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‎elements/MetagenomicsAnnotationProduct/index.html‎

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@@ -424,7 +424,7 @@ <h2 id="slots">Slots</h2>
424424
<td><a href="../sample_id/">sample_id</a></td>
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<td>0..1 <br/> <a href="../Sample/">Sample</a></td>
426426
<td>Link back to the originating sample</td>
427-
<td><a href="../ProcessedData/">ProcessedData</a>, <a href="../MetagenomicsProduct/">MetagenomicsProduct</a></td>
427+
<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a>, <a href="../ProcessedData/">ProcessedData</a></td>
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</tr>
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<tr>
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<td><a href="../provider_name/">provider_name</a></td>

‎elements/MetagenomicsBinningProduct/index.html‎

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@@ -407,7 +407,7 @@ <h2 id="slots">Slots</h2>
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<td><a href="../sample_id/">sample_id</a></td>
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<td>0..1 <br/> <a href="../Sample/">Sample</a></td>
409409
<td>Link back to the originating sample</td>
410-
<td><a href="../ProcessedData/">ProcessedData</a>, <a href="../MetagenomicsProduct/">MetagenomicsProduct</a></td>
410+
<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a>, <a href="../ProcessedData/">ProcessedData</a></td>
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</tr>
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<tr>
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<td><a href="../provider_name/">provider_name</a></td>

‎elements/MetagenomicsGenePhylogenyProduct/index.html‎

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@@ -415,7 +415,7 @@ <h2 id="slots">Slots</h2>
415415
<td><a href="../sample_id/">sample_id</a></td>
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<td>0..1 <br/> <a href="../Sample/">Sample</a></td>
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<td>Link back to the originating sample</td>
418-
<td><a href="../ProcessedData/">ProcessedData</a>, <a href="../MetagenomicsProduct/">MetagenomicsProduct</a></td>
418+
<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a>, <a href="../ProcessedData/">ProcessedData</a></td>
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</tr>
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<tr>
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<td><a href="../provider_name/">provider_name</a></td>

‎elements/acquisition_end_time/index.html‎

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@@ -533,48 +533,48 @@ <h2 id="applicable-classes">Applicable Classes</h2>
533533
<td>no</td>
534534
</tr>
535535
<tr>
536-
<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
537-
<td>Data generation activity for soil respiration analysis</td>
536+
<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
537+
<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
538538
<td>no</td>
539539
</tr>
540540
<tr>
541-
<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
542-
<td>Abstract base for plate measurement activities</td>
541+
<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
542+
<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
543543
<td>no</td>
544544
</tr>
545545
<tr>
546-
<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
547-
<td>Ecoplate absorbance measurement at a single timepoint</td>
546+
<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
547+
<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
548548
<td>no</td>
549549
</tr>
550550
<tr>
551-
<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
552-
<td>Abstract base for any data generation activity (physical to digital)</td>
551+
<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
552+
<td>Data generation activity for soil respiration analysis</td>
553553
<td>no</td>
554554
</tr>
555555
<tr>
556-
<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
557-
<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
556+
<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
557+
<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
558558
<td>no</td>
559559
</tr>
560560
<tr>
561-
<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
562-
<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
561+
<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
562+
<td>Abstract base for plate measurement activities</td>
563563
<td>no</td>
564564
</tr>
565565
<tr>
566-
<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
567-
<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
566+
<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
567+
<td>Ecoplate absorbance measurement at a single timepoint</td>
568568
<td>no</td>
569569
</tr>
570570
<tr>
571-
<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
572-
<td>A record of the mass spectrometry run that generates a raw data product</td>
571+
<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
572+
<td>Abstract base for any data generation activity (physical to digital)</td>
573573
<td>no</td>
574574
</tr>
575575
<tr>
576-
<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
577-
<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
576+
<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
577+
<td>A record of the mass spectrometry run that generates a raw data product</td>
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<td>no</td>
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</tr>
580580
</tbody>

‎elements/acquisition_start_time/index.html‎

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@@ -533,48 +533,48 @@ <h2 id="applicable-classes">Applicable Classes</h2>
533533
<td>no</td>
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</tr>
535535
<tr>
536-
<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
537-
<td>Data generation activity for soil respiration analysis</td>
536+
<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
537+
<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
538538
<td>no</td>
539539
</tr>
540540
<tr>
541-
<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
542-
<td>Abstract base for plate measurement activities</td>
541+
<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
542+
<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
543543
<td>no</td>
544544
</tr>
545545
<tr>
546-
<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
547-
<td>Ecoplate absorbance measurement at a single timepoint</td>
546+
<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
547+
<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
548548
<td>no</td>
549549
</tr>
550550
<tr>
551-
<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
552-
<td>Abstract base for any data generation activity (physical to digital)</td>
551+
<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
552+
<td>Data generation activity for soil respiration analysis</td>
553553
<td>no</td>
554554
</tr>
555555
<tr>
556-
<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
557-
<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
556+
<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
557+
<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
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<td>no</td>
559559
</tr>
560560
<tr>
561-
<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
562-
<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
561+
<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
562+
<td>Abstract base for plate measurement activities</td>
563563
<td>no</td>
564564
</tr>
565565
<tr>
566-
<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
567-
<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
566+
<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
567+
<td>Ecoplate absorbance measurement at a single timepoint</td>
568568
<td>no</td>
569569
</tr>
570570
<tr>
571-
<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
572-
<td>A record of the mass spectrometry run that generates a raw data product</td>
571+
<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
572+
<td>Abstract base for any data generation activity (physical to digital)</td>
573573
<td>no</td>
574574
</tr>
575575
<tr>
576-
<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
577-
<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
576+
<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
577+
<td>A record of the mass spectrometry run that generates a raw data product</td>
578578
<td>no</td>
579579
</tr>
580580
</tbody>

‎elements/additional_information/index.html‎

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@@ -529,8 +529,8 @@ <h2 id="applicable-classes">Applicable Classes</h2>
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</thead>
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<tbody>
531531
<tr>
532-
<td><a href="../MetagenomicsBinningProduct/">MetagenomicsBinningProduct</a></td>
533-
<td>Top-level archive (zip/tar) for binning results stored in MinIO</td>
532+
<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a></td>
533+
<td>Abstract base for all metagenomics data products</td>
534534
<td>no</td>
535535
</tr>
536536
<tr>
@@ -539,13 +539,13 @@ <h2 id="applicable-classes">Applicable Classes</h2>
539539
<td>no</td>
540540
</tr>
541541
<tr>
542-
<td><a href="../MetagenomicsGenePhylogenyProduct/">MetagenomicsGenePhylogenyProduct</a></td>
543-
<td>Top-level archive for gene-based phylogeny outputs (zip/tar stored in MinIO)</td>
542+
<td><a href="../MetagenomicsBinningProduct/">MetagenomicsBinningProduct</a></td>
543+
<td>Top-level archive (zip/tar) for binning results stored in MinIO</td>
544544
<td>no</td>
545545
</tr>
546546
<tr>
547-
<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a></td>
548-
<td>Abstract base for all metagenomics data products</td>
547+
<td><a href="../MetagenomicsGenePhylogenyProduct/">MetagenomicsGenePhylogenyProduct</a></td>
548+
<td>Top-level archive for gene-based phylogeny outputs (zip/tar stored in MinIO)</td>
549549
<td>no</td>
550550
</tr>
551551
</tbody>

‎elements/agitation_speed_rpm/index.html‎

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@@ -529,18 +529,23 @@ <h2 id="applicable-classes">Applicable Classes</h2>
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</thead>
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<tbody>
531531
<tr>
532+
<td><a href="../CultureGrowth/">CultureGrowth</a></td>
533+
<td>Abstract activity for growing cultures from samples or other cultures</td>
534+
<td>no</td>
535+
</tr>
536+
<tr>
532537
<td><a href="../PlateSetupActivity/">PlateSetupActivity</a></td>
533538
<td>Abstract base for 96-well plate setup activities</td>
534539
<td>no</td>
535540
</tr>
536541
<tr>
537-
<td><a href="../EcoplatePlateSetupActivity/">EcoplatePlateSetupActivity</a></td>
538-
<td>Ecoplate-specific plate setup</td>
542+
<td><a href="../AMP2PlateSetupActivity/">AMP2PlateSetupActivity</a></td>
543+
<td>AMP2-specific plate setup</td>
539544
<td>no</td>
540545
</tr>
541546
<tr>
542-
<td><a href="../StrainPurity/">StrainPurity</a></td>
543-
<td>Purity check of a strain culture</td>
547+
<td><a href="../PreCultureGrowth/">PreCultureGrowth</a></td>
548+
<td>Growth of a pre-culture to establish viable inoculum before</td>
544549
<td>no</td>
545550
</tr>
546551
<tr>
@@ -549,11 +554,6 @@ <h2 id="applicable-classes">Applicable Classes</h2>
549554
<td>no</td>
550555
</tr>
551556
<tr>
552-
<td><a href="../PreCultureGrowth/">PreCultureGrowth</a></td>
553-
<td>Growth of a pre-culture to establish viable inoculum before</td>
554-
<td>no</td>
555-
</tr>
556-
<tr>
557557
<td><a href="../HasIncubationConditions/">HasIncubationConditions</a></td>
558558
<td>Mixin for activities/setups that involve controlled incubation</td>
559559
<td>no</td>
@@ -564,13 +564,13 @@ <h2 id="applicable-classes">Applicable Classes</h2>
564564
<td>no</td>
565565
</tr>
566566
<tr>
567-
<td><a href="../AMP2PlateSetupActivity/">AMP2PlateSetupActivity</a></td>
568-
<td>AMP2-specific plate setup</td>
567+
<td><a href="../EcoplatePlateSetupActivity/">EcoplatePlateSetupActivity</a></td>
568+
<td>Ecoplate-specific plate setup</td>
569569
<td>no</td>
570570
</tr>
571571
<tr>
572-
<td><a href="../CultureGrowth/">CultureGrowth</a></td>
573-
<td>Abstract activity for growing cultures from samples or other cultures</td>
572+
<td><a href="../StrainPurity/">StrainPurity</a></td>
573+
<td>Purity check of a strain culture</td>
574574
<td>no</td>
575575
</tr>
576576
</tbody>

‎elements/agrochem_addition/index.html‎

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534534
<td>no</td>
535535
</tr>
536536
<tr>
537-
<td><a href="../MonetSoilSample/">MonetSoilSample</a></td>
538-
<td>A soil sample that has been collected according to the MONet soil sampling pr...</td>
537+
<td><a href="../OtherUndescribedSample/">OtherUndescribedSample</a></td>
538+
<td>A sample that does not fit into any of the other described sample types</td>
539539
<td>no</td>
540540
</tr>
541541
<tr>
542-
<td><a href="../OtherUndescribedSample/">OtherUndescribedSample</a></td>
543-
<td>A sample that does not fit into any of the other described sample types</td>
542+
<td><a href="../MonetSoilSample/">MonetSoilSample</a></td>
543+
<td>A soil sample that has been collected according to the MONet soil sampling pr...</td>
544544
<td>no</td>
545545
</tr>
546546
</tbody>

‎elements/air_temp_regm/index.html‎

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@@ -529,23 +529,18 @@ <h2 id="applicable-classes">Applicable Classes</h2>
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</thead>
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<tbody>
531531
<tr>
532-
<td><a href="../SoilSample/">SoilSample</a></td>
533-
<td>A sample of soil collected from the environment</td>
534-
<td>no</td>
535-
</tr>
536-
<tr>
537532
<td><a href="../OtherUndescribedSample/">OtherUndescribedSample</a></td>
538533
<td>A sample that does not fit into any of the other described sample types</td>
539534
<td>no</td>
540535
</tr>
541536
<tr>
542-
<td><a href="../WaterSample/">WaterSample</a></td>
543-
<td>A sample of water collected from the environment</td>
537+
<td><a href="../AerosolArmSample/">AerosolArmSample</a></td>
538+
<td>An aerosol sample collected by the ARM facility</td>
544539
<td>no</td>
545540
</tr>
546541
<tr>
547-
<td><a href="../FieldDeployedTerraformSample/">FieldDeployedTerraformSample</a></td>
548-
<td>A sample collected from a field-deployed Terraform experiment</td>
542+
<td><a href="../AerosolSample/">AerosolSample</a></td>
543+
<td>An aerosol sample collected from the environment</td>
549544
<td>no</td>
550545
</tr>
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<tr>
@@ -554,23 +549,28 @@ <h2 id="applicable-classes">Applicable Classes</h2>
554549
<td>no</td>
555550
</tr>
556551
<tr>
557-
<td><a href="../AerosolSample/">AerosolSample</a></td>
558-
<td>An aerosol sample collected from the environment</td>
552+
<td><a href="../SoilSample/">SoilSample</a></td>
553+
<td>A sample of soil collected from the environment</td>
559554
<td>no</td>
560555
</tr>
561556
<tr>
562-
<td><a href="../PureCultureSample/">PureCultureSample</a></td>
563-
<td>A sample of a culture containing a single organism</td>
557+
<td><a href="../TerraformSample/">TerraformSample</a></td>
558+
<td>A sample collected from a Terraform experiment</td>
564559
<td>no</td>
565560
</tr>
566561
<tr>
567-
<td><a href="../AerosolArmSample/">AerosolArmSample</a></td>
568-
<td>An aerosol sample collected by the ARM facility</td>
562+
<td><a href="../WaterSample/">WaterSample</a></td>
563+
<td>A sample of water collected from the environment</td>
569564
<td>no</td>
570565
</tr>
571566
<tr>
572-
<td><a href="../PlantSample/">PlantSample</a></td>
573-
<td>A sample containing plant material</td>
567+
<td><a href="../FieldDeployedTerraformSample/">FieldDeployedTerraformSample</a></td>
568+
<td>A sample collected from a field-deployed Terraform experiment</td>
569+
<td>no</td>
570+
</tr>
571+
<tr>
572+
<td><a href="../PureCultureSample/">PureCultureSample</a></td>
573+
<td>A sample of a culture containing a single organism</td>
574574
<td>no</td>
575575
</tr>
576576
<tr>
@@ -579,13 +579,13 @@ <h2 id="applicable-classes">Applicable Classes</h2>
579579
<td>no</td>
580580
</tr>
581581
<tr>
582-
<td><a href="../SedimentSample/">SedimentSample</a></td>
583-
<td>A sample of sediment collected from the environment</td>
582+
<td><a href="../PlantSample/">PlantSample</a></td>
583+
<td>A sample containing plant material</td>
584584
<td>no</td>
585585
</tr>
586586
<tr>
587-
<td><a href="../TerraformSample/">TerraformSample</a></td>
588-
<td>A sample collected from a Terraform experiment</td>
587+
<td><a href="../SedimentSample/">SedimentSample</a></td>
588+
<td>A sample of sediment collected from the environment</td>
589589
<td>no</td>
590590
</tr>
591591
</tbody>

‎elements/alkalinity/index.html‎

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@@ -534,13 +534,13 @@ <h2 id="applicable-classes">Applicable Classes</h2>
534534
<td>no</td>
535535
</tr>
536536
<tr>
537-
<td><a href="../SedimentSample/">SedimentSample</a></td>
538-
<td>A sample of sediment collected from the environment</td>
537+
<td><a href="../OtherUndescribedSample/">OtherUndescribedSample</a></td>
538+
<td>A sample that does not fit into any of the other described sample types</td>
539539
<td>no</td>
540540
</tr>
541541
<tr>
542-
<td><a href="../OtherUndescribedSample/">OtherUndescribedSample</a></td>
543-
<td>A sample that does not fit into any of the other described sample types</td>
542+
<td><a href="../SedimentSample/">SedimentSample</a></td>
543+
<td>A sample of sediment collected from the environment</td>
544544
<td>no</td>
545545
</tr>
546546
</tbody>

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