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

Is this 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?

A brief (and biased) history of the Web

Web 1.0 - basic HTML pages (personal web sites on Geosites)

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

Linking ontologies

http://lod-cloud.net/

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

Registry

500+ curated data collections

500+ curated data collections

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

BioModels

http://www.ebi.ac.uk/biomodels/http://biomodels.caltech.edu/

Model workflow within BioModels

BioModels model display

BioModels model display

BioModels model display

BioModels model classification

Quo vadis?

● Model curation is hard

● Model annotation is laborious

● We moved from lack of methods to scalability and usability issues

● Towards semi-automated annotation based on model clustering

● User-friendly tools for annotating models