Biodiversity Catalogue

Niall BeardDr Aleksandra Nenadic

Prof Carole GobleeScience Lab, University of Manchester

Overview• Motivation: Web services discovery problem• Structure of Service Metadata• Ontological Classification• Features• Site Statistics• Remarks

• http://biodiversitycatalogue.org

Web Services DiscoveryHow 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?

WebService Provider

Scientist

What is BiodiversityCatalogue?

Register a WS

Find a WS

Use a WS

Invoke a WS/Get results

Scientist

Web Service

Service Provider

Faceted Browsing

11/06/2014 5

Tags

Available filters (below)

Applied filters (top)Result/filtered services

Subscribe to these filtersFurther searchingFilters

• 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get outdated– Long term reliability– Testing on a daily basis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

Taverna WorkflowsInclude in Workflow

Taverna Workflows

Workflows in myExperiment.

org• myExperiment is

a Workflow registry

• Can integrate workflows within workflows using Taverna

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

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

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

Topic Ontology• Controlled

Vocabulary used to classify Web services

• Privately constructed CV

• Mapped to EDAM to make outwardly interoperable

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

Bio.tools Tool Description

Data or Format Operation Data or Format

NB: Classifications are not disjoint

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

Example Data Services

• Ecological Niche Modelling with OpenModeller• https://www.biodiversitycatalogue.org/serv

ices/1