1. One small(ish) step for modellers, one
giant leap for mankind
Capturing the context
Mihai Glonț
Reproducible and Citable Data and Models
Warnemuende
September 2015

2. A simple(?) question

How easy is it to find reusable models?

Reusable should entail, at least
– Reproducible
– Friendly licence
– Understandable

3. Is this understandable?

4. 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?

5. A brief (and biased) history of the Web
Web 1.0 - basic HTML pages (personal web sites on Geosites)

6. Web 2.0
●
Prevalence of content generators
●
Social media
●
Rich user interfaces
●
Folksonomies
●
Software as a service

7. 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?

8. Semantic web overview
●
Taxonomies and ontologies define
concepts (resources) and
ontologies
●
Identification through URIs
●
Data is exchanged as RDF

9. Ontologies
●
Define concepts, instances, attributes and
relationships
●
Workshop is a kind of Thing
●
Workshop hasA location

10. Linking ontologies
http://lod-cloud.net/

11. 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

12. 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/

13. Identifiers, identifiers, identifiers
●
Is http://purl.uniprot.org/taxonomy/9606
the same as
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/w
wwtax.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?

14. 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

15. Registry
500+ curated
data collections
500+ curated
data collections

16. Creating unique URIs
• Homo sapiens in Taxonomy
(9606)
http://identifiers.org/taxonomy/9606http://identifiers.org/taxonomy/9606
[Data
collection]
[Entity
identifier]

17. Creating resolvable URIs
http://identifiers.org/taxonomy/
9606
http://identifiers.org/taxonomy/
9606
• URI to identify the entity 'Homo sapiens' in the
data collection Taxonomy
http://www.ncbi.nlm.nih.go
v/Taxonomy/Browser/wwwtax.
cgi?mode=Info&id=9606
http://www.uniprot.org/taxon
omy/9606
http://www.ebi.ac.uk/ena/dat
a/view/Taxon:9606
ResourceResource ResourceResource ReferenceReference
Primary
http://info.identifiers.org/taxonomy/
9606
http://info.identifiers.org/taxonomy/
9606

18. Inter-conversion of identifier
schemes
• Registry records different identifier schemes
• Web service for inter-conversion between
identifier schemes
http://purl.obolibrary.org/obo/GO_000588
6
http://purl.obolibrary.org/obo/GO_000588
6
http://bio2rdf.org/go:0005886http://bio2rdf.org/go:0005886
http://identifiers.org/go/GO:000588
6
http://identifiers.org/go/GO:000588
6

19. Support for different formats
TaxonomyTaxonomy
htmlhtml
htmlhtml
RDFRDF
jsonjson
• The Registry records the formats provided by the
various data resources

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

21. Model workflow within BioModels

22. BioModels model display

23. BioModels model display

24. BioModels model display

25. BioModels model classification

26. 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