Martelli PL, Profiti G, Casadio R, Savojardo C

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Martelli PL

Profiti G

Casadio R

Savojardo C

Archivio istituzionale della ricerca - Alma Mater Studiorum Università di Bologna

ContactIntegrating ELIXIR Italy with ELIXIR Interoperability platform activitiesOpportunities to join ELIXIR activities are vast and cover manydifferent technical topics. ELIXIR Italy assigned to the Universityof Bologna the task of integrating the Italian node with theInteroperability platform. Thanks to the funding of theImplementation Study for new nodes integration in currentactivities, and the Staff Exchange, we were able to engage intothe platform and establish productive partnerships withcolleagues of the Spanish node.Giuseppe Profiti giuseppe.profiti2@unibo.itPier Luigi Martelli gigi@biocomp.unibo.itRita Casadio rita.casadio@unibo.itCastrense Savojardo savojard@biocomp.unibo.ithttp://www.biocomp.unibo.itA workshop for the Italian ELIXIR community, held at the BolognaBiocomputing Group on January 31st and February 1st, steered an improvementof the quality and adoption of Bioschemas, a set of semantic annotations fortools, data and samples developed by the ELIXIR Interoperability platform.Gathering a small number of different end-users and having them focus onapplying Bioschemas specifications to their tools and data resulted in havingearly adopters, annotated resources, examples for future users andimprovement suggestions.In a few hours, 6 tools and 2 databases ended up publishing Bioschemasdescriptions in their respective Web pages. This approach could be applied toother open specifications, allowing a wider adoption and the integration ofsuggestions in a bottom-up fashion.A discussion of the workshop results has been submitted for publication onF1000 Research. These best practices we described will also be helpful in the AllHands Bioschemas workshop.The Italian workshop was funded via the Implementation study for theintegration of new ELIXIR Nodes, along with other integration activities.ELIXIR Italy partnered with ELIXIR Spain for a staff exchange program focusedon the interoperability and benchmarking of tools. This was possible thanks tothe high number of Italian tools registered on bio.tools and the OpenEBenchbenchmarking platform developed by the Spanish node.Tools should be easily accessible by other automated services. This could bedone via well defined API. As an example, eDGAR, a database of disease-geneassociations, implements RD-Connect API used by the Rare Diseasecommunity. Such APIs should be easily accessible by crawlers.We collaborated with the Barcelona Supercomputing Center (BSC) of ELIXIRSpain to add OpenAPI descriptions to some of our tools. This effort highlightedhow defining APIs since day one will help in a better design, which technologiescould be adapted to existing services and the technical requirements.The staff exchange also helped the BSC in improving their OpenEBench toolsbenchmarking service. The tools from ELIXIR Italy have been used as a testcase for identifying ways to better integrate information from the ELIXIRregistry (bio.tools) and identify tools versions. A fresh perspective also helpedin identifying new sources for citation and bibliometric data.Given the Bologna Biocomputing Group experience with automated proteinfunctional annotations, the exchange also resulted in a proposal for a usingOpenEBench for continuous evaluation of such methods. The result has beenadapted to the Critical Assessment of protein Function Annotation algorithms(CAFA) and it will be discussed at the ISMB conference 2018 (Chicago, July 7th).Tools and staff exchangeInteroperability and Bioschemas Workshop results6 toolsannotated2 databasesannotated7 new examples12 suggestions for documentation improvementwww.bioschemas.orgOpenEBenchProposal for CAFA-like experiments• Stored datasets• Standard evaluations• Comparable results• Continuous evaluation• Easier publication of resultsDevelopmentEnd usersSupport and requestsFeedbacks and new ideas8 attendees from6 institutionsBologna, 31/01-01/02 2018

Integrating ELIXIR Italy with ELIXIR Interoperability platform activities

https://cris.unibo.it/bitstream/11585/651907/1/f1000research-207674.pdf

Integrating ELIXIR Italy with ELIXIR Interoperability platform activities

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Archivio istituzionale della ricerca - Alma Mater Studiorum Università di Bologna