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BioSamples Database Linked DataBioSamples Database Linked Data
Marco Brandizi, Functional Genomics Team
SWAT4LS Tutorial, Dec 9th, 2013
Find this presentation at http://tiny.cc/bsdswt13
• 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 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)
• Allows for consistency/standardisation of sample attributes/annotations
• Common IT interfaces to access sample information and links to specific
data/repositories (e.g., web, XML/REST, RDF)
Why a BioSamples Database (aka BioSD)?
• Yet another type of interface, potentially useful to application developers
and Linked Data tools
• Integration with similar/related data-sets (see example queries below!)
• Exploitation of ontologies (see below!)
– Standardisation
– A little semantics goes a long way
• Modelling of certain aspects enhanced
– e.g., numbers, intervals, dates, units are detected from string value
labels and triplified.
• Who knows?
– Apps!
– See Hackaton ideas below!
Why Linked Data for BioSD?
The BioSD Model
Sample Groups
Submission
External links
Samples
http://www.ebi.ac.uk/biosamples
The BioSD Model
Group's (or Submission's) samples
Sample's (or Groups') attribute types
and values
External links
BioSD Data (External Data Sources)
SPARQL Source: http://tinyurl.com/o95xa5v
Tag Cloud made with http://www.wordle.net
SPARQL Source: http://tinyurl.com/ocyb2ld
BioSD Data (Common Attribute Types)
SPARQL Source: http://tinyurl.com/pjgdtzs
Tag Cloud made with http://www.wordle.net
BioSD Linked Data Model (Main Entities)
Please have a look at:
http://tinyurl.com/lo33ncc
BioSD Linked Data Model (Sample Attributes)
Please have a look at:
http://tinyurl.com/n5oyvyd
SPARQL Queries
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 provenance repositories 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
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 didsbled
rdfs:subClassOf* <http://purl.obolibrary.org/obo/NCBITaxon_1637>
}
• Exercise: Use the Bioportal Service to first find all subclasses of 'alchool' (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
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
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://tinyurl.com/ln3m7nv (will take a while...)
Ideas for the Hackaton
• Refer to http://tinyurl.com/mo7wgye for details
• From geo-located samples (samples annotated with latitude/longitude) to Google
maps, e.g, by using Exhibit (http://www.simile-widgets.org/exhibit/)
• Take similar datasets (e.g., MAASTRO, Breast Cancer Data, your data), unify the
schemas (e.g., using CONSTRUCT), define federated queries
• Use the Shape or OpenPHACTS validator to define sensible rules for BioSD and
similar data-sets, e.g., must contain an organism, should have a treatment
• Design/build an App (or Web widget) that asks for eligibility criterion, i.e., pairs of
attribute value/type, and translate it into a SPARQL query (or a more complex
search based on SPARQL) to find samples
– Use common ontologies for auto-completion over property types
– Use string-based auto-completion for values
– Consider numerical values, intervals, units
– Do approximate matching, i.e., matching 8/10 of specified pairs is good.
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
And you all!
Sorry, we have 2.7M samples, but not all of them...
(Source: http://en.wikipedia.org/wiki/File:Assorted_computer_mice_-_MfK_Bern.jpg)
Contact info:
www.ebi.ac.uk/biosamples
www.marcobrandizi.info
Extras
• 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)
Main Ontologies used in BioSD / Linked Data
BioSD → RDF
Conversion
github.com/EBIBioSamples/biosd2rdf
github.com/EBIBioSamples/biosd2rdf

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BioSamples Database Linked Data, SWAT4LS Tutorial

  • 1. BioSamples Database Linked DataBioSamples Database Linked Data Marco Brandizi, Functional Genomics Team SWAT4LS Tutorial, Dec 9th, 2013 Find this presentation at http://tiny.cc/bsdswt13
  • 2. • 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 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) • Allows for consistency/standardisation of sample attributes/annotations • Common IT interfaces to access sample information and links to specific data/repositories (e.g., web, XML/REST, RDF) Why a BioSamples Database (aka BioSD)?
  • 3. • Yet another type of interface, potentially useful to application developers and Linked Data tools • Integration with similar/related data-sets (see example queries below!) • Exploitation of ontologies (see below!) – Standardisation – A little semantics goes a long way • Modelling of certain aspects enhanced – e.g., numbers, intervals, dates, units are detected from string value labels and triplified. • Who knows? – Apps! – See Hackaton ideas below! Why Linked Data for BioSD?
  • 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. BioSD Data (External Data Sources) SPARQL Source: http://tinyurl.com/o95xa5v Tag Cloud made with http://www.wordle.net SPARQL Source: http://tinyurl.com/ocyb2ld
  • 7. BioSD Data (Common Attribute Types) SPARQL Source: http://tinyurl.com/pjgdtzs Tag Cloud made with http://www.wordle.net
  • 8. BioSD Linked Data Model (Main Entities) Please have a look at: http://tinyurl.com/lo33ncc
  • 9. BioSD Linked Data Model (Sample Attributes) Please have a look at: http://tinyurl.com/n5oyvyd
  • 11. 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 provenance repositories 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
  • 12. 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 didsbled rdfs:subClassOf* <http://purl.obolibrary.org/obo/NCBITaxon_1637> } • Exercise: Use the Bioportal Service to first find all subclasses of 'alchool' (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
  • 13. 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
  • 14. 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://tinyurl.com/ln3m7nv (will take a while...)
  • 15. Ideas for the Hackaton • Refer to http://tinyurl.com/mo7wgye for details • From geo-located samples (samples annotated with latitude/longitude) to Google maps, e.g, by using Exhibit (http://www.simile-widgets.org/exhibit/) • Take similar datasets (e.g., MAASTRO, Breast Cancer Data, your data), unify the schemas (e.g., using CONSTRUCT), define federated queries • Use the Shape or OpenPHACTS validator to define sensible rules for BioSD and similar data-sets, e.g., must contain an organism, should have a treatment • Design/build an App (or Web widget) that asks for eligibility criterion, i.e., pairs of attribute value/type, and translate it into a SPARQL query (or a more complex search based on SPARQL) to find samples – Use common ontologies for auto-completion over property types – Use string-based auto-completion for values – Consider numerical values, intervals, units – Do approximate matching, i.e., matching 8/10 of specified pairs is good.
  • 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! Sorry, we have 2.7M samples, but not all of them... (Source: http://en.wikipedia.org/wiki/File:Assorted_computer_mice_-_MfK_Bern.jpg) Contact info: www.ebi.ac.uk/biosamples www.marcobrandizi.info
  • 19. • 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) Main Ontologies used in BioSD / Linked Data

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