Reusing Public and Third Party Web Services Where… can I find them? advertise mine? What… do they do? can I use them? How… do they work? up to date? reliable? Who… provides them? recommends them? knows about them?
An Open, Public, Curated, Boutique Catalogue for Web Services serving the Life Sciences for the Bioinformatics Community http://www.biocatalogue.org Launched June 2009 Nucl Acids Res, June 2010, Web Servers issue doi : 10.1093/nar/gkq394
60 operations on chemistry and chem-informatics data Protein Seq. Alignment Protein Structure Prediction Protein Function Prediction Nucleotide Seq . Alignment Rna structure prediction Gene Prediction Text Mining Ontology Phylogeny Microarray Sequence Retrieval Identifier Retrieval Structure Retrieval Literature Retrieval Genomics Proteomics Systems Biology Biostatistics Chemoinformatics
Curation Change logs Quantitative Annotations Tags Semantic Annotations Ontologies Functional Capabilities Provenance Operational Capabilities Operational Metrics Use Policy Social Status Ratings Attribution Free text Instrumentation Usable and Useful Understand able
2 year availability, responsibility migration/hole, service decay -> application decay
58% developed by students, 24% stated not maintained
(Schultheiss et al. (2010) PLoS Comp Biol (in review))
146 services archived, >90% availability
Sustainability strategy Make it portable, Provide documentation Use existing frameworks and practices Involve the community and know your users Plan sunset or migration Funding models for sustainability Preserv ation
Schultheiss et al. (2010) PLoS Comp Biol (in review)
Service Operation Operation Operation Operation Operation Operation Operation Operation Operation Operation WSDL REST DAS [Missier, et al 2010 Functional Units: Abstractions for Web Service Annotations]
Complexity because it’s a database really SABIO–RK Service only Taverna workflow find chemical reactions that are associated with a given metabolite, and the kinetics associated with those reactions.
Emerging, evolving, exciting and challenging Web service ecosystem
BioCatalogue draws together services, knowledge and community to provide intelligence.
Crowd collaboration to scale contribution, core to coordinate
Open effort – contribute or adopt
Core resource – for Alliances and Journals
Social + technical challenges
Christian Hauck’s talk 16.00 Thursday.
Credits Thomas Laurent Hamish McWilliams Franck Tanoh Jiten Bhagat Carole Goble Steve Pettifer Katy Wolstencroft Robert Stevens David De Roure Mannie Tagarira Jerzy Orlowski Sergejs Aleksejevs Rodrigo Lopez Eric Nzuobontane
Thank You http:// www.biocatalogue.org About Us - http:// wiki.biocatalogue.org API Docs - http:// apidocs.biocatalogue.org 11th July 2010 ISMB 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