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Re: Suggested Concepts for Charter

From: Paul Groth <pgroth@gmail.com>
Date: Wed, 24 Nov 2010 08:18:20 +0100
Message-Id: <711FE289-77C3-4C2E-8DD7-A212C00C38CD@gmail.com>
Cc: "<public-xg-prov@w3.org>" <public-xg-prov@w3.org>
To: Paulo Pinheiro da Silva <paulo@utep.edu>
For the grouping I was just thinking putting everything with the same concept together. E.g provenier:haspart and dc:haspart


Paul

Sent from my iPhone

On Nov 24, 2010, at 0:05, Paulo Pinheiro da Silva <paulo@utep.edu> wrote:

> Hi All,
> 
> I see that Jim added some PML concepts to the list of suggested concepts along with some comments -- thank you a lot Jim.
> 
> Considering Paul's suggestion of grouping the suggested concepts for the charter, I would like to know the group opinion about implementing a minimal grouping of the concepts into "provenance data" and "provenance metadata." Please note that the group has already discussed the relevance of these two categories during one of our meetings.
> 
> Many thanks,
> Paulo.
> 
>> Most of the concepts seem reasonable to me. I think some overlap more or
>> less with dublin core and opm. Hopefully we can pull these together in
>> groupings.
> 
> 
>> 
>> 
>> Sent from my iPad
>> 
>> On Nov 23, 2010, at 8:34 PM, Satya Sahoo <sahoo.2@wright.edu
>> <mailto:sahoo.2@wright.edu>> wrote:
>> 
>>> 
>>> Hi All,
>>> 
>>> 
>>> The following is a list of suggested terms from the Provenir ontology
>>> for submission with WG charter. I have also added the concepts to the
>>> wiki.
>>> 
>>> 
>>> Any feedback is welcome.
>>> 
>>> 
>>> Thanks.
>>> 
>>> 
>>> Best,
>>> Satya
>>> 
>>> 
>>> 1. provenir:part_of
>>> Definition: This property is used to represent parthood relation
>>> between entities (both class and instance-level).
>>> Example: A mass analyzer is part of a mass spectrometer
>>> 
>>> 
>>> 2. provenir:contained_in
>>> Definition: This property is used to represent containment relation
>>> between entities.
>>> Example: A temperature sensor is contained in an ocean buoy.
>>> 
>>> 
>>> 3. provenir:adjacent_to
>>> Definition: Spatial proximity is represented by this property. It is
>>> defined only for agent class, where the adjacent spatial location of
>>> individuals of agent class may have an effect on data values.
>>> Example: Quality of observations made by a sensor may be affected if
>>> it is adjacent to a sensor generating a magnetic field.
>>> 
>>> 
>>> 4. provenir:transformation_of
>>> Definition: This property is similar to the ro:transformation_of
>>> property that is asserted between two entities that preserve their
>>> identity between the two transformation stages.
>>> Example: An cancer cell is a transformation of a normal cell
>>> 
>>> 
>>> 5. provenir:preceded_by
>>> Definition: This property is used define a temporal ordering of
>>> processes, which may or may not be modeled be linked by a common artifact.
>>> Example: Example from RO, aging preceded by development.
>>> 
>>> 
>>> 6. provenir:located_in
>>> Definition: An instance of data or agent is associated with exactly
>>> one spatial region that is its exact location at given instance of time.
>>> Example: A sensor is located in a specific geospatial region at time
>>> instance t
>>> 
>>> 
>>> 7. provenir:has_temporal_value
>>> Definition: This property is used to explicitly associate temporal
>>> value with individuals of Provenir classes.
>>> Example: duration of a liquid chromatography process has temporal
>>> value 20 minutes.
>>> 
>>> 
>>> 8. provenir: preceded_by*
>>> Definition: Defines a temporal (and causal or non-causal) property for
>>> distinct instances of provenir:process.
>>> Example: A researcher starts a process to send email about the status
>>> of an (long-running) experiment process. The notification process is
>>> preceded by the experiment process.
>>> 
>>> 
>>> 9. provenir:has_participant @
>>> Definition: Property linking data to process, where the individual of
>>> data class participates in a process.
>>> Example: Trypsin enzyme (used to digest protein sample) participates
>>> in a proteome analysis experiment
>>> 
>>> 
>>> 10. provenir:derives_from $
>>> Definition: Property represents the derivation history of data
>>> entities as a chain or pathway.
>>> Example: The average rainfall (specific to geospatial-temporal
>>> instance) is derived from sensor readings.
>>> 
>>> 
>>> 11. provenir:temporal_parameter &
>>> Definition: This class captures the temporal details associated with
>>> individuals of provenir:data_collection, provenir:process, and
>>> provenir:agent.
>>> Example: The timestamp associated with a sensor reading
>>> Example: The duration of a protein analysis process
>>> Example: The time period during which a sensor was working correctly
>>> 
>>> 
>>> 12. provenir:spatial_parameter
>>> Definition: The spatial metadata associated with instances of
>>> provenir:process or provenir:agent or provenir:data_collection classes
>>> is represented by this class.
>>> Example: The geographical location of an ocean buoy is an example of
>>> spatial parameter.
>>> 
>>> 
>>> *Notes*:
>>> * Unlike opm:wasTriggeredBy, provenir:preceded_by property links
>>> processes that may or may not be causally dependent.
>>> @ Unlike opm:used, provenir:has_participant may or may not represent
>>> an existential relationship between the provenir:data and
>>> provenir:process, in other words the provenir:process may or may not
>>> require the existence of the provenir:data to initiate/terminate.
>>> $ Unlike opm:wasDerivedFrom, provenir:derives_from may or may not
>>> represent an existential relationship between entities.
>>> & Extensions of the Provenir ontology, such as the Janus ontology for
>>> Taverna, and Parasite Experiment ontology for biomedicine, use the
>>> OWL:Time ontology terms to represent temporal notions.
>>> 
>>> 
>>> The following Provenir terms were approximately to OPM terms during
>>> the mapping exercise, but often represented broader notions of
>>> provenance (see the mapping wiki for details). These terms need to be
>>> considered during the refinement of the corresponding OPM terms:
>>> 1. provenir:data
>>> Definition: This class models BFO continuant entities that represent
>>> the starting material, intermediate material, end products of a
>>> scientific experiment, and parameters that affect the execution of a
>>> scientific process. Data inherit the properties of continuants such as
>>> enduring or existing while undergoing changes.
>>> Example: A protein sample, digested with trypsin proteolytic enzyme,
>>> used as input in a proteome analysis experiment.
>>> 
>>> 
>>> 2. provenir:process
>>> Definition: This class models the occurrent entities that affect
>>> (process, modify, create, delete among other dynamic activities)
>>> individuals of data.
>>> Example: The proteome analysis experiment is a process and its
>>> constituent steps, are also processes
>>> 
>>> 
>>> 3. provenir:agent
>>> Definition: This class models the continuant entities that causally
>>> affect the individuals of process.
>>> Example: The researcher performing the proteome analysis experiment
>>> and microarray instrument used in the experiment are agents.
>>> 
>>> 
>>> ----- Original Message -----
>>> From: Paul Groth <pgroth@gmail.com <mailto:pgroth@gmail.com>>
>>> Date: Monday, November 22, 2010 4:43 pm
>>> Subject: Suggested Concepts for Charter
>>> To: "<public-xg-prov@w3.org <mailto:public-xg-prov@w3.org>>"
>>> <public-xg-prov@w3.org <mailto:public-xg-prov@w3.org>>
>>> Cc: Luc Moreau <L.Moreau@ecs.soton.ac.uk
>>> <mailto:L.Moreau@ecs.soton.ac.uk>>
>>> 
>>> > Hi All,
>>> >
>>> > As we discussed on the call from Friday last week, below is the
>>> > list of
>>> > core concepts from OPM that we think should be in the list that
>>> > goes
>>> > with the charter.
>>> >
>>> > I actually think there is quite a bit of overlap with the
>>> > suggested
>>> > concepts from Jim McCusker. Also, from the mappings activity, we
>>> > know
>>> > these overlap with most of the provenance ontologies.
>>> >
>>> > If no one objects, I would like to put all the concepts we are
>>> > all
>>> > sending to the mailing list on the wiki and start to group them
>>> > together.
>>> > Does that sound good to everyone?
>>> >
>>> > Comments are appreciated especially if any concept is thought to
>>> > be
>>> > unnecessary. I'm looking forward to seeing the proposed concepts
>>> > from
>>> > everyone else.
>>> >
>>> > Hopefully, we can reach a consensus soon.
>>> >
>>> > Thanks,
>>> > Paul
>>> >
>>> >
>>> > Suggest Concepts from OPM
>>> > We use opm: as a short cut for open provenance model.
>>> >
>>> > Graph:
>>> > - opm:OPMGraph
>>> > Definition: a provenance graph is defined to be a record of a
>>> > past execution
>>> > Example: Bob's Website Factory provides proof in the form
>>> > of a
>>> > provenance graph that the contract was executed as agreed.
>>> >
>>> > - opm:Account
>>> > Definition: An account of the some past execution. Accounts
>>> > offer
>>> > different levels of explanation for the same execution
>>> > Example: Bob's Website Factory and Customers Inc both provide
>>> > two
>>> > different and conflicting sets of information (i.e. accounts)
>>> > describing
>>> > the provenance of the production of the the same website.
>>> >
>>> >
>>> > Nodes:
>>> > - opm:Artifact
>>> > Definition: Immutable piece of state, which may have a physical
>>> > embodiment in a physical object, or a digital representation in
>>> > a
>>> > computer system.
>>> > Example: BlogAgg would like to know the state of an image before
>>> > and
>>> > after modification to see if it was modified appropriately
>>> >
>>> >
>>> > - opm:Process
>>> > Definition: Action or series of actions performed on or depend
>>> > upon
>>> > artifacts, and resulting in new artifacts.
>>> > Example: Alice collects data from public sources and
>>> > "natural
>>> > experiment" data. Alice then processes and interprets the
>>> > results and
>>> > writes a report summarizing the conclusions. All these steps
>>> > should be
>>> > captured.
>>> >
>>> > - opm:Agent (*1)
>>> > Definition: Contextual entity acting as a catalyst of a process,
>>> > enabling, facilitating, controlling, or affecting its execution.
>>> > Example: Alice starts and facilities the tool SPSS when doing
>>> > data analysis.
>>> >
>>> >
>>> > Edges:
>>> > - opm:Time (*2)
>>> > Example: BlogAgg wants to find the correct originator of the
>>> > microblog
>>> > who first got the word out.
>>> >
>>> > - opm:Role
>>> > Definition: A role designates an artifact’s or agent’s function
>>> > in a process
>>> > Example: Whether a data file was used as a training or test data
>>> > set
>>> > when running machine learning algorithms.
>>> >
>>> > - opm:Used, opm:UsedStar
>>> > Definition: property to express that an artifact was used by a
>>> > process.Example: The panda image was used by BlogAgg to generate
>>> > a thumbnail image.
>>> >
>>> > - opm:WasGeneratedBy, opm:WasGeneratedByStar,
>>> > Definition: property to express that an artifact was generated
>>> > by a process.
>>> > Example: A thumbnail image was generated by Blog Agg using the
>>> > panda image.
>>> >
>>> > - opm:WasControlledBy (*1)
>>> > Definition : property to express that a process was controlled
>>> > an agent.
>>> > Example: SPSS was controlled by Alice.
>>> >
>>> > - opm:WasDerivedFrom, opm:WasDerivedFromStar,
>>> > Definition: property to express that an artifact was derived
>>> > from
>>> > another artifact.
>>> > Example: The thumbnail image was derived from the panda image.
>>> >
>>> > - opm:WasTriggeredBy
>>> > Definition: property to express that a process was triggered by
>>> > another
>>> > process.
>>> > Example: Report writing was triggered by the interpretation of
>>> > results.
>>> >
>>> > Extensibility (*3):
>>> > - Some form of annotation, based on predicate-value pairs.
>>> > Example: The data is of type a customer sales records. The data
>>> > has size
>>> > 100 megabytes.
>>> >
>>> > - Profile mechanisms, including common types, common annotations,
>>> > and common graph templates
>>> > Example: The image has a creative commons attribution license.
>>> > This
>>> > pattern represents the exchange of messages in the http protocol.
>>> >
>>> >
>>> > (*) indicates terms that require refinement
>>> > (*1) Requires better, stricter guidelines for better inter-operabiltiy
>>> > (*2) To be better aligned on Time ontology
>>> > (*3) To be better specified to facilitate extensibility and to
>>> > be better aligned with RDF-like annotations
>>> >
>>> >
> 
Received on Wednesday, 24 November 2010 07:18:00 UTC

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