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Sharing Interoperable Workflows

The SHIWA (SHaring Interoperable Workflows for large-scale scientific simulations on Available DCIs) project enables publicly available workflows to be used by different research communities working on different workflow systems, and to be run on multiple distributed computing infrastructures. SHIWA and Wf4Ever are complementary projects: Wf4Ever takes a holistic view of the lifecycle of the workflow object while SHIWA brings very significant functionality in workflow execution. We are pleased to announce co-operation between these projects, and members of the Wf4Ever team will be attending the e-Science Workflows event held jointly with EGI in Budapest in February 2012.  A Memorandum of Understanding is under development.

Link for Shiwa https://www.shiwa-workflow.eu/about

Research objects

Last month, the Wf4Ever project published v0.1 of the Research Object vocabulary. This set of OWL ontologies gave us a starting point for describing workflows, data aggregations and annotations of digital artefacts. Several Wf4Ever partners are participating in the W3C Provenance working group, which have recently published the first draft for the PROV-O standard, an OWL implementation of the draft PROV-DM model.

As a first prototype for exercising both the PROV-O and RO ontologies in combination with the scientific workflow system Taverna, we have developed a set of small utillities. This blog post is a kind of technical dip showing.

Extracting abstract workflow structures

scufl2-to-wfdesc is a tool and extension of scufl2, an API for processing Taverna workflows. As a command line tool, this can extract the workflow structure from a Taverna .t2flow workflow definition, and save this as a wfdesc description, which can be uploaded as an annotation on the aggregated t2flow in the research object.

For example, the abstract structure of a (very simple) Hello World workflow looks like this (RDF/Turtle from helloworld.wfdesc.ttl):

 @base <http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/workflow/Hello_World/> .
@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
	rdfs:label "Hello_World" ;
	wfdesc:hasOutput <out/greeting> ;
	wfdesc:hasSubProcess <processor/hello/> ;
	wfdesc:hasDataLink <datalink?from=processor/hello/out/value&to=out/greeting> .

<out/greeting> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
	rdfs:label "greeting" .

<processor/hello/> a wfdesc:Process , wfdesc:Description ;
	rdfs:label "hello" ;
	wfdesc:hasOutput <processor/hello/out/value> .

<processor/hello/out/value> a wfdesc:Output , wfdesc:Description ;
	rdfs:label "value" .

<datalink?from=processor/hello/out/value&to=out/greeting> a wfdesc:DataLink ;
	wfdesc:hasSource <processor/hello/out/value> ;
	wfdesc:hasSink <out/greeting> .

wfdesc is intended as a minimal structure for describing scientific workflows from different systems. It is inspired by earlier work such as myExperiment's workflow component ontology and OPMW.

The next step for the scufl2-to-wfdesc tool is to convert it into a freestanding agent, which can submit SPARQL queries to the Research Object digital library (RODL) to find research objects which aggregate Taverna workflows, and then use the RODL REST API to upload the extracted wfdesc structure as an annotation on the workflow. This would be a stepping stone to allow other RO tools to work with workflow fragments (for instance recommendations, decay analysis and service replacement) and in particular to associate aggregated workflow results with their internal workflow provenance.

Exporting workflow provenance

Several provenance models already exists, such as OPM-V, PREMIS and SWAN, and new models such as the W3C PROV-O are under development. Wf4Ever have not currently made a deliberate choice between these, but have developed a light-weight ontology called wfprov for describing workflow provenance. This ontology is intended to be mapped to the different models, but also to the wfdesc ontology to associate workflow provenance with the abstract steps. 
 
The Third workshop on the Role of Semantic Web in Provenance Management

Members of the Wf4ever team, namely Khalid Belhajjame, Jose Manual-Jomez and Jun Zhao, are co-organizing the 3rd international workshop on the Role of Semantic Web in Provenance Management. The SWPM'12 will be co-located with the ESWC conference in May 2012. It follows on from two successful editions, co-located with the International Semantic Web Conference (ISWC). The SWPM workshop has the following complementary objectives:
(1) to explore the opportunities offered by the Semantic Web technologies in the context of the management and exploitation of provenance.
(2) to explore the role of provenance in real-world Semantic Web applications.
Additionally, we will organize in this edition a panel on PROV-DM, the provenance model that is currently being developed by the W3C provenance working group and which is on the W3C recommendation track. The aim is to discuss and to identify the opportunities PROV-DM presents in leveraging semantic web applications.

For further information visit the workshop website at:

http://sites.google.com/site/swpm2012/

or contact the organizers at : swpm2012 (at) googlegroups (dot) com

Architectural Principles and Preliminary Architecture Published

The Wf4Ever Architecture Task Force is designing and developing the Wf4Ever software architecture for the design and implementation of scientific workflow preservation systems, together with a reference implementation instantiating the architecture and enabling the preservation and efficient retrieval of scientific workflows across a range of domains. We are pleased to announce the publication of our design principles together with the preliminary architecture and early reference implementation. The architecture sets out to be compliant with standards like the OAIS reference model and the Linked Data initiative, to combine workflow lifecycle management, social networks and digital libraries, and to extend them with contributions from component-level research. Following a codesign methodology, we are building on an existing system, the myExperiment repository, to develop preservation capabilities that consider the complexity of scientific workflows and their related objects. Our ambition is that the design, software, services and methodologies established in the project will be applicable to other systems also. The Architecture is described in Wf4Ever Architecture - Phase I link to D1.3v1

Research Object Quality Preservation

 WF4Ever partners are working on how to use the provenance traces (among other data types)  to support the measurement of integrity and authenticity of  scientific research objects (RO).  The provenance of a resource is defined as: ''a record that describes entities and processes involved in producing and delivering or otherwise influencing that resource'' (see deliverable D4.1).This type of information is going to allow the evaluation of some Information Quality (IQ) criteria which later on will be used for the definition of a RO properties (R's) which have been settled for the Integrity and Authenticity measurement. 

A first prototype (screenshots)is being developed based on the open provenance model OPM and evaluating the Stability IQ dimension (see also matrixIQ-R's ) Stability is defined as the degree that a RO maintains its original characteristics throughout the time in order to be able to accomplish with its specific goals. The IQ dimension captures the trace of actions which have been done by a user over a RO and evaluates its decay degree.  At present, an algorithm based on a-priori expert knowledge is being used and is expected to be improved using end-users validation (astronomy and bioinformatics domains). In near future this process will also be adapted to the wfdesc defined as the provenance model for the WF4Ever project (wfdesc ontology) .

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Project ID card

  • Funded under: 7th FWP (Seventh Framework Programme)

  • Area: Digital Libraries and Digital Preservation. (ICT-2009.4.1)

  • Project reference: 270192

  • Total cost: 3.86 million euro

  • EU contribution: 2.94 million euro

  • Execution: From 2010-12-01 to 2013-11-30

  • Duration: 36 months

  • Project status: Execution

  • Contract type: Collaborative project (generic)

Wf4Ever was presented at the Workshop of Understanding Provenance and Linked Open Data

Wf4Ever was presented at the Workshop of Understanding Provenance and Linked Open Data in Edinburgh during March 29-30, 2011. This workshop aims to bring together key academic and non-academic...

Wf4Ever to be presented in the 7th IEEE e-Science conference

A Wf4Ever paper titled as "Fostering Scientific Workflow Preservation Through Discovery of Substitute Services" by Belhajjame et al. has been accepted in this year's IEEE e-Science conference, to...

Wf4Ever to be presented at iPRES 2011

Wf4Ever's vision about workflow preservation will be presented at the International Conference on Preservation of Digital Objects ( IPRES ) in Singapore, November 2011.The paper, titled " Towards...

Wf4Ever Started!

  The Wf4Ever project kick-off meeting took place on December 2nd and 3rd in Madrid, Spain. The 3-year EU funded project aims at providing the methods and tools required to ensure the...

Wf4Ever presented at the International Virtual Observatory Alliance

Wf4Ever was presented at the International Virtual Observatory Alliance (IVOA)&nbsp;Interop in Nara (Japan) during the&nbsp; Data&nbsp;Curation and Preservation (DCP) Session on&nbsp;December...

Wf4Ever presented at the Future Internet Assembly

Wf4Ever was presented at the Future Internet Assembly in Ghent during the Linked Data session on December 16th, 2010. The overall goal of the session was to initiate the discussion on...

Wf4Ever presented at the CERN Workshop on Innovations in Scholarly Communication

Wf4Ever was presented at the CERN Workshop on Innovations in Scholarly Communication (OAI7) , held in Geneva on the 22nd-24th June, 2011 The workshop is held every two years and is...

Wf4Ever presented at the .Astronomy Conference

Wf4Ever was presented at the third edition of the&nbsp; .Astronomy Conference &nbsp;held in Oxford New College during&nbsp;4th - 6th April 2011.&nbsp;The .Astronomy Conference aims to bring...

Wf4Ever present at the workshop of the "Landscpe and Identities"

Wf4Ever was involved in a technical workshop of the " Landscape and Identities " EngLaID project, held at Oxford e-Research Centre on 8 June 2011. The EngLaID project will explore the...

Wf4Ever at Microsoft's 2011 eScience workshop and IEEE eScience Conference

Prof. Dave De Roure spoke on Computational Research Objects at the Microsoft 2011 eScience Workshop (http://research.microsoft.com/en-us/events/escience2011/) and Khalid Belhajjame spoke on ...

Wf4Ever at Dagstuhl: The Future of Research

The Dagstuhl report is already available in http://drops.dagstuhl.de/opus/volltexte/2011/3315/ . From the report, we highlight the following excerpt of Prof. Dave De Roure's talk in the Future of...

The Third workshop on the Role of Semantic Web in Provenance Management

Members of the Wf4ever team, namely Khalid Belhajjame, Jose Manual-Jomez and Jun Zhao, are co-organizing the 3rd international workshop on the Role of Semantic Web in Provenance Management. The...

Taverna, BioCatalogue and myExperiment webinar

A live webinar on Taverna , myExperiment &nbsp;and BioCatalogue &nbsp;will be held by Paul Fisher on March 8th,&nbsp;2011 at 16:00 GMT on BitesizeBio. For details see .

Sharing Interoperable Workflows

The SHIWA (SHaring Interoperable Workflows for large-scale scientific simulations on Available DCIs) project enables publicly available workflows to be used by different research communities...

Scientific Workflows in Astronomy

Wf4Ever project was presented at ADASS - Astronomical Data Analysis Software and Systems XXI Conference , held in Paris on November 6-10 2011. A BoF interest group meeting was organized by André...

Research objects

Last month, the Wf4Ever project published v0.1 of the Research Object vocabulary . This set of OWL ontologies gave us a starting point for describing workflows, data aggregations and...

Research Object Vocabulary Specification v0.1

The first draft specification of the Research Object Vocabulary has been released as a set of interconnected ontology modules. The core of this vocabulary is the RO ontology (ro -...

Research Object Quality Preservation

&nbsp;WF4Ever partners are working on how to use the provenance traces (among other data types) &nbsp;to support the measurement of integrity and authenticity of &nbsp;scientific research...

Prof. Dave De Roure presented at the Microsoft Research workflow last week

See Dave's blog entry: http://blogs.nature.com/eresearch/2011/10/30/a-gathering-storm-of-scholarly-transformation

Carole Goble keynote at IC3K

  Wf4Ever PI Carole Goble recently presented a keynote talk at the 3rd International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management ( IC3K ). The talk...

BioCatalogue in MIRIAM

The BioCatalogue data type is now part of MIRIAM resources . It provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered...

Architectural Principles and Preliminary Architecture Published

The Wf4Ever Architecture Task Force is designing and developing the Wf4Ever software architecture for the design and implementation of scientific workflow preservation systems, together with a...

A paper named "A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data" by Garijo and Gil accepted in WORKS11

A paper named "A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data” by Garijo and Gil has been accepted in WORKS11 , to be held on November 14th in Seattle within SC...