Class: XRDPhaseProduct
X-ray Diffraction (XRD) mineral phase identification and quantification data.
One row per sample with columns for each mineral phase identified.
__
Follows the wide-format pattern with individual weight percent columns.
Individual QC flags for each mineral using ProcessedDataFlag enum.
__
Relationship to core tables:
_ - id: FK -> processedData.id (1:1 linkage)_
_ - processedData.type = 'XRDPhaseProduct'_
_ - processedData.workflow_id -> DataProcessingActivity if Rietveld refinement_
_ is computational; NULL if manual/semi-quantitative_
_ - processedData.summary_metrics = {"quartz_percent":42, "albite_percent":18, ...}_
_ - processedData.s3_key = diffractogram .xy, .xrdml, or .raw file in MinIO_
__
Standard soil mineral panel (10 major phases):
_ Primary minerals: quartz, albite, microcline_
_ Phyllosilicates: muscovite, kaolinite, chlorite_
_ Amphiboles: hornblende_
_ Sulfides and evaporites: pyrite, halite, gypsum_
__
Quantification methods:
_ - Rietveld refinement (computational, most accurate)_
_ - Reference intensity ratio (RIR) method_
_ - Semi-quantitative (manual, less precise)_
__
Computational processing workflow (if applicable):
_ XRDDataGenerationActivity acquires raw diffractogram ->_
_ DataProcessingActivity (type='xrd_rietveld_refinement') processes with_
_ HighScore Plus, GSAS-II, or FullProf ->_
_ XRDPhaseProduct (workflow_id points to refinement WEA)_
_ _
_ workflow_steps JSONB example:_
_ {"software": "HighScore_Plus", "version": "5.1", "method": "Rietveld",_
_ "r_factor": 0.042, "gof": 1.8, "amorphous_content_pct": 12}_
__
Required enum additions to enums.yaml:
_ product:_
_ XRDPhaseProduct: # Add to product permissible_values_
URI: basalt_schema:XRDPhaseProduct
classDiagram
class XRDPhaseProduct
click XRDPhaseProduct href "../XRDPhaseProduct/"
XRayDataProduct <|-- XRDPhaseProduct
click XRayDataProduct href "../XRayDataProduct/"
XRDPhaseProduct : albite_percent
XRDPhaseProduct : chlorite_percent
XRDPhaseProduct : core_section
XRDPhaseProduct --> "0..1" CoreSectionEnum : core_section
click CoreSectionEnum href "../CoreSectionEnum/"
XRDPhaseProduct : description
XRDPhaseProduct : filesize
XRDPhaseProduct : flag_albite
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_albite
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_chlorite
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_chlorite
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_gypsum
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_gypsum
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_halite
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_halite
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_hornblende
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_hornblende
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_kaolinite
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_kaolinite
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_microcline
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_microcline
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_muscovite
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_muscovite
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_pyrite
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_pyrite
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : flag_quartz
XRDPhaseProduct --> "0..1" ProcessedDataFlag : flag_quartz
click ProcessedDataFlag href "../ProcessedDataFlag/"
XRDPhaseProduct : gypsum_percent
XRDPhaseProduct : halite_percent
XRDPhaseProduct : hornblende_percent
XRDPhaseProduct : id
XRDPhaseProduct : kaolinite_percent
XRDPhaseProduct : lims_barcode
XRDPhaseProduct : md5checksum
XRDPhaseProduct : measure_type
XRDPhaseProduct --> "0..1" ProductMeasureType : measure_type
click ProductMeasureType href "../ProductMeasureType/"
XRDPhaseProduct : microcline_percent
XRDPhaseProduct : muscovite_percent
XRDPhaseProduct : name
XRDPhaseProduct : project
XRDPhaseProduct : pyrite_percent
XRDPhaseProduct : quartz_percent
XRDPhaseProduct : s3_base_url
XRDPhaseProduct : s3_bucket
XRDPhaseProduct : s3_key
XRDPhaseProduct : sample_id
XRDPhaseProduct --> "0..1" Sample : sample_id
click Sample href "../Sample/"
XRDPhaseProduct : sample_name
XRDPhaseProduct : sampling_set
XRDPhaseProduct : summary_metrics
Inheritance
- DataProduct
- ProcessedData
- XRayDataProduct
- XRDPhaseProduct
- XRayDataProduct
- ProcessedData
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| measure_type | 0..1 ProductMeasureType |
Whether the measurement recorded is a single measurement, one of a set of re... | direct |
| quartz_percent | 0..1 Float |
Quartz (SiO2) weight percent | direct |
| albite_percent | 0..1 Float |
Albite (NaAlSi3O8) weight percent | direct |
| microcline_percent | 0..1 Float |
Microcline (KAlSi3O8) weight percent | direct |
| muscovite_percent | 0..1 Float |
Muscovite (KAl2(AlSi3O10)(OH)2) weight percent | direct |
| kaolinite_percent | 0..1 Float |
Kaolinite (Al2Si2O5(OH)4) weight percent | direct |
| chlorite_percent | 0..1 Float |
Chlorite ((Mg,Fe)3(Si,Al)4O10(OH)2 (Mg,Fe)3(OH)6) weight percent | direct |
| hornblende_percent | 0..1 Float |
Hornblende (Ca,Na)2-3(Mg,Fe,Al)5(Al,Si)8O22(OH)2 weight percent | direct |
| pyrite_percent | 0..1 Float |
Pyrite (FeS2) weight percent | direct |
| halite_percent | 0..1 Float |
Halite (NaCl) weight percent | direct |
| gypsum_percent | 0..1 Float |
Gypsum (CaSO4 2H2O) weight percent | direct |
| flag_quartz | 0..1 ProcessedDataFlag |
direct | |
| flag_albite | 0..1 ProcessedDataFlag |
direct | |
| flag_microcline | 0..1 ProcessedDataFlag |
direct | |
| flag_muscovite | 0..1 ProcessedDataFlag |
direct | |
| flag_kaolinite | 0..1 ProcessedDataFlag |
direct | |
| flag_chlorite | 0..1 ProcessedDataFlag |
direct | |
| flag_hornblende | 0..1 ProcessedDataFlag |
direct | |
| flag_pyrite | 0..1 ProcessedDataFlag |
direct | |
| flag_halite | 0..1 ProcessedDataFlag |
direct | |
| flag_gypsum | 0..1 ProcessedDataFlag |
direct | |
| summary_metrics | 0..1 String |
Lightweight per-product summary for common queries that avoid full file downl... | ProcessedData |
| lims_barcode | 0..1 String |
LIMS barcode identifier | ProcessedData |
| sample_id | 0..1 Sample |
Link back to the originating sample | ProcessedData |
| name | 1 String |
Human-readable name for the entity or activity | DataProduct |
| description | 0..1 String |
Human-readable description for the entity or activity | DataProduct |
| project | 0..1 Integer |
Identifier for the user project associated with the entity or activity | DataProduct |
| sampling_set | 0..1 Integer |
Sampling set number for grouping related samples collected together | DataProduct |
| core_section | 0..1 CoreSectionEnum |
The section of the core | DataProduct |
| sample_name | 0..1 String |
The name or label that is present on the shipped sample | DataProduct |
| s3_base_url | 0..1 String |
DataProduct | |
| s3_bucket | 0..1 String |
DataProduct | |
| s3_key | 1 String |
MinIO/S3 object key; required for all data products | DataProduct |
| filesize | 0..1 Integer |
Size of the file in bytes | DataProduct |
| md5checksum | 0..1 String |
DataProduct | |
| id | 1 Uuid |
DataProduct |
Identifier and Mapping Information
Schema Source
- from schema: https://EMSL-Computing.github.io/BASALT-Schema
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | basalt_schema:XRDPhaseProduct |
| native | basalt_schema:XRDPhaseProduct |
LinkML Source
Direct
name: XRDPhaseProduct
description: "X-ray Diffraction (XRD) mineral phase identification and quantification\
\ data.\nOne row per sample with columns for each mineral phase identified.\n\n\
Follows the wide-format pattern with individual weight percent columns.\nIndividual\
\ QC flags for each mineral using ProcessedDataFlag enum.\n\nRelationship to core\
\ tables:\n - id: FK -> processedData.id (1:1 linkage)\n - processedData.type\
\ = 'XRDPhaseProduct'\n - processedData.workflow_id -> DataProcessingActivity if\
\ Rietveld refinement\n is computational; NULL if manual/semi-quantitative\n\
\ - processedData.summary_metrics = {\"quartz_percent\":42, \"albite_percent\"\
:18, ...}\n - processedData.s3_key = diffractogram .xy, .xrdml, or .raw file in\
\ MinIO\n\nStandard soil mineral panel (10 major phases):\n Primary minerals: quartz,\
\ albite, microcline\n Phyllosilicates: muscovite, kaolinite, chlorite\n Amphiboles:\
\ hornblende\n Sulfides and evaporites: pyrite, halite, gypsum\n\nQuantification\
\ methods:\n - Rietveld refinement (computational, most accurate)\n - Reference\
\ intensity ratio (RIR) method\n - Semi-quantitative (manual, less precise)\n\n\
Computational processing workflow (if applicable):\n XRDDataGenerationActivity\
\ acquires raw diffractogram ->\n DataProcessingActivity (type='xrd_rietveld_refinement')\
\ processes with\n HighScore Plus, GSAS-II, or FullProf ->\n XRDPhaseProduct (workflow_id\
\ points to refinement WEA)\n \n workflow_steps JSONB example:\n {\"software\"\
: \"HighScore_Plus\", \"version\": \"5.1\", \"method\": \"Rietveld\",\n \"r_factor\"\
: 0.042, \"gof\": 1.8, \"amorphous_content_pct\": 12}\n\nRequired enum additions\
\ to enums.yaml:\n product:\n XRDPhaseProduct: # Add to product permissible_values"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: XRayDataProduct
slots:
- measure_type
attributes:
quartz_percent:
name: quartz_percent
description: Quartz (SiO2) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
albite_percent:
name: albite_percent
description: Albite (NaAlSi3O8) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
microcline_percent:
name: microcline_percent
description: Microcline (KAlSi3O8) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
muscovite_percent:
name: muscovite_percent
description: Muscovite (KAl2(AlSi3O10)(OH)2) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
kaolinite_percent:
name: kaolinite_percent
description: Kaolinite (Al2Si2O5(OH)4) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
chlorite_percent:
name: chlorite_percent
description: Chlorite ((Mg,Fe)3(Si,Al)4O10(OH)2 (Mg,Fe)3(OH)6) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
hornblende_percent:
name: hornblende_percent
description: Hornblende (Ca,Na)2-3(Mg,Fe,Al)5(Al,Si)8O22(OH)2 weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
pyrite_percent:
name: pyrite_percent
description: Pyrite (FeS2) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
halite_percent:
name: halite_percent
description: Halite (NaCl) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
gypsum_percent:
name: gypsum_percent
description: Gypsum (CaSO4 2H2O) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: float
flag_quartz:
name: flag_quartz
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_albite:
name: flag_albite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_microcline:
name: flag_microcline
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_muscovite:
name: flag_muscovite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_kaolinite:
name: flag_kaolinite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_chlorite:
name: flag_chlorite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_hornblende:
name: flag_hornblende
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_pyrite:
name: flag_pyrite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_halite:
name: flag_halite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_gypsum:
name: flag_gypsum
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
Induced
name: XRDPhaseProduct
description: "X-ray Diffraction (XRD) mineral phase identification and quantification\
\ data.\nOne row per sample with columns for each mineral phase identified.\n\n\
Follows the wide-format pattern with individual weight percent columns.\nIndividual\
\ QC flags for each mineral using ProcessedDataFlag enum.\n\nRelationship to core\
\ tables:\n - id: FK -> processedData.id (1:1 linkage)\n - processedData.type\
\ = 'XRDPhaseProduct'\n - processedData.workflow_id -> DataProcessingActivity if\
\ Rietveld refinement\n is computational; NULL if manual/semi-quantitative\n\
\ - processedData.summary_metrics = {\"quartz_percent\":42, \"albite_percent\"\
:18, ...}\n - processedData.s3_key = diffractogram .xy, .xrdml, or .raw file in\
\ MinIO\n\nStandard soil mineral panel (10 major phases):\n Primary minerals: quartz,\
\ albite, microcline\n Phyllosilicates: muscovite, kaolinite, chlorite\n Amphiboles:\
\ hornblende\n Sulfides and evaporites: pyrite, halite, gypsum\n\nQuantification\
\ methods:\n - Rietveld refinement (computational, most accurate)\n - Reference\
\ intensity ratio (RIR) method\n - Semi-quantitative (manual, less precise)\n\n\
Computational processing workflow (if applicable):\n XRDDataGenerationActivity\
\ acquires raw diffractogram ->\n DataProcessingActivity (type='xrd_rietveld_refinement')\
\ processes with\n HighScore Plus, GSAS-II, or FullProf ->\n XRDPhaseProduct (workflow_id\
\ points to refinement WEA)\n \n workflow_steps JSONB example:\n {\"software\"\
: \"HighScore_Plus\", \"version\": \"5.1\", \"method\": \"Rietveld\",\n \"r_factor\"\
: 0.042, \"gof\": 1.8, \"amorphous_content_pct\": 12}\n\nRequired enum additions\
\ to enums.yaml:\n product:\n XRDPhaseProduct: # Add to product permissible_values"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: XRayDataProduct
attributes:
quartz_percent:
name: quartz_percent
description: Quartz (SiO2) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: quartz_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
albite_percent:
name: albite_percent
description: Albite (NaAlSi3O8) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: albite_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
microcline_percent:
name: microcline_percent
description: Microcline (KAlSi3O8) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: microcline_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
muscovite_percent:
name: muscovite_percent
description: Muscovite (KAl2(AlSi3O10)(OH)2) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: muscovite_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
kaolinite_percent:
name: kaolinite_percent
description: Kaolinite (Al2Si2O5(OH)4) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: kaolinite_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
chlorite_percent:
name: chlorite_percent
description: Chlorite ((Mg,Fe)3(Si,Al)4O10(OH)2 (Mg,Fe)3(OH)6) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: chlorite_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
hornblende_percent:
name: hornblende_percent
description: Hornblende (Ca,Na)2-3(Mg,Fe,Al)5(Al,Si)8O22(OH)2 weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: hornblende_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
pyrite_percent:
name: pyrite_percent
description: Pyrite (FeS2) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: pyrite_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
halite_percent:
name: halite_percent
description: Halite (NaCl) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: halite_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
gypsum_percent:
name: gypsum_percent
description: Gypsum (CaSO4 2H2O) weight percent
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: gypsum_percent
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: float
flag_quartz:
name: flag_quartz
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_quartz
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_albite:
name: flag_albite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_albite
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_microcline:
name: flag_microcline
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_microcline
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_muscovite:
name: flag_muscovite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_muscovite
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_kaolinite:
name: flag_kaolinite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_kaolinite
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_chlorite:
name: flag_chlorite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_chlorite
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_hornblende:
name: flag_hornblende
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_hornblende
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_pyrite:
name: flag_pyrite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_pyrite
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_halite:
name: flag_halite
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_halite
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
flag_gypsum:
name: flag_gypsum
from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
rank: 1000
alias: flag_gypsum
owner: XRDPhaseProduct
domain_of:
- XRDPhaseProduct
range: ProcessedDataFlag
measure_type:
name: measure_type
description: Whether the measurement recorded is a single measurement, one of
a set of replicate measurements, or an average of several replicate measurements.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: measure_type
owner: XRDPhaseProduct
domain_of:
- BulkDensityProduct
- ElementalAnalysisProduct
- EnzymeProduct
- GWCMoistureProduct
- HydraulicPropertiesProduct
- IonsAnalysisProduct
- MAOMProduct
- MicrobialBiomassProduct
- NitrogenAnalysisProduct
- PhosphorusAnalysisProduct
- RespirationProduct
- TextureProduct
- TomographyProduct
- WEOMProduct
- pHProduct
- XRFElementalProduct
- XRDPhaseProduct
range: ProductMeasureType
summary_metrics:
name: summary_metrics
description: "Lightweight per-product summary for common queries that avoid full\
\ file download.\nDirection: structured key-value pairs; per-type schemas TBD:\n\
\ ecoplate: well-level absorbance summaries (position, timepoint, absorbance)\n\
\ xrf: per-element concentration results + QC flag\n lcms: feature\
\ count, identification count, MSI-2 fraction\nInterim DB storage: JSONB column\
\ retained until formal typed class exists."
todos:
- make this inined/multivalued?
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: summary_metrics
owner: XRDPhaseProduct
domain_of:
- ProcessedData
range: string
required: false
lims_barcode:
name: lims_barcode
description: LIMS barcode identifier
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: lims_barcode
owner: XRDPhaseProduct
domain_of:
- ProcessedData
- Sample
range: string
required: false
sample_id:
name: sample_id
description: Link back to the originating sample
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: sample_id
owner: XRDPhaseProduct
domain_of:
- ProcessedData
- AMP2WellMetadata
- MetagenomicsProduct
range: Sample
required: false
name:
name: name
description: Human-readable name for the entity or activity.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: name
owner: XRDPhaseProduct
domain_of:
- Activity
- Entity
- DataProduct
- DataGenerationActivity
- Instrument
- OntologyClass
- ContainerAxis
- Configuration
- MobilePhaseSegment
- MassSpectrometryStandardRun
- PurchasedMaterial
- LabProcessingActivity
- organism
- Site
- Sample
- SamplingActivity
- SoilSamplingActivity
- Study
- SoftwareControlledTermValue
range: string
required: true
description:
name: description
description: Human-readable description for the entity or activity
title: description
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: description
owner: XRDPhaseProduct
domain_of:
- Activity
- Entity
- DataProduct
- DataGenerationActivity
- DataProcessingActivity
- OntologyClass
- ContainerType
- LabDevice
- Configuration
- MassSpectrometryStandardRun
- PurchasedMaterial
- LabProcessingActivity
- organism
- Site
- Sample
- SamplingActivity
- SoilSamplingActivity
- Study
- TimestampValue
- TextValue
- SoftwareControlledTermValue
- ControlledTermValue
- QuantityValue
range: string
project:
name: project
description: 'Identifier for the user project associated with the entity or activity. '
title: Project
todos:
- should this be an ID? CURIE can use the one NMDC has https://bioregistry.io/reference/emsl.project:60141
where emsl.project is the CURIE prefix
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
aliases:
- study
- study_id
- project_id
- proposal
- proposal_id
rank: 1000
alias: project
owner: XRDPhaseProduct
domain_of:
- DataProduct
- AerosolArmSample
- AerosolSample
- CommerciallyPurchasedSample
- CultureEnvironmentalSample
- FieldDeployedTerraformSample
- MixedCultureSample
- MonetSoilSample
- OtherUndescribedSample
- PlantSample
- PureCultureSample
- SedimentSample
- SoilSample
- SynthesizedMaterialSample
- TerraformSample
- WaterSample
- SamplingActivity
range: integer
sampling_set:
name: sampling_set
description: 'Sampling set number for grouping related samples collected together.
This is a user-defined sequential integer that can be used to link samples collected
in the same sampling event or campaign.'
title: sampling set
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: sampling_set
owner: XRDPhaseProduct
domain_of:
- DataProduct
- MonetSoilSample
range: integer
core_section:
name: core_section
description: The section of the core.
title: core section
examples:
- value: TOP
- value: MID
- value: BTM
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: core_section
owner: XRDPhaseProduct
domain_of:
- DataProduct
- CoreSection
range: CoreSectionEnum
sample_name:
name: sample_name
description: 'The name or label that is present on the shipped sample. This should
be a human readable name.'
title: sample name
notes:
- This is typically an alias for the inherited 'name' slot on Sample classes.
Defined separately for compatibility with source data files using 'sample_name'
column headers.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
aliases:
- samp_name
rank: 1000
alias: sample_name
owner: XRDPhaseProduct
domain_of:
- DataProduct
- AerosolArmSample
- AerosolSample
- CommerciallyPurchasedSample
- CultureEnvironmentalSample
- FieldDeployedTerraformSample
- MixedCultureSample
- MonetSoilSample
- OtherUndescribedSample
- PlantSample
- PureCultureSample
- SedimentSample
- SoilSample
- SynthesizedMaterialSample
- TerraformSample
- WaterSample
range: string
s3_base_url:
name: s3_base_url
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: s3_base_url
owner: XRDPhaseProduct
domain_of:
- DataProduct
range: string
s3_bucket:
name: s3_bucket
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: s3_bucket
owner: XRDPhaseProduct
domain_of:
- DataProduct
range: string
s3_key:
name: s3_key
description: MinIO/S3 object key; required for all data products
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: s3_key
owner: XRDPhaseProduct
domain_of:
- DataProduct
range: string
required: true
filesize:
name: filesize
description: Size of the file in bytes
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: filesize
owner: XRDPhaseProduct
domain_of:
- DataProduct
range: integer
md5checksum:
name: md5checksum
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
rank: 1000
alias: md5checksum
owner: XRDPhaseProduct
domain_of:
- DataProduct
range: string
id:
name: id
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
identifier: true
alias: id
owner: XRDPhaseProduct
domain_of:
- Activity
- Entity
- DataProduct
- DataGenerationActivity
- DataProcessingActivity
- AlternativeIdentifier
- FunctionalAnnotationIdentifier
- Instrument
- OntologyClass
- ContainerType
- Custodian
- InstrumentAlternativeIdentifier
- LabDevice
- SampleProcessing
- ProcessingSampleLink
- Configuration
- MobilePhaseSegment
- MassSpectrometryStandardRun
- PurchasedMaterial
- LabProcessingActivity
- organism
- MAOMProduct
- WEOMProduct
- Site
- Sample
- AerosolArmSample
- AerosolSample
- AMP2UserSample
- CommerciallyPurchasedSample
- CultureEnvironmentalSample
- EngineeredStrainSample
- FieldDeployedTerraformSample
- MixedCultureSample
- MonetSoilSample
- OtherUndescribedSample
- PlantSample
- PureCultureSample
- SedimentSample
- SoilSample
- SynthesizedMaterialSample
- TerraformSample
- WaterSample
- ProcessedSample
- CoreSection
- SamplingActivity
- AerosolArmSamplingActivity
- AerosolSamplingActivity
- CommerciallyPurchasedSamplingActivity
- CultureEnvironmentalSamplingActivity
- EngineeredStrainSamplingActivity
- FieldDeployedTerraformSamplingActivity
- MixedCultureSamplingActivity
- MonetSoilSamplingActivity
- OtherUndescribedSamplingActivity
- PlantSamplingActivity
- PureCultureSamplingActivity
- SedimentSamplingActivity
- SoilSamplingActivity
- SynthesizedMaterialSamplingActivity
- TerraformSamplingActivity
- WaterSamplingActivity
- Study
- ProjectParticipant
- TimestampValue
- TextValue
- SoftwareControlledTermValue
- ControlledTermValue
- PersonValue
- QuantityValue
- ConditioningValue
- zipDownload
range: uuid
required: true