MP
HP
NDR
WDO-It! 101 Workshop:
Creating an abstraction of a process
UTEP’s Trust Laboratory
Cyber-ShARE Center of Excellence
• Established at UTEP in
2007 with NSF funding
• Focused
– Cross-disciplinary research
in science, engineering,
and technology at UTEP
– Training workshops on
using cyberinfrastructure
– Education and outreach
– Resource acquisition and
sharing (documentation of
processes)
Sharing resources via Cyberinfrastructure to advance research and education.
Objectives of workshop
• This workshop will go over the basics of creating
Semantic Abstract Workflows (SAWs).
– SAWs are useful to formalize your understanding of a
process and communicate it to others in a graphical
format.
• After completing this workshop, you will be able to
use the WDO-It! tool to create SAWs about processes
that you use in your every-day work.
Overview
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•
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•
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Motivation
Purpose of creating a process abstraction
Guiding example: Description of a process
Task 1: Identify process vocabulary
Task 2: Create a process abstraction
Group exercise
What is next…
Motivation
• How easy is it for scientists to publish their scientific
data and artifacts (e.g., map) on the web?
– How easy would it be for programmers to publish their latest
code on the web?
• How easy is it for scientists to publish their raw data
and tool parameters and to link them to their derived
product?
– How easy would it be for programmers to publish
documentation about their code on the web and to maintain
them linked?
Provenance: An Example (1/2)
How
accurate is
this map?
isMemberOf
isMemberOf
What are the
sources for
this map?
isMemberOf
hasCreator
hasAgent
hasCreator
Can I trust
that this is a
hasCreator
quality
map?
isMemberOf
hasSource
isConsequentOf
(http://utep.edu/myDataSet.xls)
(http://utep.edu/myGravityMap.gif)
Provenance: An Example (2/2)
How
accurate is
this map?
isMemberOf
How isMemberOf
accurate is hasCreator
this sensor?
hasAgent
hasCreator
isMemberOf
Can I trust
that this is a
hasCreator
quality
map?
isMemberOf
hasSource
isConsequentOf
How reliable
is this tool?
(http://utep.edu/myDataSet.xls)
(http://utep.edu/myGravityMap.gif)
On the Use of Provenance
• How to Represent Provenance?
– PML ontology (UTEP team has 7 years of
experience representing provenance)
• How to Capture Provenance?
– One needs to understand scientific processes to
capture provenance
Side note:
• What is Ontology?
– Branch of philosophy that deals with what entities
exist and how those entities relate to each other
– The computer science version
• An inventory of concepts about a specific domain of
interest, and the relation between those concepts
• Encoded in a computer language, e.g., OWL
• E.g., Ontology of vehicles:
<owl:Class Vehicle />
<owl:Class SUV>
<owl:subClassOf Vehicle />
</owl:Class>
CI-Miner
• A comprehensive approach to facilitate
provenance encoding in PML:
WDO-It! 101
workshop
Overview
•
•
•
•
•
•
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Motivation
Purpose of creating a process abstraction
Guiding example: Description of a process
Task 1: Identify process vocabulary
Task 2: Create a process abstraction
Group exercise
What is next…
Purpose of creating a process
abstraction
• Purpose
– Model your understanding of a process
– Identify appropriate vocabulary for describing a process
– Identify the parts of a process that are of interest to you
• Benefits
– Share your understanding of a process with others
– Guide the development of systems that implement your
understanding of a process
– Enhance existing systems to provide functionality aligned
to your understanding of a process
Overview
•
•
•
•
•
•
•
Motivation
Purpose of creating a process abstraction
Guiding example: Description of a process
Task 1: Identify process vocabulary
Task 2: Create a process abstraction
Group exercise
What is next…
Guiding example: A process (1/2)
• Description:
– Geo-referenced datasets usually are built from sparse
field measurements , where the location of each point
is given by Longitude/Latitude coordinates
– To create a map model of a geo-referenced dataset,
e.g., a contour map, the dataset usually needs to:
1. Be pre-processed to create a grid of uniformly-spaced data
points
2. Create the map model from the uniformly distributed
dataset
Guiding example: A process (2/2)
1. Sparse geo-referenced dataset
Longitude
-074.4244296
-074.9746118
-074.4245976
-074.7647730
-074.7647730
-074.3714268
-074.3714268
-074.2129201
-074.3237562
-074.3237562
Latitude
40.0049488
40.0051130
40.0051168
40.0059447
40.0059447
40.0099501
40.0101141
40.0109512
40.0139483
40.0139483
OBS
4176.40
4189.60
4176.40
4199.07
4199.10
4173.71
4173.69
4159.90
4172.05
4172.10
2. Uniformly distributed dataset (Grid)
ncols 5
nrows 5
cellsize=2
4604 4599
4619 4618
4596 4599
4551 4562
4532 4512
4598
4611
4598
4575
4482
4602
4586
4593
4572
4449
4606
4566
4585
4535
4459
3. Map model
Overview
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•
•
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Motivation
Purpose of creating a process abstraction
Guiding example: Description of a process
Task 1: Identify process vocabulary
Task 2: Create a process abstraction
Group exercise
What is next…
Task1: Identify process vocabulary
• Launch WDO-It!
– Download from
http://trust.utep.edu/wdo/downloads
• Capture process vocabulary in a WorkflowDriven Ontology (WDO)
• WDOs:
– OWL document
– Can import vocabulary terms from other existing
OWL ontologies
Task1: Identify process vocabulary
1. Click
2. Enter a namespace
(URI-like format)
Recommendation: Use a
namespace that matches the URL
where you will publish the WDO
Example: http://trust.utep.edu/2009/ContourMapWDO
You can change namespaces later with a text editor
that supports the “Replace All” operation.
Task1: Identify process vocabulary
Loaded OWL Documents Tree
WDO namespace on the root
Imported Ontologies subtree
reflects <owl:imports> statement
of OWL document
Note1: All WDO’s import the wdo.owl
ontology
Note2: The WDO in the root of the tree is
the one being edited, imported ontologies
are not modified.
Task1: Identify process vocabulary
• WDOs capture the vocabulary of a process in
two main categories:
– Data
– Method
• What are the data concepts of our process?
– ContourMap, GriddedDataset
• What are the method concepts of our
process?
– Gridding, Contouring
Task1: Identify process vocabulary
Adding Data and Method
concepts to the WDO
1. Click
2. Choose type
3. Add label (<rdfs:label>)
and optionally a comment
(<rdfs:comment>)
Note: URIs automatically generated by
WDO-It! in reference to namespace
assigned to the WDO document.
Facilitates renaming!
Task1: Identify process vocabulary
Start with the more general
concepts of your process and start
building your WDO hierarchies.
To add a child concept: Select a
concept from the Data or Method
tree, then click the Add Concept Icon
You can remove concepts that do not
have children by selecting them and
clicking the Remove Concept Icon
You can rename and add comments
to concepts by selecting them and
clicking the Edit Concept Icon
Note: Concept Hierarchy shows
ALL concepts defined in the
selected OWL document
Overview
•
•
•
•
•
•
•
Motivation
Purpose of creating a process abstraction
Guiding example: Description of a process
Task 1: Identify process vocabulary
Task 2: Create a process abstraction
Group exercise
What is next…
Task2: Create process abstraction
• Now that process vocabulary was captured in
a WDO, create process abstraction in a
Semantic Abstract Workflow (SAW)
• SAWs:
– are OWL documents
– do not include vocabulary (or class) definitions
– reuse vocabulary definitions from a WDO
• i.e., import a ‘Source WDO’
• e.g., <owl:imports rdfs:resource=“ContourMapWDO”>
– use a graphical notation
Task2: Create process abstraction
1. Click
2. Enter a namespace
(URI-like format)
Recommendation: Use a
namespace that matches
the URL where you will
publish the SAW
Example: http://trust.utep.edu/2009/CreateGravityContourMapSAW
Task2: Create process abstraction
Loaded OWL Documents Tree
WDO namespace on the root
(Source WDO)
Workflows subtree reflects
<owl:imports> statement of OWL
document w.r.t. source WDO
SAWs do not contain concept
definitions, hence, concept hierarchy
empty when SAW selected
Workflow area enabled when SAW
selected
Task2: Create process abstraction
Adding instances to the SAW
1. Click and hold on a WDO concept
2. Drag and drop on the Workflow area
Data concepts are rendered as
directed edges with beginning
and ending ‘Sources’
Note: ‘Sources’ are instances of the
‘pmlp:Source’ class
Methods are rendered as rectangles
Task2: Create process abstraction
Removing instances from the SAW
1. Select an Data or a Method instance
2. Press the Delete key
Note: ‘Source’ instances cannot be
individually deleted, since Data
instances depend on them
Edit instances
1. Select an Data, Method, or Source
instance
2. Click the Edit Instance Icon
Task2: Create process abstraction
Editing SAW instances:
pmlp:Source instances
Source instances can
be specialized into
other subtypes, as per
the pmlp ontology,
e.g., pmlp:Person
wdo:Data instances
Data instances can be
assigned a pmlp:Format
instance (URI), which will be
used during the creation of
data annotators to encode
provenance with PML
wdo:Method instances
Method instances can be
assigned a
pmlp:InferenceEngine
instance (URI), which will be
used during the creation of
data annotators to encode
provenance with PML
Task2: Create process abstraction
Assembling the process graph: No control-flow, just data-flow!
Connecting edges and nodes:
1. Click on a Source instance and hold
2. Drag and drop on top of a Method instance to connect
(Dropping Method instances into Source instances works too)
Note: Data instances need to be attached to
a Source instance or to a Method instance on
each side of the edge
Disconnecting edges and nodes:
1. Select and hold an endpoint of an edge
2. Drag and drop on another part of the
workflow area to disconnect
Note: ‘Sources’ cannot be disconnected
from Data edges
Task2: Create process abstraction
• Sources can be merged, as long as they are
attached to the same direction of their
corresponding edges
Task2: Create process abstraction
Exercise: Build the following SAW
Lets describe
Contouring in more
detail
Task2: Create process abstraction
Creating a ‘subworkflow’:
1.
2.
3.
4.
Right Click on the Contouring method instance
Select ‘Edit DetailedBy property…’
Select ‘New Workflow…’
Enter namespace for new workflow and start creating new abstract workflow
E.g., http://trust.utep.edu/2009/ContouringSAW
5. Notice the updated Workflow subtree in the Loaded OWL Documents section
Task2: Create process abstraction
Exercise: Build the following subworkflow for ‘Contouring’
Overview
•
•
•
•
•
•
•
Motivation
Purpose of creating a process abstraction
Guiding example: Description of a process
Task 1: Identify process vocabulary
Task 2: Create a process abstraction
Group exercise
What is next…
Group exercise
• As a group
– Choose a volunteer to drive the WDO-It! tool
– Identify a common process
Group exercise
• As a group
– Build a WDO for the process
– Hint:
• Data and Method concepts are intended to classify
things from a perspective that is meaningful to the end
user of the process
• Ex1. Digital Elevation Map and Gravity Map are
probably good Data concepts for a geophysicist
• Ex2. PDF Map and JPG Map are probably not good
classifications for a geophysicist
Group exercise
• As a group
– Build a SAW for the process
– Hint:
• Focus on the valid flows of data as input/output of
Methods
• Disregard control structures such as selection and
iteration
Overview
•
•
•
•
•
•
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Motivation
Purpose of creating a process abstraction
Guiding example: Description of a process
Task 1: Identify process vocabulary
Task 2: Create a process abstraction
Group exercise
What is next…
What is next? (1/3)
• Create HTML reports of your WDOs and SAWs
– On the menu toolbar
• Choose Tools/Generate Reports…
• Select OWL documents for which to generate a report
• Select a store location
What is next? (2/3)
• Use SAWs to capture provenance
– Use WDO-It! to generate provenance-annotator
modules to instrument existing systems
– Use WDO-It! to manually link artifacts to
document provenance of manually executed
processes
• Look for follow-up workshop: Using process
abstractions to capture provenance
What is next? (3/3)
• Collaborate with others to make your process
abstractions more robust
– CI-Server/CI-Client
– WF-Talk
• Publish your CI resources
– CI-Server/CI-Client
• Look for follow up workshop: Using the CIServer collaboration framework to develop
and publish CI resources
Feedback
• Please take a few minutes to complete the
following surveys:
– Feedback about the approach
• Contact information optional
• handout
– Feedback about the presentation of the workshop
• Anonymous feedback
• Online: http://trust.utep.edu/wdo/doc
Thank you!
For more information please contact:
Leonardo Salayandia, leonardo@utep.edu
Paulo Pinheiro da Silva, paulo@utep.edu
Aida Gandara, agandara1@miners.utep.edu
Nick Del Rio, ndel2@miners.utep.edu