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Building Block Types

last updated at 2024-04-25

Swate and the ARC feature a set of defined building block types. They can be split into input, descriptive and output building blocks and you can find additional information on the DataPLANT website and the ISA-XLSX specification. Additionally, different protocol columns are available to facilitate submission to endpoint repositories.

Input Building Block

Definition: Each Annotation Table MUST contain ONE Input column, which defines the input of your annotation table. Different input types can be selected, which include Source name, Sample name, Material, Raw Data File, Derived Data File and Image File.

Expected Values: Unique identifier for input.

Examples:

Example | Sample pooling.

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

Example | From physical sample to data file.

Input Sample Name Parameter [...] Output Raw Data File
MinimalChlamyProteins1 ... minimal1.mzLite
MinimalChlamyProteins2 ... minimal2.mzLite
MinimalChlamyProteins3 ... minimal3.mzLite
MinimalChlamyProteins4 ... minimal4.mzLite

Example | From data file to data file.

Input Raw Data File Parameter [...] Output Derived Data File
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 TSR (PATO:0000146) TAN (PATO:0000146)
12,00 degree Celsius degree Celsius UO UO:0000027
Component [instrument model] TSR (MS:1000031) TAN (MS:1000031)
SCIEX instrument model MS MS:1000121
Component [instrument model] TSR (MS:1000031) TAN (MS:1000031)
free text input


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

Example | Centrifugation Time.

Parameter [Centrifugation Time] Unit TSR (NCIT:C178881) TAN (NCIT:C178881)
1,00 minute minute UO UO:0000031

Example | Free text input.

Parameter [Very important unknown parameter] TSR () TAN ()
very important unknown value


Component

Definition: Anything 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] TSR (MS:1000031) TAN (MS:1000031)
SCIEX instrument model MS 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 growth. 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.

Input [Source Name] Factor [temperature] Parameter [biological replicate] Output 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.

Input [Source Name] Factor [temperature] Unit TSR (PATO:0000146) TAN (PATO:0000146) Parameter [biological replicate] TSR (MS:1001809) TAN (MS:1001809) Output Sample Name
plant1 10,00 degree Celsius degree Celsius UO UO:0000027 1 extract1
plant2 10,00 degree Celsius degree Celsius UO UO:0000027 1 extract2
plant3 10,00 degree Celsius degree Celsius UO UO:0000027 1 extract3
plant4 28,00 degree Celsius degree Celsius UO UO:0000027 2 extract4
plant5 28,00 degree Celsius degree Celsius UO UO:0000027 2 extract5
plant6 28,00 degree Celsius degree Celsius UO UO:0000027 2 extract6


Characteristic

Definition: Any characteristics describing the source sample.

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

Examples

Example | Plant Growth template.

Characteristic [Organism part] Characteristic [age] Characteristic [plant structure development 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.

Characteristic [Organism part] TSR (DPBO:0000032) TAN (DPBO:0000032) Characteristic [age] TSR (DPBO:0000033) TAN (DPBO:0000033) Characteristic [plant structure development stage] TSR (PO:0009012) TAN (PO:0009012)
Leaf PO PO:0025034 28 days after germination Mature
Leaf PO PO:0025034 28 days after germination Mature
Leaf PO PO:0025034 28 days after germination Mature
Leaf PO PO:0025034 28 days after germination Mature
Leaf PO PO:0025034 28 days after germination Mature
Leaf PO PO:0025034 28 days after germination Mature


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 string, in the form of free text or an ontology term.

Examples

Example | Growth Protocol.

Protocol Type TSR () TAN ()
growth protocol DPBO DPBO:1000162


Protocol REF

Definition: The name of the protocol. This building block comprises only one column.

Expected Values: MUST be string.

Output Building Block

General Definition: Each annotation table MUST contain exactly one Output column.

Expected Values: as in Input.

Examples: as in Input.

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 data files you have produced.

Derived Data File

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

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