Solution: see examples on such page

9.
Samples about a given organism
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel
WHERE {
?smp biosd-terms:has-bio-characteristic ?pv.
?pv biosd-terms:has-bio-characteristic-type ?pvType;
rdfs:label ?pvLabel.
?pvType a ?pvTypeClass.
# Listeria
?pvTypeClass
rdfs:label ?propTypeLabel;
# '*' gives you transitive closure, even when inference is disabled
rdfs:subClassOf* <http://purl.obolibrary.org/obo/NCBITaxon_1637>
}
• Exercise: Use the Bioportal Service to first find all subclasses of 'alcohol' (obo:CHEBI_30879)
and then search samples annotated with such subclasses
– Hint: Use SERVICE <http://sparql.bioontology.org/ontologies/sparql/?apikey=KEY>
Try it at: http://www.ebi.ac.uk/rdf/services/biosamples/sparql
Excercise Solution: see one of the examples on such page

10.
Geo-located Samples/Sample Groups
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX sio: <http://semanticscience.org/resource/>
SELECT DISTINCT ?item ?latVal ?longVal WHERE {
?item biosd-terms:has-bio-characteristic ?latPv, ?longPv.
?latPv
biosd-terms:has-bio-characteristic-type [ rdfs:label ?latLabel];
sio:SIO_000300 ?latVal. # sio:has value
FILTER ( REGEX ( ?latLabel, "latitude", "i" ) ).
?longPv
biosd-terms:has-bio-characteristic-type [ rdfs:label ?longLabel ];
sio:SIO_000300 ?longVal. # sio:has value
FILTER ( REGEX ( ?longLabel, "longitude", "i" ) ).
}
• Find all samples having an attribute of type temperature, with a numerical value and a unit
specified. Hint: use sio:SIO_000221 (has unit), sio:SIO_000300 (has value)
• Find samples/groups annotated with intervals, which use the properties biosd-terms:has-low-value
and has-high-value and optionally have a unit.
Try it at: http://www.ebi.ac.uk/rdf/services/biosamples/sparql
Excercise Solutions: see examples on that page

11.
Expressed Genes and Samples
• For http://purl.uniprot.org/uniprot/P04637 (P53 in Human)
• Find the EFO classes for which it is up-regulated in the Atlas (p-value < 1E-9)
• And show the Atlas expression value label . Hints:
– Start from the example http://tinyurl.com/kvvhw6b,
– Use the Atlas endpoint: http://www.ebi.ac.uk/rdf/services/atlas/sparql
• Find the samples having attributes that are instances of such EFO classes
• Which comes from a repository other than 'ArrayExpress'
• Hints:
– Use SERVICE <http://www.ebi.ac.uk/rdf/services/biosamples/sparql> and a sub-query
– Search property values linked to prop. types that are instances of the e.f. found by the
Atlas
– Then link to the samples, the samples to the submissions, the submissions to the web
records
● OR JUST HAVE A LOOK: http://goo.gl/kOfE1r (will take a while...)

12.
New Ideas and Alike

13.
Geo-Samples, Google Map Integration
• Exercise: From geo-located samples to Google Map. Think how to do it:
● Gmaps supports the KML format (https://developers.google.com/kml)
● You can type a KML-returning URL into maps.google.com
(or pass it via GET, q=<kml-url>)
● The SPARQL endpoint can return results in XML format
● There are on line XSLTs: http://services.w3.org/xslt?xslfile=<url>&xmlfile=<url>
http://tinyurl.com/kzd2pg4
http://tinyurl.com/lf2623l
http://tinyurl.com/lltqy2u
http://goo.gl/maps/CMRrk
Many thanks to Costanza Romano

14.
Search-by-Feature Similarity (ongoing)
SELECT DISTINCT ?smp ? smpDescr (COUNT (DISTINCT ?pv) AS ?score)
WHERE {
{
?smp a biosd-terms:Sample;
rdfs:comment ?smpDescr.
?smp biosd-terms:has-bio-characteristic ?pv.
?pv biosd-terms:has-bio-characteristic-type ?pvType.
?pvType a <http://purl.obolibrary.org/obo/NCBITaxon_10090>.
} UNION {
?smp a biosd-terms:Sample;
rdfs:comment ?smpDescr.
...
?pvType a <http://purl.obolibrary.org/obo/NCBITaxon_10090>.
} UNION ...
}
GROUP BY ?smp ?smpDescr
HAVING (COUNT (DISTINCT ?pv) > 0)
ORDER BY DESC (COUNT (DISTINCT ?pv))
• Many thanks to AbdulShakur Abdullah, Eric Hillaert, Prasad Nuli
(https://github.com/CapStoneEBI2014/biosd_similarity_search)

15.
More (possibly for the hackathon)
• Continuing with the similarity search
• Improving linkage with other data sets
– e.g., targeting samples in ArrayExpress/Atlas
– e.g., links to EPMC data sets (PMID->PMC conversion), Bio2RDF
publications, LLD publications
• Aiming at supporting similar datasets
– Interested in the on-going HCLS' work about HL7->RDF
– Collaborating with the European biobank community
● Interested in the BBMRI-ontology (http://tinyurl.com/qjttyge)
• Visualisations/widgets
– Geo-located samples on a map
– Samples on body map
– Using the BioJS library

16.
Acknowledgements
• BioSD Team - Alvis Brazma, Tony Burdett, Adam
Faulconbridge, Mike Gostev, Helen Parkinson, Rui Perreria,
Ugis Sarkans, Drashtti Vasant
• Tony Burdett for the help with Zooma
• Simon Jupp, Andy Jenkinson, James Malone, for their great
help with developing and setting up BioSD/RDF
– The rest of the Linked Data team @EBI
(http://www.ebi.ac.uk/rdf)
• BiomedBridges FP7 project (http://www.biomedbridges.eu), for
funding us

17.
And you all!
Contact info:
www.ebi.ac.uk/biosamples
www.marcobrandizi.info
Sorry, we have grown to ~4M samples, yet we don't have all of them,
not even this year...
(Sources: http://en.wikipedia.org/wiki/File:Assorted_computer_mice_-_MfK_Bern.jpg,
http://tinyurl.com/otfnhk6, http://tinyurl.com/odkadvn, http://tinyurl.com/pyrqrdf)

18.
Extras

19.
BioSD Data (External Data Sources)
SPARQL Source: http://tinyurl.com/o95xa5v
Tag Cloud made with http://www.wordle.net
(2013)
submissions sampleGroups samples
126490 126492 3925151
Computed on v20141205, SPARQL Source: http://tinyurl.com/ocyb2ld
Total number of triples is 190637851 (http://tinyurl.com/pkyvmnc)

20.
BioSD Data (Common Attribute Types)
SPARQL Source: http://goo.gl/wk0RHp
Tag Cloud made with http://www.wordle.net
(2013)

21.
Main Ontologies used in BioSD / Linked Data
• See Doc Page http://www.ebi.ac.uk/rdf/documentation/biosamples
• biosd-terms (http://tiny.cc/biosd_terms)
– a small application ontology defining specific classes and properties, e.g., sample,
sample group, has-knowledgeable-person
• Experimental Factors Ontology (EFO)
– mainly to define/annotate sample attributes
• Ontology for Biomedical Investigations (OBI)
• Information Artefacts Ontology (IAO)
• Semantic Science Ontology (SIO)
– to define main classes in BioSD/RDF
• Bibliographic Ontology (BIBO)
– We link publications about submissions/sample sets
• Dublin Core, schema.org, FOAF
– for general categories and in the Linked Data spirit
• Linked automatically by Zooma: many more (e.g., CHEBI, NCBI-Tax, GO)