specification.xml

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      <level>
        <types>
          <type name="Users" prefix="U">
            <contentType class="Requirement"/>
            <content>
              <comparator class="IdComparator"/>
              <req id="1" manuallyValidated="false">
                <title>Governments</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="2" manuallyValidated="false">
                <title>NGOs</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="3" manuallyValidated="false">
                <title>Parties to the convention</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="4" manuallyValidated="false">
                <title>Citizen groups</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="5" manuallyValidated="false">
                <title>Researchers</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="6" manuallyValidated="false">
                <title>BON</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="7" manuallyValidated="false">
                <title>Data providers</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="8" manuallyValidated="false">
                <title>Developers</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="9" manuallyValidated="false">
                <title>GeoBON members</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="10" manuallyValidated="false">
                <title>Funding organisms</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
            </content>
          </type>
        </types>
      </level>
      <level>
        <types>
          <type name="Needs" prefix="N">
            <contentType class="Requirement"/>
            <content>
              <comparator class="IdComparator"/>
              <req id="1" manuallyValidated="false">
                <title>Know the state of biodiversity</title>
                <desc>Currently:
- Small set of indicators provided my major actors (NGOs, etc.) ex: LPI, Redlist. 
- Ad-hoc reporting.
- Realtime dashboard and annual reports.
- Parties are disagreeing on baselines and indicators.

New system : 
- Use generic data and agreed-upon indicators to show a basic result.
- Use additionnal data sources to get a more accurate result.
- Intergrated in UN Biodiversity Lab and Target Tracker (WCMC, mandated by CBD).
- For SHI, the species will need to be specified.

</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="2" manuallyValidated="false">
                <title>Trace the source of this answer</title>
                <desc>(supported by which publications, scientists/organisations involved, based on which data)

Currently: 
- Look your answer... according to the system.

New system: 
- The process is trasparent.
- Give the sources for each steps of the pipeline.
- Know the people / organisations that provided the data for a specific answer.</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="3" manuallyValidated="false">
                <title>Know uncertainty of the answer</title>
                <desc>Dimensions: spatial, temporal
Types: human footprint, calculations, data, etc.

Currently: what we have doesn&apos;t mean much.

New system: 
- We want to find a way to communicate uncertainty for everything we show.
- Tell if the monitoring network can detect the trend.
</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="4" manuallyValidated="false">
                <title>Predict the future state of biodiversity</title>
                <desc>Planning:
SDM (eg Maria Isabel testing with plant data in Colombia)
Yan Boulanger - tree species and biomass for QC (he has data for 17spp) combined with info drivers (QC has very good monitoring data)
Issue: present and future predictions are different in terms of pipelines (debatable maybe?)
Major gap to be discussed: SDM connected with biodiversity metrics!!! (separate discussion on this point)
How we go from SDMs to indicators and then compound the uncertainty

New system : 
Visualize the projection.
How do you change the monitoring network to reduce prediction uncertainty? ==&gt; N05
Provide a feedback for better models for the current state ==&gt; N01

(we must decide what trigger a re-run of the model)

</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="5" manuallyValidated="false">
                <title>Where should we sample</title>
                <desc>Criteria could be : 
- minimize cost of sampling;
- minimize uncertainty of prediction or uncertianty current state of biodiversity.

Currently: Historically-based reasons, or designed for other things than *detecting change*.

New system: Recommend sites to sample to reduce prediction uncertainty or current state uncertainty.


</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="6" manuallyValidated="true">
                <title>What can I sample</title>
                <desc>NOT OUR DECISION

Sampling methods: Sound, DNA, direct observations, camera traps, satellite images
The model needs both large scale generic information, and reliable/specific observations.

Currently: Depending on who is doing it, can be cost-effective or a brute force approach.


</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="7" manuallyValidated="false">
                <title>Who is sampling </title>
                <desc>Know the people / organisations that provide data for a specific species.

Currently: Contact each country one by one. Often leads to overlooking data collectors.

New system: Search for &quot;frogs&quot;, get the organisations observing frogs on a map.
(separate system from the indicator &quot;answer&quot;, but will be used in conjuction)</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="9" manuallyValidated="false">
                <title>Identify research needs</title>
                <desc>(data / algorithms)

Currently: Cite papers specifically, rarely region specific.

New system:
- Use the uncertainty output to justify reseach needs, to get funding, etc.
- Data-based and region specific.</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="10" manuallyValidated="false">
                <title>Expand the system</title>
                <desc>Currently:
- No need to reach out to people most of the time, it is on github repos. 
- There is no coherent generalized pipeline. Every code uses their own pipeline/resolution.

New system:
- Coherent pipeline that can be extended.
- Can add a specific step without coding everyting.
- There must be a gatekeeper process to asses the quality and relevance of what is merged.
- We want to show a working proof of concept before we allow external researchers to expand the system.
</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="11" manuallyValidated="false">
                <title>See intermediate results</title>
                <desc>Currently:

New system: 
-  Anything that can be mapped that is passed between pipeline steps.
- Any other variable passed between steps (variable dump/graph).
</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="12" manuallyValidated="false">
                <title>Impact &amp; outreach</title>
                <desc>Currently: Publications, direct contact with deciders.

New system: 
- Deciders can make queries themselves (uncertainty must be VERY clear)
- Other scientists will see my research through this platform as well.</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="13" manuallyValidated="false">
                <title>Contibute analysis</title>
                <desc>Researchers can communicate their analysis of the system or its result to Geo BON or the community.</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="14" manuallyValidated="false">
                <title>Contibute data</title>
                <desc>New system: 
- We are not hosting anything, the data should be uploaded to another repository.
- The contributor should add a step to fetch this specific data when needed (for ex GBIF country node).</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="15" manuallyValidated="false">
                <title>Learning &amp; training</title>
                <desc>About biodiversity:
-

About the code and pipeline:
- The framework must be very clear.
- Inside each step, scientists will be responsible... but we can ask for clarifications in merge requests.
- Documentation should be REALLY simple and easily available.</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="16" manuallyValidated="true">
                <title>Connect with other members</title>
                <desc>(this is out of MS Project scope, more Geo BON stuff that can be adressed with the secretariat)</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="17" manuallyValidated="false">
                <title>Tracking progress</title>
                <desc>Is the capacity to monitor the indacators getting better?
(going towards the CBD goals)

Currently: Have a researcher grab data and process it in an ad-hoc way. In almost every case, it is not properly designed for purpose (repurposing data / algorithms).

New system: 
- Must give more confidence, with repeatable results!
- Tracking the new sites vs previous sampling
- Impact of these new sites on indicator uncertainty
- Impact on prediction
- Can track progress towards the GBF targets.
</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="18" manuallyValidated="false">
                <title>View alternative models</title>
                <desc>The type of model that we use makes a big difference in prediction.
Might depend on the need of the user... some model will give better results for some needs.

** This needs to be discussed in-depth!!

New system : 
- Region-specific when available, else choose the best generic model.
- Front-end user would not need to bother that choice, but in that case it must be explained.</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="20" manuallyValidated="false">
                <title>Know what species are missing in the analysis</title>
                <desc>Currently: Normally, published calculations are only done on those species that have enough data. Those with less data are not highlighted.

New system:
- For species with low data, we should show only what we can. The intermediate results panel would be used to show what we can show if the query was specific.
- If the indicator query gave a result: be able to know which species were left out / or show at which step the species stopped. 
- Explain the decision process.</desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
            </content>
          </type>
        </types>
      </level>
      <level>
        <types>
          <type name="User stories" prefix="S">
            <contentType class="Requirement"/>
            <content>
              <comparator class="IdComparator"/>
              <req id="1" manuallyValidated="true">
                <title>Dev: Choose the basis for our pipeline</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="2" manuallyValidated="false">
                <title>Dev: Create a very simple pipeline</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="3" manuallyValidated="false">
                <title>Scientist: Use valid data for Quebec</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="4" manuallyValidated="false">
                <title>Scientist: Use heterogenous sources in the SDM</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="5" manuallyValidated="false">
                <title>Scientist: Visualize the pipeline and references</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="6" manuallyValidated="false">
                <title>Decider: know uncertainty</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="7" manuallyValidated="false">
                <title>Decider: See unbiaised data</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="8" manuallyValidated="false">
                <title>Scientist: Use the pre-calculated SDMs from BioModelos</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="9" manuallyValidated="false">
                <title>User: Visualise connectivity (and its uncertainty)</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="10" manuallyValidated="false">
                <title>User: Visualise land cover change (and its uncertainty)</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="11" manuallyValidated="false">
                <title>User: Visualize the Species Habitat Index (and its uncertainty)</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="12" manuallyValidated="false">
                <title>BON: Suggest BON structure to detect change</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="13" manuallyValidated="false">
                <title>BON: Suggest BON structure to accurately reflect current situation</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="14" manuallyValidated="false">
                <title>Scientist: I want to publish a new version of a script</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
              <req id="15" manuallyValidated="false">
                <title>Scientist: Choose the appropriate methodology for Connectivity</title>
                <desc></desc>
                <manualValidationRef></manualValidationRef>
                <referenceFile></referenceFile>
              </req>
            </content>
          </type>
        </types>
      </level>
      <level>
        <types>
          <type name="Tests" prefix="T">
            <contentType class="Requirement"/>
            <content>
              <comparator class="IdComparator"/>
            </content>
          </type>
        </types>
      </level>
    </levels>
  </specification>
  <links>
    <from id="N10">
      <to>S14</to>
    </from>
    <from id="N01">
      <to>S01</to>
      <to>S02</to>
      <to>S03</to>
      <to>S04</to>
      <to>S07</to>
      <to>S08</to>
      <to>S09</to>
      <to>S10</to>
      <to>S11</to>
      <to>S13</to>
    </from>
    <from id="N11">
      <to>S09</to>
      <to>S10</to>
    </from>
    <from id="N03">
      <to>S06</to>
      <to>S09</to>
      <to>S10</to>
      <to>S11</to>
    </from>
    <from id="N02">
      <to>S03</to>
      <to>S04</to>
      <to>S05</to>
      <to>S08</to>
    </from>
    <from id="N05">
      <to>S12</to>
      <to>S13</to>
    </from>
    <from id="N04">
      <to>S12</to>
    </from>
    <from id="U10">
      <to>N17</to>
    </from>
    <from id="N06"/>
    <from id="U02">
      <to>N01</to>
      <to>N02</to>
      <to>N03</to>
      <to>N04</to>
      <to>N05</to>
      <to>N06</to>
      <to>N07</to>
      <to>N17</to>
      <to>N18</to>
      <to>N20</to>
    </from>
    <from id="N09">
      <to>S05</to>
      <to>S06</to>
    </from>
    <from id="U01">
      <to>N01</to>
      <to>N02</to>
      <to>N03</to>
      <to>N04</to>
      <to>N05</to>
      <to>N06</to>
      <to>N07</to>
      <to>N17</to>
      <to>N18</to>
      <to>N20</to>
    </from>
    <from id="U04">
      <to>N01</to>
      <to>N05</to>
      <to>N06</to>
      <to>N07</to>
      <to>N18</to>
      <to>N20</to>
    </from>
    <from id="U03">
      <to>N01</to>
      <to>N02</to>
      <to>N03</to>
      <to>N04</to>
      <to>N05</to>
      <to>N06</to>
      <to>N07</to>
      <to>N17</to>
      <to>N18</to>
      <to>N20</to>
    </from>
    <from id="U06">
      <to>N01</to>
      <to>N02</to>
      <to>N03</to>
      <to>N04</to>
      <to>N05</to>
      <to>N06</to>
      <to>N07</to>
      <to>N12</to>
      <to>N17</to>
      <to>N20</to>
    </from>
    <from id="U05">
      <to>N01</to>
      <to>N02</to>
      <to>N03</to>
      <to>N04</to>
      <to>N05</to>
      <to>N06</to>
      <to>N07</to>
      <to>N09</to>
      <to>N10</to>
      <to>N11</to>
      <to>N12</to>
      <to>N13</to>
      <to>N14</to>
      <to>N15</to>
      <to>N17</to>
      <to>N18</to>
      <to>N20</to>
    </from>
    <from id="U08">
      <to>N10</to>
      <to>N11</to>
    </from>
    <from id="U07">
      <to>N14</to>
    </from>
    <from id="U09">
      <to>N16</to>
    </from>
  </links>
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