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Re: Suggested Concepts for Charter

From: Satya Sahoo <sahoo.2@wright.edu>
Date: Tue, 23 Nov 2010 14:34:28 -0500
To: Paul Groth <pgroth@gmail.com>
Cc: "<public-xg-prov@w3.org>" <public-xg-prov@w3.org>, Luc Moreau <L.Moreau@ecs.soton.ac.uk>
Message-id: <69b0c10b1e36.4cebd0f4@wright.edu>

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>
Date: Monday, November 22, 2010 4:43 pm
Subject: Suggested Concepts for Charter
To: "<public-xg-prov@w3.org>" <public-xg-prov@w3.org>
Cc: Luc Moreau <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 artifactís or agentís 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 Tuesday, 23 November 2010 19:35:19 UTC

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