Niall Beards presentation about the BiodiversityCatalogue and how it facilitates web service discoverability, its interaction with Taverna, and it's interoperability with the bio.tools registry.

1. Biodiversity Catalogue
Niall Beard
Dr Aleksandra Nenadic
Prof Carole Goble
eScience Lab, University of Manchester

2. Overview
• Motivation: Web services discovery problem
• Structure of Service Metadata
• Ontological Classification
• Features
• Site Statistics
• Remarks
• http://biodiversitycatalogue.org

3. Web Services Discovery
How can I advertise
my Web services? What information do
people need about
them?
What can this Web
service do? How do I
use it? How do I know the
Web service will still
be working
tomorrow?
How can I find the
right Web service?
Web
Service
Provide
r
Scientist

4. What is BiodiversityCatalogue?
Register a WS
Find a WS
Use a WS
Invoke a WS/Get results
Scienti
st
Web
Service
Service Provider

5. Faceted Browsing
11/06/2014 5
Tag
s
Available filters (below)
Applied filters (top)
Result/filtered services
Subscribe to these filters
Further searchingFilters

6. • Web service
MONITORING
– Services change and
get outdated
– Long term reliability
– Testing on a daily basis
Monitoring
11/06/2014 pro-iBiosphere Final Event, Brussels 6

7. Taverna Workflows
Include in Workflow

8. Taverna Workflows

9. Workflows in
myExperiment.
org
• myExperiment is
a Workflow
registry
• Can integrate
workflows within
workflows using
Taverna

10. Other Features
• Data Search – Search using your data to find
services with corresponding input output
types
• Script Testing (Defunct) – Write tests to check
the operational functionality of the web
service

11. Structure of Service Metadata
• Profile
• Documentation URL
• Description
• License
• Cost
• Contact Info
• Usage Conditions
• How to cite
• Publications about service
• Example workflows
• Maturity

12. Structure of Service Metadata
• Technical
•Description of endpoints/operations
•Example endpoints
•Documentation URLs
• Input Parameters
– Description
– Default Value
– Constrained Values
– Example Data
– Required or Optional
• Output Representations
– Content Type (e.g. text/csv)
– Example data
– Data formats
– Data Schemas
– Tags

13. Topic Ontology
• Controlled
Vocabulary used to
classify Web
services
• Privately
constructed CV
• Mapped to EDAM
to make outwardly
interoperable

14. Bio.tools Integration
• BioCatalogue exports its
tools to the bio.tools
registry
• Bio.tools uses the EDAM
ontology to annotate.
• Topic
• Data
• Format
• Operation
• Unfortunately no such
detail ontology tagging
beyond topics

15. Bio.tools Tool Description
Data or Format Operation Data or Format

16. NB: Classifications are not disjoint

17. Remarks
• Annotations work well for assisting
construction of workflows
– Structured enough to help humans read
– Free text annotations mean no service type or
domain knowledge needed.
• Semantic annotations would work better
– Automated workflow construction would be the
holy grail
– Curation costs prohibitive

18. Example Data Services
• Ecological Niche Modelling with
OpenModeller
• https://www.biodiversitycatalogue.org/ser
vices/1