Day 2 Vocamp Physical Sample

<h2>Started discussion Using Geolink modular Oceanorgraphy Ontology as a source of ideas </h2>

There is an issue on what is an event in this ontology and if it has been defined well enough to distinguish from process.
Myaybe see DOLCE on this.
Agent types.  Collector is one of them and DataCite has some roles including Publisher....
Agent and activity are tied together by "wasAssociated With. See more in definitions

Used Definitions:
Features (DOLCE) are 'parasitic entities', that exist insofar their host exists. Typical examples of features are holes, bumps, boundaries, 
or spots of color. Features may be relevant parts of their host, like a bump or an edge, or dependent regions like a hole in a piece 
of cheese, the underneath of a table, the front of a house, or the shadow of a tree, which are not parts of their host. 
All features are essential wholes, but no common unity criterion may exist for all of them. However, typical features have a 
topological unity, as they are singular entities.Here only features of physical endurants are considered.

Feature of interest: a feature (so a representation of a real-world object) that carries the property which is observed.
This can be either a domain feature (aka sampled feature), 
e.g. “Mississippi”, or a sampling feature, e.g. “water gage X" at Mississippi river.

Place (from DOLCE)
A location, in a very generic sense: a political geographic entity (Roma, Lesotho), a non-material location determined by the 
presence of other entities ("the area close to Roma"), pivot events or signs ("the area where the helicopter fell"), 
complements of other entities ("the area under the table"), etc. 
In this generic sense, a Place is an "approximate" location. For an "absolute" location, see the class SpaceRegion


Process subClassOf Event

This is a placeholder for events that are considered in their evolution, or anyway not strictly dependent on agents, tasks, and plans. 
See Event class for some thoughts on classifying events. See also 'Transition'
A process may also be defined as the workflows and sequence of events inherent in processes.

Event (DOLCE)
 Events are said to occur or happen. They are considered perduring entities that unfold over time, i.e., they take up time and have 
 particupating objects.
 An occurrence-type is stative or eventive according to whether it holds of the mereological sum of two of its instances, 
 i.e. if it is cumulative or not. A sitting occurrence (is an event) is stative since the sum of two sittings is still a sitting occurrence.
 In general, events differ from situations because they are not assumed to have a description from which they depend. 
 They can be sequenced by some course, but they do not require a description as a unifying criterion.
 On the other hand, at any time, one can conceive a description that asserts the constraints by which an event of a certian type 
 is such, and in this case, it becomes a situation.
 Since the decision of designing an explicit description that unifies a perdurant depends on context, task, interest, application, etc.
 
 Workflow (DOLCE)
A Plan that defines Role(s), Task(s), and a specific structure for tasks to be executed, usually supporting the work of an Organization

Agents, are entiteis acting on its environment. 
An Agent's responsibility for an Activity or Entity is described using the properties prov:wasAssociatedWith and prov:wasAttributedTo,
respectively. Agents can also be responsible for other Agents' actions. In this case of delegation, 
the influencing Agent prov:actedOnBehalfOf another Agent that also bears responsibility for the influenced Activity or Entity.

There are some possible sub-types when non-human agents are considered:
Rational agents chooses to act to fulfil its own best interests; 
autonomous (agent that should achieve autonomously goals by making decisions and carrying out
actions in an environment; 
mobile (agents can move freely in an electronic network, communicating with objects of the environment such
as information resources of other agents; 
cognitive(an autonomous agent with human-like cognitive features but, in general, any agent that exploits
explicit knowledge

Roles
Some  distinguish three role types with the following informal definitions: 
• A  social role  corresponds to the involvement of a social object within some society.  
    the collector role is understood within a scientific organizational context but also a sampling process.
    But a Sampling Feature can be a role in that some entity exists before playing a Sampling Feature role.  It is not a  "rigid" identity.
    
• A  relational role  corresponds to the way in which an argument participates in some relation; 
       This may apply to some relations among information artifacts
• A  processual   role  corresponds   to   the   manner   in   which   a   single   participant behaves in some process; 
      the collector role is understood within a scientific organizational context but also a sampling process.
       Processual roles  have processes as their contexts. As such they are processes themselves, and one may identify them as 
       special layers of a process, because role­of is understood as a part­of relationship


<u>Our Competency Questions see snapshot</u>
1. Given that we are doing a chemicla analysis, where was the sample under analysis collected?
Scenario - There might be 3 jars of water that was collected from a Feature of Interest - a Lake..The sample is from part of the lake.
It does raise the Q of the difference bwtween pulling out one water jar of many as the Feature of Interest being (representatively) analyzed.
How do we get between agregated samples and observations?
Maybe sampling feature is the site where the sample is collected?
      Site - a place where a sample is collected. 
      Sites provide information giving the spatial location at which values have been collected. 
      A facility or location at which observations have been collected. A site may have instruments or equipment installed and
      may contain multiple other sampling features (e.g., a stream gage, weather station, observation well, etc.). 
      Additionally, many specimen sampling features may be collected at a site. Sites are also often referred to as stations. 
      A site is represented as a point, but it may have a geographical footprint that is not a point. 
      The site coordinates serve as a reference for the site and offsets may be specified from this reference location.
Can a site have a borehole??
Q was how do we define "place" ?  it has an identifyable location...?
      We may be equating sampling feature with Site. But Site is a Place and Sampling Feature is a Feature. So Feature of Interest 
      has a larger place and the SampleFeature is contained withing that.  

Is what we are calling Collection a  Sampling Feature Complex?  
No, that refers to the idea of a Core and other samples collected around a point of that core. Say 3 jars of water.
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What is the context for samples - it involves things we see in the data such as Geological age (time setting), place and featuress 
and propoerties. See SESAR data with link provided by Steve. 
See http://www.geosamples.org/help/vocabularies for vocabularies and also http://www.geosamples.org/search

Sample types page describes the different samples that can be registered. The sample type vocabulary is listed below. 
  Core - long cylindrical cores
  Core Half Round - half-cylindrical products of along-axis split of a whole round
  Core Piece - material occurring between unambiguous [as curated] breaks in recovery. 
  Core Quarter Round - quarter-cylindrical products of along-axis split of a half round.
  Core Section - arbitrarily cut segments of a "core"
  Core Section Half  - half-cylindrical products of along-axis split of a section or its component fragments through a selected diameter.
  Core Sub-Piece - unambiguously mated portion of a larger piece noted for curatorial management of the material. 
  Core Whole Round - cylindrical segments of core or core section material.
  CTD - a CTD (Conductivity, Temperature, and Depth) cast sample.
  Cuttings - loose, coarse, unconsolidated material suspended in drilling fluid.
  Dredge  - a group of rocks collected by dragging a dredge along the seafloor.
  Grab - a sample (sometimes mechanically collected) from a deposit or area, not intended to be representative of the deposit or area.
  Hole - hole cavity and walls surrounding that cavity.  
  Individual Sample - a sample that is an individual unit, including rock hand samples, a biological specimen, or a bottle of fluid.
                    (seemed like a top level, but then what about multiple samples?)
  Oriented Core - core that can be positioned on the surface in the same way that it was arranged in the borehole before extraction. 
  Other - a sample that does not fit any of the existing type designations. It is expected that further detailed description of the particular sample will be provided.
  Rock Powder - a sample created from pulverizing a rock to powder.
  Site - a place where a sample is collected.(stange to have this here rather than by itself)
  Terrestrial Section - a sample of a section of the near-surface Earth, generally in the critical zone.

<b>SESAR Sample types: What Samples Can Be Registered in SESAR?</b>
The System for Earth Sample Registration registers specimens and related sampling features collected from the natural environment. These include, but are not limited to:
Rock, mineral, or fossil specimens, and sub-samples thereof (e.g. thin sections, mineral concentrates)
Dredges
Cores (rock, sediment, ice) and related core sections, section halves, and samples from cores
Fluid samples (seawater, river or lake water, hydrothermal fluids, porewater)
Drill holes and wells
Soil pedons and samples thereof
Macro- and micro-biology samples

<b>Materials Type </b>
  Biology
  Gas
  Ice
  Liquid>aqueous
  Liquid>organic
  Mineral
  NotApplicable
  Other
  Particulate
  Rock
  Sediment
  Soil
  Synthetic
  
  Note: ODM2 has a tissue type.

<b>Sub-object types listed below are used by the International Ocean Drilling Program-United States Implementing Organization 
(IODP-USIO).</b>
 
      Bead- bead pressed from a powder.
      Chemical Fraction- Parts of a parent sample separated chemically.
      Cube- Equidimensional prism of material.
      Culture- Biological material cultured in geological material.
      Cylinder- Cylinders of material.
      Mechanical Fraction- Parts of a parent sample separated mechanically.
      Powder- Fine-grained (<62 micron), dry, granular material.
      Slab- Rectangular prism of material where one dimension is significantly shorter than the others.
      Smear- A toothpick sample suspended in liquid and fixed on slide.
      Specimen- Material of any shape or form selected for specific characteristics of interest.
      Squeeze Cake- Solid fraction remaining after forced expulsion of interstitial fluids from a source sample; typically has the shape of a cylindrical disc.
      Thin Section- A sub-millimeter thick slice of material mounted on a glass slide.
      Toothpick- Minute amount of material taken for observation.
      U-Channel- Long rectangular prism of material.
      Wedge- Sample form factor named for the tool used to extract it. Typically 5-20 ml in volume.


<u>Steve's Competency questions</>
Given that we have a Chemical analysis on a sample
 Where was this sample collected?
. What is the provenance (history) of  the analyzed sample material.
 Given a Sample, what  analytic data was derived?
Given a Fossil Sample
Are there any isotopic age data from within 1 km  of where sample was acquired.
Given video mosaic
Are there any bottom samples in the field of view?
Where did Geologist X collect samples in 1970?

SESAR vocabulary and issues with Sample type.
We see many different types of entities in this list.  it included individual sample and core and site.
It might be somewhat hierarchical but seems like a confused hierarchy.

Material category - classification (sub-type of Material)  and field name (free text)  Descriotion
2 types.  One high level (Rock) and one more specific (igneous).

<b>Notes of Feature</b>
A feature is something that has identity, location, and unity.

Some use a broad Feature concept such as SSN and O & M.
The 'Feature' is the fundamental unit of geospatial information, so the Feature Model is the fundamental meta-model used for developing 
an Application Schema.
Features are typed objects with identity. This is often referred to as "vector" data in traditional GIS.
Feature types are defined by a characteristic set of properties (i.e. their attributes, associations, operations). 
A feature type is usually specific to an application domain, and will be part of a Feature Type Catalogue (FTC) 
that describes a key part of the language of a domain. Features often correspond with objects that are 
recognisable in the real world, such as road, mine, truck, storm. However, spatial properties are not mandatory, 
so a feature type could be defined for any item of interest within a domain. 
This potentially allows data access for both spatial and non-spatial information to be unified through a common interface.
The General Feature Model is formally defined in ISO 19101 and ISO 19109. For a more detailed discussion, see FeatureModel.
The OGC Web Feature Service is the primary interface for feature data.

‘feature’ defined in the ‘Reference Model’ used by OGC and ISO Technical Committee 211 – Geographic Information referring to a
conceptualization of an entity in the real world. 
“Sampling features are distinctive compared with other features from application domains by having navigable associations to 
observations. ”

Examples from ODM2  bore hole, flight line....
GeoFeatures are often distinguished from other features.

SWEET ontology (Steve it is a Wordnet with no definitions) has properties for objects: “temperature”, “pressure”, “height”, “albedo” .
We seem to agree that  these  not feature of Interest but are propertie of Features (of Interest).

Sampling Feature a cruise is a type of a sampling feature
Also: (Simon Cox and O And M see ISO figure for this and https://www.seegrid.csiro.au/wiki/AppSchemas/ObservationsAndSampling)
Sub-types of point, surface, etc.

A sampling feature is established in order to make observations concerning some domain feature. The association Intention shall link
the SF_SamplingFeature to the feature which the sampling feature was designed to sample.
 The target of this association has the role sampledFeature with respect to the sampling feature, and shall not be a sampling feature
 or observation.
 It is usually a real-world feature from an application domain.

EXAMPLE A profile typically samples a water- or atmospheric-column; a well samples the water in an aquifer;
a tissue specimen samples a part of an organism

Observation Model
  Feature of interest
    Observation location
    Observation time
    Observed property and result type
      Scalar-valued properties
      Complex-valued properties
      Variable properties
      Time Series
  Sampling model
    Sampling features classified by shape
    Specimens
    Relationships of sampling features to other features
  
  Observations vs. Interpretations
  Examples
    Observations
    Sampling features
      Wells and aquifers
      Sampling on a ferry track
      Borehole and outcrop
      Assay suite on a specimen collected from an outcrop

  
  OGCInformationModels
    Observations and Measurements specification documents
    parent_gray FeatureModel
    ObservationsAndSampling


<B>Notes on Medium</b>
Sample Medium   The medium in which the sample was collected [e.g. water (Surface Water such as a stream, river, lake, pond, reservoir,
ocean ), air, sediment, etc.  from CUAHSI Community Observations Data Model Working Design Specifications Document
Are MaterialType and Medium the same thing (?)  we may be able to distinguish them.


Notes on Sampling site info
See Basic Observations and Sampling Feature Ontology
http://www.semantic-web-journal.net/system/files/swj890.pdf

Discsussing:
Listing 4 – A specimen with provenance and preparation information
<http://handle.net/10273/IGSN.SIOabc123> a saml:Specimen , my:splitCore ,
 <http://www.opengis.net/def/material/OGC-OM/2.0/rock> ;
 rdfs:label "SIO specimen abc123"^^xsd:string ;
 saml:sampledFeature my:midAtlanticRidge ;
 saml:samplingMethod <http://ldeo.columbia.edu/sampling/ghostbuster> ;
 saml:samplingTime "2013-06-12T09:25:00.00+11:00"^^xsd:dateTime ;
 saml:samplingLocation [ a w3geo:Point ;
 w3geo:alt -1272.0 ;
w3geo:lat 24.97 ;
w3geo:long -45.87
 ] ;
 saml:currentLocation <http://example.org/various/Warehouse3/shelf9/box67> ;
 saml:size [ a saml:Measure ;
 rdf:value "0.46"^^saml:Number ;
 saml:uom <http://qudt.org/vocab/unit#Kilogram>
 ] ;
 saml:samplingFeatureComplex [ a saml:SamplingFeatureComplex ;
 saml:relatedSamplingFeature <http://handle.net/10273/IGSN.SIOxyz456> ;
saml:role my:parent
 ] ;
 prov:wasDerivedFrom <http://handle.net/10273/IGSN.SIOxyz456> ;
 prov:wasGeneratedBy [ a prov:Activity ;
 prov:endedAtTime "2013-08-02T08:15:00.00+11:00"^^xsd:dateTime ;
 prov:used <http://handle.net/10273/IGSN.SIOxyz456> ;
prov:wasAssociatedWith my:JohnDoe ;
prov:wasInformedBy <http://example.org/various/sf-process/jkl987>
 ] .


Spatial sampling has a sample point orsampling surface.