ismb 2010 biocatalogue presentation

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Jiten Bhagat University of Manchester [email protected] ISMB 2010 July 2010 | Boston, MA USA http://www.biocatalogue.org

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The slides were presented by Jiten Bhagat at ISMB 2010 in Boston (US)

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Page 1: ISMB 2010 BioCatalogue presentation

Jiten BhagatUniversity of Manchester

[email protected]

ISMB 2010July 2010 | Boston, MA USA

http://www.biocatalogue.org

Page 2: ISMB 2010 BioCatalogue presentation

• A public centralised and curated registry of Life Science Web Services

• ‘Web 2.0’-style website and API

• Allow anyone to register, discover and curate Web Services

• Community oriented with expert guidance

• Open content, open source, open platform11th July 2010 2ISMB 10

Page 3: ISMB 2010 BioCatalogue presentation

Public launched a year ago at ISMB 2009

11th July 2010 3ISMB 10

Page 4: ISMB 2010 BioCatalogue presentation

Who

11th July 2010 4ISMB 10

Page 5: ISMB 2010 BioCatalogue presentation

Revisiting the Motivations (I)

Guesstimate 3000+ publicly available online services in Life Sciences

Where?can I find them? advertise them?

What?do they do? can I use them?the cost? the licenses?

How?do they work? up to date?

Who?provides them? uses them? recommends them?11th July 2010 5ISMB 10

Page 6: ISMB 2010 BioCatalogue presentation

Revisiting the Motivations (II)

Discover “Web Services are hard to find”

Register “My Web Services are not visible”

Annotate “Web Services are poorly described”

Monitor “Web Services can be volatile”

11th July 2010 6ISMB 10

Page 7: ISMB 2010 BioCatalogue presentation

Where Are We Now

• Project is active and going strong

• Building up content and metadata

• Constant, iterative development and releases

• Full time curator with a focus group of users

• Active community involvement & outreach

11th July 2010 7ISMB 10

Page 8: ISMB 2010 BioCatalogue presentation

Reach

• 11K unique visitors from over 120 countries

11th July 2010 8ISMB 10

Page 9: ISMB 2010 BioCatalogue presentation

Stats

• 390+ registered members

• 120+ service providers

• 1.7K Web Services with over 11K SOAP operations and 1K REST endpoints

• Almost 50K annotations 33K from providers (and WSDL docs) 9K from users

11th July 2010 9ISMB 10

Page 10: ISMB 2010 BioCatalogue presentation

Started With...

• Simple Web Service registration

• Annotation Descriptions, Tags, Categories, Example Data

• Keyword search

• Filtering

• Basic monitoring

11th July 2010 10ISMB 10

Page 11: ISMB 2010 BioCatalogue presentation

Now (I)

• Features and Improvements Brand new more "active" homepage More monitoring features • EMBRACE test scripts

Automatic service update checker Better support for describing REST services More annotation fields for metadata Activity feeds & monitoring status changes Improved website interface

11th July 2010 11ISMB 10

Page 12: ISMB 2010 BioCatalogue presentation

Now (II)

• Programmatic access to the BioCatalogue data and features (API) Read only• Write API coming soon

Used in:• NCRI's ONIX platform• Taverna plugin• BioCatalogue Mass Curation app (using spreadsheets)• myExperiment integration

Follows REST principles (XML & JSON outputs)

11th July 2010 12ISMB 10

Page 13: ISMB 2010 BioCatalogue presentation

Now (II)

• Content Acquisition, Outreach & Papers Merged the data from the EMBRACE registry NAR paper published (featured in top 5%)Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S.,

Stevens, R., Pettifer, S., Lopez, R., Goble, C.A.: BioCatalogue: a universal catalogue of web services for the life sciences, Nucl. Acids Res., 2010. doi:10.1093/nar/gkq394

Annotation jamboree with 15 folks• Providers and consumers

Presentations and posters at events

11th July 2010 13ISMB 10

Page 14: ISMB 2010 BioCatalogue presentation

DEMO

11th July 2010 14ISMB 10

Page 15: ISMB 2010 BioCatalogue presentation

NCRI ONIX Resource Catalogue

11th July 2010 ISMB 10 15

Page 16: ISMB 2010 BioCatalogue presentation

BioCatalogue in Taverna

11th July 2010 ISMB 10 16

Page 17: ISMB 2010 BioCatalogue presentation

Mass Curation Tool

11th July 2010 18ISMB 10

Page 18: ISMB 2010 BioCatalogue presentation

EdUnify Registry

11th July 2010 ISMB 10 19

https://demo.edunify.pesc.org/ - Web Services for Education

https://wiki.service.emory.edu/display/er/EdUnify+-+Useful+Links

Page 19: ISMB 2010 BioCatalogue presentation

Some Lessons Learnt

1. Describing Web Services is HARD

2. We need to provide comprehensive APIs to the registry

3. The SOAP/REST technical view over services is not enough Need a more functional / task-oriented view

11th July 2010 20ISMB 10

Page 20: ISMB 2010 BioCatalogue presentation

Where We’re Heading

11th July 2010 ISMB 10 21

• Functional Units What tasks/functionality does this Web Service

provide?

• Testing services directly on the BioCatalogue

• Better support for developers Both for the BioCatalogue codebase and API use

• Carrying on with curation and community building

Page 21: ISMB 2010 BioCatalogue presentation

How Can You Get Involved?

• Join in the curation of Web Services Describe how they work Tag and categorise

• Join in the development of the software

• Build applications / integrate using the API

• Install your own BioCatalogue instance

• Provide feedback and suggestions

11th July 2010 22ISMB 10

Page 22: ISMB 2010 BioCatalogue presentation

Acknowledgements

Thomas LaurentHamish McWilliams

Franck Tanoh

Jiten Bhagat

Carole Goble

Rodrigo LopezEric Nzuobontane

Steve Pettifer

Katy Wolstencroft

Robert Stevens

David De Roure

11th July 2010 23ISMB 10Mannie Tagarira

Sergejs Aleksejevs

Jerzy Orlowski

Page 23: ISMB 2010 BioCatalogue presentation
Page 24: ISMB 2010 BioCatalogue presentation

Thank You

http://www.biocatalogue.org

About Us - http://wiki.biocatalogue.org

API Docs - http://apidocs.biocatalogue.org

11th July 2010 25ISMB 10

Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S., Lopez, R., Goble, C.A.: BioCatalogue: a

universal catalogue of web services for the life sciences, Nucl. Acids Res., 2010. doi:10.1093/nar/gkq394