Author: gnaylor
Date: Wed Jul 13 17:25:34 2016
New Revision: 1752464
URL: http://svn.apache.org/viewvc?rev=1752464&view=rev
Log:
Edit and add attribution to intro quote
Modified:
incubator/taverna/site/trunk/content/documentation/provenance/index.md
Modified: incubator/taverna/site/trunk/content/documentation/provenance/index.md
URL:
http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/documentation/provenance/index.md?rev=1752464&r1=1752463&r2=1752464&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/documentation/provenance/index.md
(original)
+++ incubator/taverna/site/trunk/content/documentation/provenance/index.md Wed
Jul 13 17:25:34 2016
@@ -16,10 +16,10 @@ Notice: Licensed to the Apache Softwa
specific language governing permissions and limitations
under the License.
-> Provenance is information about entities, activities, and people
+> "Provenance is information about entities, activities, and people
> involved in producing a piece of data or thing, which can be used to
-> form assessments about its quality, reliability or trustworthiness.
-- <small><a href="http://www.w3.org/TR/prov-overview/";>W3C
PROV-Overview</a>*</small>
+> form assessments about its quality, reliability or trustworthiness."
+[W3.org, PROV Overview](http://www.w3.org/TR/prov-overview/)
For a scientific workflow system, provenance can have several aspects:
@@ -29,44 +29,43 @@ For a scientific workflow system, proven
##Provenance of workflow definitions
-Taverna does not capture provenance of editing a *workflow definition*,
- but assume the scientist manages the evolution of workflow definitions
through existing
- means for versioning files, such as filenames and folders,
- version control systems like
[git](https://help.github.com/articles/set-up-git),
+Taverna does not capture provenance of editing a *workflow definition*,
+ but assumes the scientist manages the evolution of workflow definitions
through existing
+ means for versioning files, such as filenames and folders,
+ version control systems like
[Git](https://help.github.com/articles/set-up-git),
or workflow sharing websites like
[myExperiment](http://www.myexperiment.org/).
-Within Taverna, a
- [workflow can be
annotated](http://dev.mygrid.org.uk/wiki/display/taverna/Annotations)
- to give *attribution* to the **Authors** of a workflow (or nested
workflow).
-We recommend using comma or linefeed for multiple authors.
-
-Taverna's workflow fileformat has an internal workflow identifier (UUID) which
is updated for
- every workflow change.
-A log of previous workflow identifiers is included within the workflow
definition formats
-
[t2flow](http://taverna.googlecode.com/svn/taverna/dev/xsd/trunk/t2flow/t2flow.xsd)
and
+Within Taverna, a
+ [workflow can be
annotated](http://dev.mygrid.org.uk/wiki/display/taverna/Annotations)
+ to give *attribution* to the **Authors** of a workflow (or nested workflow).
+We recommend using comma(s) or linefeed(s) to separate multiple authors.
+
+Taverna's workflow file format has an internal workflow identifier (UUID)
which is updated for
+ every workflow change.
+A log of previous workflow identifiers is included within the workflow
definition formats
+
[t2flow](http://taverna.googlecode.com/svn/taverna/dev/xsd/trunk/t2flow/t2flow.xsd)
and
[Taverna 3 workflow
bundle](http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle),
- allowing
- [detection of workflows with common
ancestry](http://www.myexperiment.org/workflows/2899)>.
+ allowing
+ [detection of workflows with common
ancestry](http://www.myexperiment.org/workflows/2899).
##Provenance of workflow runs
-Taverna can
+Taverna can
[capture provenance of workflow
runs](http://dev.mygrid.org.uk/wiki/display/taverna/Data+and+provenance+preferences),
- including individual processor iterations and their inputs and outputs.
-This provenance is kept in an internal database,
- which is used to populate *Previous runs* and *Intermediate results* in the
- [Results
perspective](http://dev.mygrid.org.uk/wiki/display/taverna/Result+Perspective)
- in the Taverna Workbench.
+ including individual processor iterations and their inputs and outputs.
+This provenance is kept in an internal database,
+ which is used to populate *Previous runs* and *Intermediate results* in the
Taverna Workbench
+ [Results
perspective](http://dev.mygrid.org.uk/wiki/display/taverna/Result+Perspective).
-The provenance trace can be used by the
+The provenance trace can be used by the
[Taverna-PROV plugin](https://github.com/wf4ever/taverna-prov)
- to export the workflow run, including the output and intermediate values,
- and the provenance trace as a [PROV-O](http://www.w3.org/TR/prov-o/) RDF
graph which can
- be queried using [SPARQL](http://www.w3.org/TR/sparql11-overview/) and
processed with other
+ to export (1) the *workflow run*, including the output and intermediate
values,
+ and (2) the *provenance trace* as a [PROV-O](http://www.w3.org/TR/prov-o/)
RDF graph which can
+ be queried using [SPARQL](http://www.w3.org/TR/sparql11-overview/) and
processed with other
PROV tools, such as the [PROV
Toolbox](https://github.com/lucmoreau/ProvToolbox/).
-We are planning to extend myExperiment to handle uploading of such provenance
traces,
- which would give a mechanism to present and browse values and details of a
workflow runs
+We are planning to extend myExperiment to handle uploading of such provenance
traces,
+ which would give a mechanism to present and browse values and details of a
workflow run
within the browser.
This [presentation about Taverna's provenance
support](http://www.slideshare.net/soilandreyes/20130529-taverna-provenance)
@@ -74,78 +73,80 @@ This [presentation about Taverna's prove
##Provenance of data
-Scientists using Taverna to perform analysis are often less concerned about
the detailed provenance of a workflow run, which semantically just describes
inputs and outputs to a chain of processes, but are rather interested in
*derivation* and *attribution* of the data that is involved in a workflow. For
instance, a workflow might be performing text-mining on a biomedical article to
extract gene names, and then retrieve the genome sequences for those genes by
looking up in a database. The sequences can then be said to be derived from
that database and should (according to the license of the web service) also be
attributed to its maintainers. The *list* of sequences can be said to be
derived from the biomedical article.
+Scientists using Taverna to perform analyses are often more interested in
*derivation and attribution of workflow data* and less concerned about the
detailed workflow run provenance. For example, a workflow may perform
text-mining on a biomedical article to extract gene names, and then retrieve
the genome sequences for those genes using a database lookup. The workflow in
effect *derives the sequences from the database.* Consequently, the sequences
should (according to the license of the web service) be attributed to its
maintainers. Similarly, *the sequence list is derived from the biomedical
article* and also requires attribution.
-The typical world of Taverna workflows is to combine web services “in
the wild” (say found on <a href="">http://www.biocatalogue.org/</a>
BioCatalogue) with local tools. Neither of these will typical have any facility
to provide such “science-level provenance”. myGrid is planning a
facility for such data provenance in different ways:
+Taverna workflows typically use local tools to combine web services found
“in the wild”
+(e.g., <a href="">http://www.biocatalogue.org/</a> BioCatalogue). This
approach will not usually
+provide “science-level provenance.” myGrid is planning a
capability for such data provenance
+in different ways:
-1. Merging and propagation of [PROV-AQ](http://www.w3.org/TR/prov-aq/)
provided provenance
- traces for [REST
services](http://dev.mygrid.org.uk/wiki/display/taverna/REST)
+1. Merging and propagation of
[PROV-AQ](http://www.w3.org/TR/prov-aq/)-provided provenance
+ traces for [REST
services](http://dev.mygrid.org.uk/wiki/display/taverna/REST)
(including matching data identity) -- âwhite-box serviceâ
-2. A provenance âbackchannelâ for [Components](/documentation/components),
- which can be populated either by the underlying service directly or by
shims within the
- component.
- This allows higher level provenance that is meaningful for a set of
components instead of
+2. A provenance âbackchannelâ for [Components](/documentation/components),
+ which can be populated either by the underlying service directly or by
shims within the
+ component.
+ This allows higher-level provenance that is meaningful for a set of
components instead of
service-specific execution details.
-3. Annotation of workflow fragments by
+3. Annotation of workflow fragments by
[common
motifs](http://www.slideshare.net/dgarijo/common-motifs-in-scientific-workflows-an-empirical-analysis),
which can provide higher-level provenance for data generated by the
workflow
-The paper [Enhancing and Abstracting Scientific Workflow Provenance for Data
+The paper [Enhancing and Abstracting Scientific Workflow Provenance for Data
Publishing](http://www.edbt.org/Proceedings/2013-Genova/papers/workshops/a45-alper.pdf)
- (doi
[10.1145/2457317.2457370](http://dx.doi.org/10.1145/2457317.2457370)) details
these
+ (doi
[10.1145/2457317.2457370](http://dx.doi.org/10.1145/2457317.2457370)) details
these
approaches.
##Collaborations
-myGrid actively participated in the
+myGrid actively participated in the
[W3C Provenance Working Group](http://www.w3.org/2011/prov/wiki/Main_Page)
- which developed the [PROV family of
standards](http://www.w3.org/TR/prov-overview/).
-The [Taverna-PROV plugin](https://github.com/wf4ever/taverna-prov) has been
developed for
- Taverna that allows the export of workflow run provenance as
+ which developed the [PROV family of
standards](http://www.w3.org/TR/prov-overview/).
+The [Taverna-PROV plugin](https://github.com/wf4ever/taverna-prov) has been
developed for
+ Taverna and allows the export of workflow run provenance as
[PROV-O RDF](http://www.w3.org/TR/prov-o/).
-The [wf4ever project](http://www.wf4ever-project.org) is investigating the
sharing of workflows
- and workflow runs as [research objects](http://www.researchobject.org/), in
particular for
- Taverna is the development of the [Research Object
Bundle](https://w3id.org/bundle),
- which will form a single archive of a workflow run, including run
*provenance*, *inputs*,
- *outputs*, *intermediate values*, *workflow definition* and (for Taverna 3)
+The [wf4ever project](http://www.wf4ever-project.org) is investigating the
sharing of workflows
+ and workflow runs as [research objects](http://www.researchobject.org/). Of
particular importance for
+ Taverna is the development of the [Research Object
Bundle](https://w3id.org/bundle),
+ which will form a single archive of a workflow run, including run
*provenance*, *inputs*,
+ *outputs*, *intermediate values*, *workflow definition* and (for Taverna 3)
information about the *run environment*.
##Past collaborations
-Since early 2010, we are invited partners of the [NSF DataONE
project](https://dataone.org/),
- dedicated to large-scale preservation of scientific data, and founding
members of the
- Worklow and Provenance Working Group promoted by the project, along with
Prof. Ludaescher
+Since early 2010, we have been invited partners of the [NSF DataONE
project](https://dataone.org/),
+ dedicated to large-scale preservation of scientific data, and founding
members of the
+ Worklow and Provenance Working Group promoted by the project, along with
Prof. Ludaescher
at UC Davis, USA and Juliana Freire at University of Utah, USA.
-Historically, work on provenance within the myGrid consortium and Taverna team
has been
- focusing on multiple aspects, beginning with the design and implementation
of *Janus*,
- a data model and software component for provenance capture and analysis for
Taverna.
+Historically, work on provenance within the myGrid consortium and Taverna team
has been
+ focusing on multiple aspects, beginning with the design and implementation
of *Janus*,
+ a data model and software component for provenance capture and analysis for
Taverna.
Our research in this area is often pursued in collaboration with external
partners:
- - A model and architecture for capturing provenance.
- We have designed a data model for *Janus* that is at the same time
specific to Taverna,
- but can also be exported to other models,
- notably the [Open Provenance Model](http://openprovenance.org/) (OPM),
- to enable interoperability with third party provenance-generating
systems.
- Taverna has been retrofitted with provenance generation capabilities.
- - An expressive provenance query language and efficient query processing
model for large
+ - **Provenance capture.** A model and architecture for capturing provenance.
+ We have designed a data model for *Janus* that is at the same time
specific to Taverna,
+ but can also be exported to other models,
+ notably the [Open Provenance Model](http://openprovenance.org/) (OPM),
+ to enable interoperability with third party provenance-generating systems.
+ Taverna has been retrofitted with provenance-generating capabilities.
+ - **Provenance processing** An expressive provenance query language and
efficient query-processing model for large
provenance graphs.
- - Investigation into provenance interoperability and exchange, using the OPM.
- The Taverna provenance component now exports data as OPM graphs,
- and can also import OPM graphs (with basic features) received from third
parties.
- We have also been working with the Kepler group on a project to promote
provenance
- interoperability, in collaboration with Prof. Ludaescher at UC Davis, CA,
and
- Ilkay Antintas at UCSD, CA .
- - Investigation into the role of semantics and of Linked Open Data (LOD) in
provenance
- modelling and management, in collaboration with the Knoesis Centre at
Wright University,
+ - **Provenance interoperability.** Investigation into provenance
interoperability and exchange, using the OPM.
+ The Taverna provenance component now exports data as OPM graphs,
+ and can also import OPM graphs (with basic features) received from third
parties.
+ We have also been working with the Kepler group on a project to promote
provenance
+ interoperability, in collaboration with Prof. Ludaescher at UC Davis, CA,
and
+ Ilkay Antintas at UCSD, CA.
+ - **Provenance modeling and management.** Investigation into the role of
semantics and of Linked Open Data (LOD) in provenance
+ modelling and management, in collaboration with the Knoesis Centre at
Wright University,
Ohio (Prof. Amit Sheth, Dr. Satya Sahoo) and with Jun Zhao of Oxford
University.
Other past collaborations on the topic of provenance include:
- - Participation in the
+ - Participation in the
[Third Provenance
Challenge](http://twiki.ipaw.info/bin/view/Challenge/ThirdProvenanceChallenge)
- [The Semantic Provenance
project](http://www.mygrid.org.uk/projects/semantic-provenance-project/),
with Ely Lilly and IU
-
