Inserting new speciments

istSOS 3 supports the insertion of speciment observation.

Specimen Observation

A Specimen is a physical sample, obtained for observation(s) usually carried out ex situ, often in a laboratory [1].

When the Observation represents a measurement of a property of a Specimen at a single point in time the specialised observation ‘SpecimenObservation’ SHOULD be used [2].

[1] OGC 07-002r3 - Cap. 7.3

[2] http://inspire.ec.europa.eu/id/document/tg/d2.9-o%26m-swe - Cap. 6.2.5.1.

Considerations

When inserting speciment observations, the observation table will contains not only the results of the laboratory procedure but also some informations contained into the SF_Specimen feature of interest.

There are different cases on how to register and insert speciment observations. For instance you can define a procedure that will contain all the results derived from a particular speciment type. Imagine a chemical survey of water quality of a lake. In this case the feature of interest is the lake and the speciments are the water collected in differrent location of that lake. Every speciment observation will have information on the speciment, the position, the sampling method, the material class, etc. and the obtained observation(s) carried out ex-situ.

Example of a speciment (to be expanded)

<?xml version="1.0"?>
<sp:SF_Specimen
    gml:id="pr1_s1"
    xmlns:sf="http://www.opengis.net/sampling/2.0"
    xmlns:sp="http://www.opengis.net/samplingSpecimen/2.0"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:xlink="http://www.w3.org/1999/xlink"
    xmlns:gml="http://www.opengis.net/gml/3.2"
    xsi:schemaLocation="http://www.opengis.net/samplingSpecimen/2.0 http://schemas.opengis.net/samplingSpecimen/2.0/specimen.xsd">
    <gml:description>Rock sample collected on traverse</gml:description>
    <gml:name
        codeSpace="http://my.geology.example.org/samples/2007">pr1_s1</gml:name>
    <sf:type xlink:href="http://www.opengis.net/def/samplingFeatureType/OGC-OM/2.0/SF_Specimen"/>
    <sf:sampledFeature
        xlink:href="http://my.geology.example.org/unit/g345"/>
    <sp:materialClass xlink:href="http://www.opengis.net/def/material/OGC-OM/2.0/rock"/>
    <sp:samplingTime>
        <gml:TimeInstant
            gml:id="pr1_s1_t">
            <gml:timePosition>2007-01-24T12:14:50.00+09:00</gml:timePosition>
        </gml:TimeInstant>
    </sp:samplingTime>
    <sp:samplingLocation>
        <gml:Point
            gml:id="pr1_s1_p">
            <gml:pos
                srsName="http://www.opengis.net/def/crs/EPSG/0/4347">-30.706 134.196 272.</gml:pos>
        </gml:Point>
    </sp:samplingLocation>
    <sp:size
        uom="kg">2.16</sp:size>
    <sp:currentLocation
        xlink:href="http://my.geology.example.org/storage/shelf/s234_8"/>
</sp:SF_Specimen>

  <?xml version="1.0"?>
  <sp:SF_Specimen xmlns:sf="http://www.opengis.net/sampling/2.0"
          xmlns:sp="http://www.opengis.net/samplingSpecimen/2.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema‐instance"
          xmlns:xlink="http://www.w3.org/1999/xlink"
          xmlns:gml="http://www.opengis.net/gml/3.2"
          gml:id="pr1_s2"
          xsi:schemaLocation="http://www.opengis.net/samplingSpecimen/2.0
          http://schemas.opengis.net/samplingSpecimen/2.0/specimen.xsd">
      <gml:description>Rock sample collected on traverse</gml:description>
      <gml:name codeSpace="http://my.geology.example.org/samples/2007">pr1_s2</gml:name>
      <sf:type xlink:href="http://www.opengis.net/def/samplingFeatureType/OGC-OM/2.0/SF_Specimen"/>
      <sf:sampledFeature xlink:href="http://my.geology.example.org/unit/g345"/>
      <sf:relatedSamplingFeature>
          <sf:SamplingFeatureComplex>
              <sf:role xlink:href="http://www/example/org/sampling/parentSpecimen"/>
              <sf:relatedSamplingFeature xlink:href="http://my.geology.example.org/projects/2007/pr1_s1"/>
          </sf:SamplingFeatureComplex>
      </sf:relatedSamplingFeature>
      <sp:materialClass xlink:href="http://www.opengis.net/def/material/OGC-OM/2.0/rock"/>
      <sp:samplingTime>
          <gml:TimeInstant gml:id="pr1_s2_t">
              <gml:timePosition>2007-01-29T12:19:55.00+09:00</gml:timePosition>
          </gml:TimeInstant>
      </sp:samplingTime>
      <sp:samplingMethod xlink:href="http://geochemistry.example.org/splits/biased/density/greaterThan/2.9"/>
      <sp:samplingLocation>
          <gml:Point gml:id="pr1_s2_p">
              <gml:pos srsName="http://www.opengis.net/def/crs/EPSG/0/4347">30.706 134.196 272.</gml:pos>
          </gml:Point>
      </sp:samplingLocation>
      <sp:size uom="kg">2.16</sp:size>
      <sp:currentLocation xlink:href="http://www.opengis.net/def/nil/OGC-OM/2.0/destroyed"/>
  </sp:SF_Specimen>

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json_schema
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15-100r1_OGC_Observations_and_Measurements_-_JSON_implementation.pdf

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Inserting new observations
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When inserting new observations related to specimens, istSOS promote a
two-step procedure which follow the field work work-flow:

1. In the field the sample is collected and its metadata are registered
2. The operator insert the specimen information into the database
   (using the WAlib)
3. The specimen is sent to laboratory for specific analyses
4. when results of analyses are available the operator insert the values of
   desired observedProperties to the database (using the istsoslib)


Alternatively, the operator can store all the information locally and insert
into the database all at once both the specimen metadata and the analyses results.
Beware that this approach may prevent the registration of other