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Re: Suggested Concepts for Charter

From: JunZhao <jun.zhao@zoo.ox.ac.uk>
Date: Wed, 24 Nov 2010 10:58:42 +0000
Message-ID: <4CECEFE2.609@zoo.ox.ac.uk>
To: Paul Groth <pgroth@gmail.com>
CC: "<public-xg-prov@w3.org>" <public-xg-prov@w3.org>
Dear all,

I just added the concepts from the Provenance Vocabulary on the wiki 
page [1].

* prv:Actor - It is broader than opm:Agent. Each opm:Agent is directly 
related to a process (OPM defines opm:Agent as "a catalyst of a 
process"). A prv:Actor can be basically any active entity. This includes 
entities that are directly involved in the processes described (as 
represented by opm:Agent) but also entities that are not directly 
involved (e.g. the person who maintains the Web server that served a 
prv:DataItem in a prv:DataAccess execution).

* prv:involvedActor - prv:involvedActor refers to active entities that 
were somehow involved in the execution of a process. It is broader than 
opm:wasControlledBy because this involvement does not necessarily mean 
that the referent was responsible for controlling the execution.

* prv:containedBy - refers to a data item that contained a data item.

* prv:operatedBy - refers to a human actor who was operating a non-human 
actor at the time the provenance description refers to. OPM does not 
have any properties between opm:Agent.

* prv:usedBy - refers to a data publisher (a human actor) who used a 
data providing services (a non-human actor) at the time the provenance 
description refers to. Again, OPM does not properties between opm:Agent.




Paul Groth wrote:
> 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

Dr Jun Zhao
Image Bioinformatics Research Group
Department of Zoology
University of Oxford
OX33 1SL
Email: jun.zhao@zoo.ox.ac.uk
Phone: +44 (0) 1865 281 094
Received on Wednesday, 24 November 2010 10:59:13 UTC

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