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Updated the methods vocabs for Opportune module as per version-2 #570

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Sep 17, 2024
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Updated the methods vocabs for Opportune module as per version-2 #570

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43fe73c
Updated the methods vocabs for Opportune module as per version-2
arunherb Jun 17, 2024
41caab9
Merge branch 'main' into opportune_methods_v2
junrongYu Jun 18, 2024
f41f48c
Merge branch 'main' into opportune_methods_v2
junrongYu Sep 17, 2024
b1076e8
Added reference links of other modules and appendix; Added optional m…
junrongYu Sep 17, 2024
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256 changes: 128 additions & 128 deletions ...servations/opportunistic-observations.ttl → ...e-observations/opportune-observations.ttl
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,39 @@ species.</p></li>
<li><p><a href="https://linked.data.gov.au/def/nrm/f0123418-c565-45a6-be01-c5c332c727e5">Camera Trapping Module</a> – opportune observations of particular species
may warrant the use of camera trapping.</p></li>
</ul>
"""^^rdf:HTML ;
<h2 id="field-collection">Field collection</h2>
<h3 id="pre-requisites">Pre-requisites</h3>
<p>Pre-requisites for completing this protocol:</p>
<ul>
<li><p>Opportune observations can be recorded at any stage of a project
and are not dependent on other modules.</p></li>
</ul>
<h3 id="time-requirements">Time requirements</h3>
<p>Time estimates vary depending on the level of detail recorded and
whether voucher specimens are collected. As a general guide, allow:</p>
<ul>
<li><p>2 – 5 minutes to record an opportune flora observation in the
Monitor app, depending on if a voucher specimen is collected.</p></li>
<li><p>2 – 10 minutes to record an opportune fauna observation in the
app, depending on if a voucher specimen is collected.</p></li>
<li><p>5 minutes processing time per flora voucher specimen (barcode and
press).</p></li>
<li><p>5 – 30 minutes processing time per fauna voucher specimen (e.g.
tissue sampling, preservation, labelling, barcode).</p></li>
<li><p>5 minutes per record to upload any photos/videos/audio recordings
collected outside of the app.</p></li>
</ul>
<h3 id="personnel-requirements">Personnel requirements</h3>
<p>Number of personnel and skills:</p>
<ul>
<li><p>Opportune observations can be completed by one person but is
easier with two, so one can make the observations and the other can
record the data directly into the app.</p></li>
<li><p>The surveyor making the observations is ideally familiar with and
experienced in identifying the flora and fauna within the area.</p></li>
<li><p>Scientific permits may be required for the collection of voucher
specimens. Land access permissions are required.</p></li>
</ul>"""^^rdf:HTML ;
dcterms:source """
<h1 id="references">References</h1>
<p>ABARES (2016) The Australian Land Use and Management Classification
Expand Down Expand Up @@ -512,37 +544,37 @@ specimens). Vertebrate vouchering is not covered in the EMSA Modules
voucher specimens (animal remains or signs) include when:</p></li>
</ul>
<ul>
<li><p>species identification is uncertain</p></li>
<li><p>a record is considered important (e.g. the species has a limited
<li><p>Species identification is uncertain</p>
<p>A record is considered important (e.g. the species has a limited
occurrence, there are few existing records, the record represents a
range extension (including introduced species), the specimen has
atypical characteristics)</p></li>
<li><p>the voucher is in better condition or has more scientific value
(e.g. more likely to provide species identification) than previously
collected specimens</p></li>
<li><p>animal remains or signs are considered important for other
studies (e.g. genetics, diet, parasites and zoonoses)</p></li>
<li><p>advised by the relevant museum to address scientific knowledge
atypical characteristics)</p>
<p>The voucher is in better condition or has more scientific value (e.g.
more likely to provide species identification) than previously collected
specimens</p>
<p>Animal remains or signs are considered important for other studies
(e.g. genetics, diet, parasites and zoonoses)</p></li>
<li><p>Advised by the relevant museum to address scientific knowledge
gaps and improve representation within their collection</p></li>
<li><p>it is a required condition of permits, approved by an animal
<li><p>It is a required condition of permits, approved by an animal
ethics committee</p></li>
<li><p>a dead specimen or sign is of a threatened or presumed extinct
<li><p>A dead specimen or sign is of a threatened or presumed extinct
species, no matter what the quality/condition.</p></li>
</ul>
<ul>
<li><p>Unless there are overriding circumstances, fauna voucher
specimens should only be collected if they are considered a suitable
condition for accessioning and if they can be prepared, preserved,
stored and transported appropriately. As a guide, suitable specimen
quality should be interpreted as:</p></li>
quality should be interpreted as:</p>
<p>Road kill, beach washed and freshly deceased: whole, with the skull
intact, clean (no blood stains) and not decomposing (strong odour, fur,
feathers or skin easily fall off) or desiccated.</p>
<p>Skeletal material: dry, whole and partial skeletal material may be
useful, depending on species and condition. Broken or fractured
bones/skulls are not useful.</p></li>
</ul>
<ul>
<li><p>Road kill, beach washed and freshly deceased: whole, with the
skull intact, clean (no blood stains) and not decomposing (strong odour,
fur, feathers or skin easily fall off) or desiccated.</p></li>
<li><p>Skeletal material: dry, whole and partial skeletal material may
be useful, depending on species and condition. Broken or fractured
bones/skulls are not useful.</p></li>
<li><p>Eggs and nests: abandoned nests or eggs are a good record of
breeding data for birds. Alternatively, a photo and measurements of the
eggs and/or nest can be used as an observational record (DPaW
Expand All @@ -557,7 +589,8 @@ was dead before the tissues were sampled. This will assist in
interpreting potentially anomalous results in the lab (Owens 2000).
Photos can be taken of the specimen (with scale) to accompany the
record. Ideally include close-ups showing features, any tags/microchip
numbers etc., as well as photos of the surrounding environment.</p></li>
numbers, etc., as well as photos of the surrounding
environment.</p></li>
<li><p>If a specimen is not required, is not of a suitable condition for
collection, or animal ethics approval has not been obtained, then take
photos (with scale) instead (DPaW 2013).</p></li>
Expand Down Expand Up @@ -588,7 +621,7 @@ to the Post-field sample curation protocol in the Invertebrate Fauna
Module. Also consult with the relevant museum for guidance.</p></li>
</ul>"""^^rdf:HTML ;
skos:prefLabel "Opportune Module" ;
schema:url "https://github.com/ternaustralia/dawe-rlp-vocabs/tree/main/vocab_files/methods_by_module/opportunistic-observations/opportunistic-observations.ttl"^^xsd:anyURI ;
schema:url "https://github.com/ternaustralia/dawe-rlp-vocabs/tree/main/vocab_files/methods_by_module/opportune-observations/opportune-observations.ttl"^^xsd:anyURI ;
tern:appendix """
<h1 id="appendices">Appendices</h1>
<p><span class="anchor" id="appendix-1"></span><h4>Appendix 1. Collection
Expand Down Expand Up @@ -2244,41 +2277,23 @@ measurements</h3>
<td></td>
</tr>
<tr class="even">
<td>Teats</td>
<td>Drop-down list</td>
<td>Number in Pouch</td>
<td>Enter number of young observed in pouch</td>
<td></td>
<td></td>
<td></td>
<td>X</td>
<td></td>
</tr>
<tr class="odd">
<td>Testes</td>
<td>Drop-down list</td>
<td></td>
<td></td>
<td></td>
<td>X</td>
<td></td>
</tr>
<tr class="even">
<td>Pouch</td>
<td>Testes size</td>
<td>Drop-down list</td>
<td></td>
<td></td>
<td></td>
<td>X</td>
<td></td>
</tr>
<tr class="odd">
<td>Number in Pouch</td>
<td>Enter number of young observed in pouch</td>
<td></td>
<td></td>
<td></td>
<td>X</td>
<td></td>
</tr>
<tr class="even">
<td>Head length</td>
<td>mm</td>
Expand Down Expand Up @@ -3047,113 +3062,88 @@ knife, scraper (for collection)</p></li>
pencil, scissors (for storing specimens).</p></li>
</ul>"""^^rdf:HTML ;
tern:instructions """
<h2 id="field-collection">Field collection</h2>
<h3 id="pre-requisites">Pre-requisites</h3>
<p>Pre-requisites for completing this protocol:</p>
<ul>
<li><p>Opportune observations can be recorded at any stage of a project
and are not dependent on other modules.</p></li>
</ul>
<h3 id="time-requirements">Time requirements</h3>
<p>Time estimates vary depending on the level of detail recorded and
whether voucher specimens are collected. As a general guide, allow:</p>
<ul>
<li><p>2 – 5 minutes to record an opportune flora observation in the
Monitor app, depending on if a voucher specimen is collected.</p></li>
<li><p>2 – 10 minutes to record an opportune fauna observation in the
app, depending on if a voucher specimen is collected.</p></li>
<li><p>5 minutes processing time per flora voucher specimen (barcode and
press).</p></li>
<li><p>5 – 30 minutes processing time per fauna voucher specimen (e.g.
tissue sampling, preservation, labelling, barcode).</p></li>
<li><p>5 minutes per record to upload any photos/videos/audio recordings
collected outside of the app.</p></li>
</ul>
<h3 id="personnel-requirements">Personnel requirements</h3>
<p>Number of personnel and skills:</p>
<ul>
<li><p>Opportune observations can be completed by one person but is
easier with two, so one can make the observations and the other can
record the data directly into the app.</p></li>
<li><p>The surveyor making the observations is ideally familiar with and
experienced in identifying the flora and fauna within the area.</p></li>
<li><p>Scientific permits may be required for the collection of voucher
specimens. Land access permissions are required.</p></li>
</ul>
<h3 id="instructions-and-procedures">Instructions and procedures</h3>
<h3 id="instructions-and-procedures">Instructions and procedures</h3>
<ol type="1">
<li><p>Open the Monitor app and select the Opportune Module from the
projects page or via the yellow quick-access <em>opportune</em> button
located in the top right corner of the screen.</p></li>
<li><p>Select <em>add observation record</em>, A unique sequential
<em>observation ID</em> is automatically assigned to the
record.</p></li>
<li><p>Add <em>photos, video</em> or <em>audio</em> for the observation
(if applicable) using the in-app camera/audio recorder or selecting from
the camera roll/audio recorder on your device. If files are on another
device, enter a <em>media ID</em> (i.e. the unique photo ID on the
external device) so the files can be uploaded later when accessing the
app from a computer. Enter a <em>description</em> (free text) to
accompany each file, e.g. <em>close up of thorns</em>.</p></li>
projects page or via the quick-access opportune button located in the
app menu.</p></li>
<li><p>Since the opportune collection is not plot-based, and therefore
not associated with a plot visit, record the <em>start date time</em>
(yyyy-mm-dd hh:mm:ss) of the opportune survey. This is only required
prior to recording the first opportune record.</p>
<p>Save the opportune survey (start) component. The first opportune
record will open. A unique sequential <em>observation ID</em> is
automatically assigned to the record.</p></li>
<li><p>Media including <em>photos, video</em> or <em>audio</em> can be
recorded for the observation. Enter a <em>comment</em> to accompany each
file (e.g. <em>close up of thorns</em>).</p></li>
<li><p>The <em>date</em>, <em>time</em> and <em>location</em> of the
observation are automatically recorded but can be changed as necessary
(i.e. if entering a record after the event). To change the location,
select <em>choose on map</em> or enter specific coordinates. If the
location is recorded on a stand-alone GPS, enter a <em>GPS ID</em> so
the coordinates can be uploaded later.</p></li>
<li><p>Select the <em>taxa type</em> from the drop-down list.</p></li>
<li><p>Select the <em>species</em> or the lowest taxonomic level known
using the search function and drop-down list (as you type, options will
be provided by species, genus, class, order, and family). The common
name and scientific name are shown for each species. If the
select <em>choose on map</em> or enter specific coordinates.</p></li>
<li><p>Select the <em>taxa type</em> from the drop-down list. This
filters the species and other drop-down lists.</p></li>
<li><p>Record the <em>species</em> from the drop-down list. Begin typing
the scientific or common name to query the species list. If the
identification is unknown and pending the review of evidence collected,
then manually enter a descriptive field name instead e.g. <em>Acacia
spiky</em>. The field name given during this step should be used as the
then manually enter a descriptive field name instead (e.g. Acacia
spiky). The field name given during this step should be used as the
field name every time that species is encountered within a survey
event.</p></li>
<li><p>Switch the <em>confident</em> toggle to <em>off</em> if the
identification is uncertain. The default is <em>on</em> (see <a href="#additional-guidelines">Additional Guidelines</a>).</p></li>
identification is uncertain. The default is <em>on</em> (see Additional
guidelines).</p></li>
<li><p>Record the <em>number of individuals</em> observed (zero, blank
and no selection are invalid) and select if the number of individuals is
<em>exact</em> or an <em>estimate</em>.</p></li>
<li><p>Select the <em>observation method</em> (tier 1 to tier 3) from
the drop-down list (refer to <a href="#appendix-1">Appendix 1</a> for the full list of
the drop-down list (refer to Appendix 1 for the full list of
options).</p></li>
<li><p>Select the <em>observer/s</em> (drop-down list, multiple
<li><p>Select the <em>observers</em> (drop-down list, multiple
selections allowed, or manually enter first name, middle initial and
last name).</p></li>
<li><p>If observed outside of a plot, record the <em>habitat (major
vegetation group)</em> from the drop-down list.</p></li>
<li><p>Record <em>observation notes</em> (optional) as free text (e.g.
additional habitat information, condition, fauna behaviour, presumed
cause of death, appearance, signs of disease, tag details (ID
number/colour/Bluetooth ID).</p></li>
<li><p>Toggle on to record <em>advanced details</em> (optional; refer to
<a href="#appendix-2">Appendix 2</a>). Relevant fields will be visible based on the selection of
taxa type in Step 5. For flora, select the <em>growth form</em> and
<em>life stage</em> (multiple selections allowed) from the drop-down
lists. For direct observations of fauna, select the <em>sex</em>,
<em>age class</em> and <em>breeding status</em> from the drop-down lists
and record <em>fauna measurements</em> (where relevant).</p></li>
<li><p>If a <em>voucher specimen</em> is collected, switch the toggle to
<em>on</em>. Assign a unique barcode label to the specimen and <em>scan
<li><p>Record the <em>habitat (major vegetation group)</em> (optional)
from the drop-down list.</p></li>
<li><p>Record any <em>comments</em> (optional) (e.g. additional habitat
information, condition, fauna behaviour, presumed cause of death,
appearance, signs of disease, tag details (ID number/colour/Bluetooth
ID).</p></li>
<li><p>For flora, select the <em>growth form</em> and <em>life
stage</em> (multiple selections allowed) from the drop-down
lists.</p></li>
<li><p>For fauna, check the checkbox to record <em>additional fauna
details</em> (optional; refer to Appendix 2). Relevant fields will be
visible based on the selection of taxa type in Step 5. For direct
observations of fauna, select the <em>sex</em>, <em>age class</em> and
<em>breeding status</em> from the drop-down lists and record <em>fauna
measurements</em> (where relevant).</p></li>
<li><p>If a <em>voucher specimen</em> is collected, check the checkbox.
Assign a unique <em>voucher barcode</em> to the specimen and <em>scan
the barcode</em> (see section 3.2.2 Voucher specimen collection). Select
<em>voucher type</em> (tier 1 and tier 2) from the drop-down list (refer
to <a href="#appendix-3">Appendix 3</a>. for the full list of options). For vertebrate fauna
remains (i.e. carcasses), select the <em>condition of the specimen</em>
from the drop-down list. Select the <em>preservative type</em>
(drop-down list) and specify the <em>% concentration</em> if relevant
(e.g. 95% undenatured ethanol). Record any <em>voucher comments</em>
(optional) as free text (e.g. physical description of the specimen,
linked voucher IDs, prey/parasites collected with samples).</p></li>
<li><p>Select the <em>add voucher specimen</em> to add additional
voucher specimens for the same observation (e.g. a plant voucher and a
plant tissue voucher). Each specimen is allocated a unique
barcode.</p></li>
<li><p>Select <em>save</em> to save the opportune record. Repeat from
Step 3.1.5 to add another observation.</p></li>
<li><p>At the end of a survey event, select <em>complete protocol</em>.
The observation records can be edited as necessary.</p></li>
(drop-down list) and specify the <em>concentration</em> if relevant
(e.g. 95% undenatured ethanol). Record a <em>voucher comment</em>
(optional) (e.g. physical description of the specimen, linked voucher
IDs, prey/parasites collected with samples).</p></li>
<li><p>Add additional voucher specimens for the same observation (e.g. a
plant voucher and a plant tissue voucher) if required. Each specimen is
allocated a unique barcode.</p></li>
<li><p>Save the opportune record. Add another opportune record for the
current location if required. A new opportune record will open. The next
unique sequential <em>observation ID</em> is automatically assigned to
the record. Repeat steps 4–18.</p></li>
<li><p>After all opportune records for the current location are saved,
select the back button at the top of page to return to the project
page.</p></li>
<li><p>Record additional records by selecting the Opportune Module and
then the edit button.</p></li>
<li><p>At the end of the survey, complete the opportune component and
then record the <em>end date time</em> (yyyy-mm-dd hh:mm:ss) of the
opportune survey. Check the summary of the data and queue the collection
for submission.</p></li>
</ol>"""^^rdf:HTML ;
tern:purpose """
<h2 id="rationale">Rationale</h2>
Expand Down Expand Up @@ -3247,6 +3237,16 @@ not intended to cover the capture or euthanasia of vertebrate fauna;
thus, fauna voucher specimens are restricted to those collected from
deceased animals or observed signs such as scats and hair.</p>
"""^^rdf:HTML ;
tern:undertakenComplementarily
<https://linked.data.gov.au/def/nrm/0771a99f-27f4-4ff7-bf6d-aa70fe22ae51> ,
<https://linked.data.gov.au/def/nrm/0ad98270-707f-4a78-acd1-666faa2c124e> ,
<https://linked.data.gov.au/def/nrm/1f2ac884-2177-403a-a6c3-27e109b1fc95> ,
<https://linked.data.gov.au/def/nrm/2b5c2281-e0f4-4ef5-8ae0-8ae745af9a7e> ,
<https://linked.data.gov.au/def/nrm/420ce0a7-9364-4bf4-861c-ef5f710e31b9> ,
<https://linked.data.gov.au/def/nrm/8e7c86ce-e283-4cea-aca7-44ed7a22629c> ,
<https://linked.data.gov.au/def/nrm/cd04526e-7455-45c1-8a44-55575a4a7b2d> ,
<https://linked.data.gov.au/def/nrm/dd2da1e0-edbe-4f20-a1ae-b860876c1837> ,
<https://linked.data.gov.au/def/nrm/f0123418-c565-45a6-be01-c5c332c727e5> ;
tern:undertakenConcurrently
<https://linked.data.gov.au/def/nrm/0771a99f-27f4-4ff7-bf6d-aa70fe22ae51> ,
<https://linked.data.gov.au/def/nrm/0ad98270-707f-4a78-acd1-666faa2c124e> ,
Expand Down
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