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‎about/index.html‎

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@@ -549,7 +549,8 @@ <h2 id="contacts">Contacts</h2>
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<h2 id="credits">Credits</h2>
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<p>This material is free to use, and attribution is always appreciated. Attribution may read as follows:</p>
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<p>Authored by Conrad Mearns, Maia Kapur, Montana Smith, Beata Meluch, Aramy Truong, and Yuri E. Corilo at the Pacific Northwest National Laboratory, operated by Battelle for the U.S. Department of Energy.</p>
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<p>(Optional, if applicable): Please cite the following in your work: (Place Holder Zenodo)</p>
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<p>Please cite the following in your work: </p>
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<p>Prymolennna, A., Zalmanek, B., Kapur, M. S., Meluch, B. J., Smith, M., Mearns, C., Truong, A.&amp; Corilo, Y. (2026). EMSL-Computing/BASALT-Schema: v0.1.0 — Initial public release of BASALT schema (Version v0.1.0) [Computer software]. Zenodo. <a href="https://doi.org/10.5281/zenodo.21893602">https://doi.org/10.5281/zenodo.21893602</a></p>
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‎elements/MetagenomicsAnnotationProduct/index.html‎

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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>
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<td>Link back to the originating sample</td>
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<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a>, <a href="../ProcessedData/">ProcessedData</a></td>
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<td><a href="../ProcessedData/">ProcessedData</a>, <a href="../MetagenomicsProduct/">MetagenomicsProduct</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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<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>
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<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a>, <a href="../ProcessedData/">ProcessedData</a></td>
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<td><a href="../ProcessedData/">ProcessedData</a>, <a href="../MetagenomicsProduct/">MetagenomicsProduct</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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<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>
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<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a>, <a href="../ProcessedData/">ProcessedData</a></td>
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<td><a href="../ProcessedData/">ProcessedData</a>, <a href="../MetagenomicsProduct/">MetagenomicsProduct</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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</thead>
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<tbody>
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<tr>
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<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
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<td>Abstract base for plate measurement activities</td>
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<td><a href="../NucleotideSequencing/">NucleotideSequencing</a></td>
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<td>A lab activity in which DNA or RNA that was extracted from a sample is sequen...</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
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<td>Ecoplate absorbance measurement at a single timepoint</td>
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<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
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<td>Data generation activity for soil respiration analysis</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
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<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
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<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
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<td>Abstract base for plate measurement activities</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
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<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
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<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
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<td>Ecoplate absorbance measurement at a single timepoint</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
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<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
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<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
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<td>Abstract base for any data generation activity (physical to digital)</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
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<td>Data generation activity for soil respiration analysis</td>
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<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
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<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../NucleotideSequencing/">NucleotideSequencing</a></td>
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<td>A lab activity in which DNA or RNA that was extracted from a sample is sequen...</td>
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<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
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<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
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<td>A record of the mass spectrometry run that generates a raw data product</td>
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<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
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<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
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<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
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<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
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<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>
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<tr>
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<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
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<td>Abstract base for any data generation activity (physical to digital)</td>
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<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
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<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
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<td>no</td>
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</tr>
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</tbody>

‎elements/acquisition_start_time/index.html‎

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</thead>
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<tbody>
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<tr>
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<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
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<td>Abstract base for plate measurement activities</td>
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<td><a href="../NucleotideSequencing/">NucleotideSequencing</a></td>
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<td>A lab activity in which DNA or RNA that was extracted from a sample is sequen...</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
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<td>Ecoplate absorbance measurement at a single timepoint</td>
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<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
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<td>Data generation activity for soil respiration analysis</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
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<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
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<td><a href="../PlateDataGenerationActivity/">PlateDataGenerationActivity</a></td>
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<td>Abstract base for plate measurement activities</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
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<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
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<td><a href="../EcoplateDataGenerationActivity/">EcoplateDataGenerationActivity</a></td>
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<td>Ecoplate absorbance measurement at a single timepoint</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
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<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
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<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
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<td>Abstract base for any data generation activity (physical to digital)</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../RespirationDataGenerationActivity/">RespirationDataGenerationActivity</a></td>
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<td>Data generation activity for soil respiration analysis</td>
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<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
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<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../NucleotideSequencing/">NucleotideSequencing</a></td>
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<td>A lab activity in which DNA or RNA that was extracted from a sample is sequen...</td>
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<td><a href="../XRayDataGenerationActivity/">XRayDataGenerationActivity</a></td>
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<td>Abstract base class for X-ray analytical methods including XRF (elemental)</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
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<td>A record of the mass spectrometry run that generates a raw data product</td>
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<td><a href="../AMP2DataGenerationActivity/">AMP2DataGenerationActivity</a></td>
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<td>AMP2 plate measurement (OD, fluorescence, flow cytometry)</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../XRFDataGenerationActivity/">XRFDataGenerationActivity</a></td>
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<td>X-ray Fluorescence (XRF) elemental analysis activity</td>
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<td><a href="../MassSpectrometryDataGenerationActivity/">MassSpectrometryDataGenerationActivity</a></td>
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<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>
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<tr>
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<td><a href="../DataGenerationActivity/">DataGenerationActivity</a></td>
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<td>Abstract base for any data generation activity (physical to digital)</td>
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<td><a href="../XRDDataGenerationActivity/">XRDDataGenerationActivity</a></td>
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<td>X-ray Diffraction (XRD) mineralogical analysis activity</td>
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<td>no</td>
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</tr>
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</tbody>

‎elements/additional_information/index.html‎

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</thead>
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<tbody>
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<tr>
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<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a></td>
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<td>Abstract base for all metagenomics data products</td>
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<td><a href="../MetagenomicsBinningProduct/">MetagenomicsBinningProduct</a></td>
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<td>Top-level archive (zip/tar) for binning results stored in MinIO</td>
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<td>no</td>
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</tr>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../MetagenomicsBinningProduct/">MetagenomicsBinningProduct</a></td>
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<td>Top-level archive (zip/tar) for binning results stored in MinIO</td>
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<td><a href="../MetagenomicsGenePhylogenyProduct/">MetagenomicsGenePhylogenyProduct</a></td>
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<td>Top-level archive for gene-based phylogeny outputs (zip/tar stored in MinIO)</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../MetagenomicsGenePhylogenyProduct/">MetagenomicsGenePhylogenyProduct</a></td>
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<td>Top-level archive for gene-based phylogeny outputs (zip/tar stored in MinIO)</td>
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<td><a href="../MetagenomicsProduct/">MetagenomicsProduct</a></td>
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<td>Abstract base for all metagenomics data products</td>
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<td>no</td>
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</tr>
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‎elements/agitation_speed_rpm/index.html‎

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</thead>
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<tr>
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<td><a href="../HasIncubationConditions/">HasIncubationConditions</a></td>
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<td>Mixin for activities/setups that involve controlled incubation</td>
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<td><a href="../PlateSetupActivity/">PlateSetupActivity</a></td>
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<td>Abstract base for 96-well plate setup activities</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../PreCultureGrowth/">PreCultureGrowth</a></td>
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<td>Growth of a pre-culture to establish viable inoculum before</td>
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<td><a href="../EcoplatePlateSetupActivity/">EcoplatePlateSetupActivity</a></td>
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<td>Ecoplate-specific plate setup</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../EcoplatePlateSetupActivity/">EcoplatePlateSetupActivity</a></td>
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<td>Ecoplate-specific plate setup</td>
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<td><a href="../StrainPurity/">StrainPurity</a></td>
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<td>Purity check of a strain culture</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../PlateSetupActivity/">PlateSetupActivity</a></td>
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<td>Abstract base for 96-well plate setup activities</td>
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<td><a href="../StockCulturePreparation/">StockCulturePreparation</a></td>
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<td>Preparation of a stock culture from user samples for long-term storage</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../ExperimentalCulture/">ExperimentalCulture</a></td>
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<td>Growth of an experimental culture for downstream analysis</td>
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<td><a href="../PreCultureGrowth/">PreCultureGrowth</a></td>
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<td>Growth of a pre-culture to establish viable inoculum before</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../CultureGrowth/">CultureGrowth</a></td>
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<td>Abstract activity for growing cultures from samples or other cultures</td>
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<td><a href="../HasIncubationConditions/">HasIncubationConditions</a></td>
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<td>Mixin for activities/setups that involve controlled incubation</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../AMP2PlateSetupActivity/">AMP2PlateSetupActivity</a></td>
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<td>AMP2-specific plate setup</td>
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<td><a href="../ExperimentalCulture/">ExperimentalCulture</a></td>
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<td>Growth of an experimental culture for downstream analysis</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../StockCulturePreparation/">StockCulturePreparation</a></td>
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<td>Preparation of a stock culture from user samples for long-term storage</td>
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<td><a href="../AMP2PlateSetupActivity/">AMP2PlateSetupActivity</a></td>
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<td>AMP2-specific plate setup</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../StrainPurity/">StrainPurity</a></td>
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<td>Purity check of a strain culture</td>
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<td><a href="../CultureGrowth/">CultureGrowth</a></td>
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<td>Abstract activity for growing cultures from samples or other cultures</td>
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<td>no</td>
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</tr>
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</tbody>

‎elements/agrochem_addition/index.html‎

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</thead>
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<tbody>
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<tr>
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<td><a href="../SoilSample/">SoilSample</a></td>
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<td>A sample of soil collected from the environment</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../MonetSoilSample/">MonetSoilSample</a></td>
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<td>A soil sample that has been collected according to the MONet soil sampling pr...</td>
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<td>no</td>
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<td>A sample that does not fit into any of the other described sample types</td>
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<td>no</td>
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</tr>
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<td><a href="../SoilSample/">SoilSample</a></td>
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<td>A sample of soil collected from the environment</td>
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<td>no</td>
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</tr>
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</tbody>
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</table>
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<h2 id="properties">Properties</h2>

‎elements/air_temp_regm/index.html‎

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</thead>
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<tr>
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<td><a href="../OtherUndescribedSample/">OtherUndescribedSample</a></td>
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<td>A sample that does not fit into any of the other described sample types</td>
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<td><a href="../SoilSample/">SoilSample</a></td>
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<td>A sample of soil collected from the environment</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../MixedCultureSample/">MixedCultureSample</a></td>
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<td>A sample containing multiple cultured organisms</td>
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<td><a href="../OtherUndescribedSample/">OtherUndescribedSample</a></td>
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<td>A sample that does not fit into any of the other described sample types</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../PureCultureSample/">PureCultureSample</a></td>
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<td>A sample of a culture containing a single organism</td>
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<td><a href="../WaterSample/">WaterSample</a></td>
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<td>A sample of water collected from the environment</td>
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<td>no</td>
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</tr>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../TerraformSample/">TerraformSample</a></td>
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<td>A sample collected from a Terraform experiment</td>
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<td><a href="../MixedCultureSample/">MixedCultureSample</a></td>
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<td>A sample containing multiple cultured organisms</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../AerosolArmSample/">AerosolArmSample</a></td>
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<td>An aerosol sample collected by the ARM facility</td>
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<td><a href="../AerosolSample/">AerosolSample</a></td>
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<td>An aerosol sample collected from the environment</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../WaterSample/">WaterSample</a></td>
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<td>A sample of water collected from the environment</td>
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<td><a href="../PureCultureSample/">PureCultureSample</a></td>
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<td>A sample of a culture containing a single organism</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../CultureEnvironmentalSample/">CultureEnvironmentalSample</a></td>
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<td>A sample containing organisms cultured from an environmental sample</td>
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<td><a href="../AerosolArmSample/">AerosolArmSample</a></td>
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<td>An aerosol sample collected by the ARM facility</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../AerosolSample/">AerosolSample</a></td>
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<td>An aerosol sample collected from the environment</td>
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<td><a href="../PlantSample/">PlantSample</a></td>
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<td>A sample containing plant material</td>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../PlantSample/">PlantSample</a></td>
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<td>A sample containing plant material</td>
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<td><a href="../CultureEnvironmentalSample/">CultureEnvironmentalSample</a></td>
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<td>A sample containing organisms cultured from an environmental sample</td>
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<td>no</td>
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</tr>
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<tr>
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<td>no</td>
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</tr>
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<tr>
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<td><a href="../SoilSample/">SoilSample</a></td>
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<td>A sample of soil collected from the environment</td>
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<td><a href="../TerraformSample/">TerraformSample</a></td>
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<td>A sample collected from a Terraform experiment</td>
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<td>no</td>
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</tr>
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</tbody>

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