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One small(ish) step for modellers, one giant leap for mankind
Capturing the context
Mihai Glonț
Reproducible and Citable Data and ModelsWarnemuendeSeptember 2015
A simple(?) question
How easy is it to find reusable models? Reusable should entail, at least
– Reproducible
– Friendly licence
– Understandable
Problems
How do we recognise concepts? Is adenosine5PrimePhospate a better variable name than a? Do all modellers know the same amount information about ATP?
How can we uniquely identify the concepts involved in a modelling exercise?
Web 2.0
● Prevalence of content generators● Social media● Rich user interfaces● Folksonomies● Software as a service
Web 3.0
● Semantic Web
● “The Semantic Web provides a common framework that allows data to be shared and reused across application, enterprise, and community boundaries" (W3C)
● Machines understand the data on the web and can reason about it
● Implicit knowledge is captured in a machine-processable manner
● What holiday options are there for a family of four for 10 days, somewhere sunny and close to the sea, with good food and a budget of EUR 3000?
Semantic web overview
● Taxonomies and ontologies define concepts (resources) and ontologies
● Identification through URIs● Data is exchanged as RDF
Ontologies
● Define concepts, instances, attributes and relationships● Workshop is a kind of Thing
● Workshop hasA location
RDF Primer
● Resource Description Framework● Documents consist of a series of statements
● Statements (triples) follow the following syntax● Subject - Predicate – Object
https://sems.uni-rostock.de/reproducible-and-citable-data-and-models/http://example.com/someOntology/hasLocation
https://en.wikipedia.org/wiki/Warnemunde
A selection of ontologies for life scientists
● ChEBI: http://www.ebi.ac.uk/chebi/
● GO: http://geneontology.org/
● BRENDA Tissue Ontology: http://www.brenda-enzymes.org/
● FMA: http://bioportal.bioontology.org/ontologies/FMA
● Human disease ontology: http://disease-ontology.org/
● TEDDY: http://purl.bioontology.org/ontology/TEDDY/
● KiSAO: http://co.mbine.org/standards/kisao
● SBO: http://www.ebi.ac.uk/sbo/
https://www.ebi.ac.uk/ontology-lookup/
Identifiers, identifiers, identifiers
● Is http://purl.uniprot.org/taxonomy/9606
the same as http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606 or
http://taxonomy.bio2rdf.org/describe/?url=http://bio2rdf.org/taxonomy:9606
● What if the URIs change?● What if the URIs don't point to anything?
Introducing identifiers.org
● The aim of the identifiers.org project is to provide unique, stable, resolvable and location-independent URIs to identify and to locate scientific data
● Community-driven
● Free to use
Creating unique URIs
• Homo sapiens in Taxonomy (9606)
http://identifiers.org/taxonomy/9606http://identifiers.org/taxonomy/9606
[Data collection]
[Entity identifier]
Creating resolvable URIs
http://identifiers.org/taxonomy/9606http://identifiers.org/taxonomy/9606
• URI to identify the entity 'Homo sapiens' in the data collection Taxonomy
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606
http://www.uniprot.org/taxonomy/9606
http://www.ebi.ac.uk/ena/data/view/Taxon:9606
ResourceResource ResourceResource ReferenceReference
Primary
http://info.identifiers.org/taxonomy/9606http://info.identifiers.org/taxonomy/9606
Inter-conversion of identifier schemes• Registry records different identifier schemes
• Web service for inter-conversion between identifier schemes
http://purl.obolibrary.org/obo/GO_0005886
http://purl.obolibrary.org/obo/GO_0005886
http://bio2rdf.org/go:0005886http://bio2rdf.org/go:0005886
http://identifiers.org/go/GO:0005886
http://identifiers.org/go/GO:0005886
Support for different formats
TaxonomyTaxonomy
htmlhtml
htmlhtml
RDFRDF
jsonjson
• The Registry records the formats provided by the various data resources