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Building Block Types

last updated at 2023-02-15

Swate and the ARC feature a set of six defined Building Block types. They can be split into input, descriptive and output Building Blocks and you can find additional information on the nfdi4plant website.

Input Building Block/Source Name

Definition: This is the only input column type and each Annotation Table MUST contain this column once.

Expected Values: Unique identifier for input.

Examples:

Example | Sample pooling.

Source Name Parameter [...] Sample Name
MinimalChlamy1 ... MinimalChlamyHarvested1
MinimalChlamy2 ... MinimalChlamyHarvested1
MinimalChlamy3 ... MinimalChlamyHarvested2
MinimalChlamy4 ... MinimalChlamyHarvested2

Example | From physical sample to data file.

Source Name Parameter [...] Data File Name
MinimalChlamyProteins1 ... minimal1.mzLite
MinimalChlamyProteins2 ... minimal2.mzLite
MinimalChlamyProteins3 ... minimal3.mzLite
MinimalChlamyProteins4 ... minimal4.mzLite

Example | From data file to data file.

Source Name Parameter [...] Data File Name
minimal1.mzLite ... minimal1.prot
minimal2.mzLite ... minimal2.prot
minimal3.mzLite ... minimal3.prot
minimal4.mzLite ... minimal4.prot


Descriptive Building Blocks

General Definition:

Additional in-depth information.

About Table Headers

About Table Body
Parameter [temperature] Unit Term Source REF (PATO:0000146) Term Accession Number (PATO:0000146)
12,00 degree Celsius degree Celsius UO http://purl.obolibrary.org/obo/UO_0000027
Parameter [instrument model] Term Source REF (MS:1000031) Term Accession Number (MS:1000031)
SCIEX instrument model MS http://purl.obolibrary.org/obo/MS_1000121
Parameter [instrument model] Term Source REF (MS:1000031) Term Accession Number (MS:1000031)
free text input user-specific user-specific
Parameter [day light exposure] Unit Term Source REF (PECO:0007163) Term Accession Number (PECO:0007163)
12,00 bananas bananas user-specific user-specific


Parameter

Definition: Any workflow parameters defining the exact workflow.

Expected Values: MAY be any from text, integer or float numbers with or without unit.

Examples

Centrifugation Time

Example | Centrifugation Time.

Parameter [Centrifugation Time] Unit Term Source REF (NCIT:C178881) Term Accession Number (NCIT:C178881)
1,00 minute minute UO http://purl.obolibrary.org/obo/UO_0000031

Example | Free text input.

Parameter [Very important unknown parameter] Term Source REF () Term Accession Number ()
very important unknown value user-specific user-specific


Component

Definition: Aynthing physical, which can also be used up during the experiment, e.g. instrument names, software names, and reagents names.

Expected Values: MAY be any from text, integer or float numbers with or without unit.

Examples

Example | Instrument Model.

Component [instrument model] Term Source REF (MS:1000031) Term Accession Number (MS:1000031)
SCIEX instrument model MS http://purl.obolibrary.org/obo/MS_1000121


Factor

Definition: While Parameter and Characteristic will be used to describe so called controlled variables, Factor MUST be used to describe independent variable of your experiment

Example: Effect of fertilizer on plant growths. In a study measuring the influence of different quantities of fertilizer on plant growth, the independent variable would be the amount of fertilizer used. The dependent variable would be the growth in height or mass of the plant. The controlled variables would be the type of plant, the type of fertilizer, the amount of sunlight the plant gets, the size of the pots, etc. (source)

Expected Values: MAY be any from text, integer or float numbers with or without unit.

Examples

Example | Temperature.

Source Name Factor [temperature] Parameter [biological replicate] Sample Name
plant1 10.00 degree Celsius 1 extract1
plant2 10.00 degree Celsius 1 extract2
plant3 10.00 degree Celsius 1 extract3
plant4 28.00 degree Celsius 2 extract4
plant5 28.00 degree Celsius 2 extract5
plant6 28.00 degree Celsius 2 extract6

Extended table.

Source Name Factor [temperature] Unit Term Source REF (PATO:0000146) Term Accession Number (PATO:0000146) Parameter [biological replicate] Term Source REF (MS:1001809) Term Accession Number (MS:1001809) Sample Name
plant1 10,00 degree Celsius degree Celsius UO http://purl.obolibrary.org/obo/UO_0000027 1 user-specific user-specific extract1
plant2 10,00 degree Celsius degree Celsius UO http://purl.obolibrary.org/obo/UO_0000027 1 user-specific user-specific extract2
plant3 10,00 degree Celsius degree Celsius UO http://purl.obolibrary.org/obo/UO_0000027 1 user-specific user-specific extract3
plant4 28,00 degree Celsius degree Celsius UO http://purl.obolibrary.org/obo/UO_0000027 2 user-specific user-specific extract4
plant5 28,00 degree Celsius degree Celsius UO http://purl.obolibrary.org/obo/UO_0000027 2 user-specific user-specific extract5
plant6 28,00 degree Celsius degree Celsius UO http://purl.obolibrary.org/obo/UO_0000027 2 user-specific user-specific extract6


Characteristic

Definition: Any workflow parameters describing the source sample.

Expected Values: MAY be any from text, integer or float numbers with or without unit.

Examples

Example | Plant Growth template.

Characteristics [Organism part] Characteristics [age] Characteristics [Developmental Stage]
Leaf 28 days after germination Mature
Leaf 28 days after germination Mature
Leaf 28 days after germination Mature
Leaf 28 days after germination Mature
Leaf 28 days after germination Mature
Leaf 28 days after germination Mature

Extended table.

Characteristics [Organism part] Term Source REF (DPBO:0000032) Term Accession Number (DPBO:0000032) Characteristics [age] Term Source REF (DPBO:0000033) Term Accession Number (DPBO:0000033) Characteristics [Developmental Stage] Term Source REF (DPBO:0000070) Term Accession Number (DPBO:0000070)
Leaf PO http://purl.obolibrary.org/obo/PO_0025034 28 days after germination user-specific user-specific Mature user-specific user-specific
Leaf PO http://purl.obolibrary.org/obo/PO_0025034 28 days after germination user-specific user-specific Mature user-specific user-specific
Leaf PO http://purl.obolibrary.org/obo/PO_0025034 28 days after germination user-specific user-specific Mature user-specific user-specific
Leaf PO http://purl.obolibrary.org/obo/PO_0025034 28 days after germination user-specific user-specific Mature user-specific user-specific
Leaf PO http://purl.obolibrary.org/obo/PO_0025034 28 days after germination user-specific user-specific Mature user-specific user-specific
Leaf PO http://purl.obolibrary.org/obo/PO_0025034 28 days after germination user-specific user-specific Mature user-specific user-specific


Protocol Columns

These columns have been added to better support conversion to endpoint repositories.

Protocol Type

Definition: The type of protocol described with the assay. This building block is handled by Swate as a descriptive building block.

Expected Values: MUST be a Protocol Type child term.

Examples

Example | Growth Protocol.

Protocol Type Term Source REF (DPBO:1000161) Term Accession Number (DPBO:1000161)
growth protocol DPBO http://purl.obolibrary.org/obo/DPBO_1000162


Protocol REF

Definition: The name of the protocol. By default the name is inferred by the name of the Excel worksheet. To circumvent some limitations (lenght, etc.) we also offer this column as alternative. This building block comprises only one column.

Expected Values: MUST be string.

Output Building Blocks

General Definition: Each Annotation Table MUST contain exactly one output column.

Expected Values: as in Source Name.

Examples: as in Source Name.

Sample Name

Definition: Use this building block type to reference any samples your experimental workflow produced.

Raw Data File

Definition: Use this building block type to reference any untransformed and unprocessed samples you have produced.

Derived Data File

Definition: Use this building block type to reference any samples your computational workflow produced.

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