Building Block Types

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

• 👀 This example shows a sample pooling, in which two input samples are pooled into one output sample. This can also be done in reverse, where one input can be split into multiple output samples.

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

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

About Table Headers

• The main column MUST start with Parameter, Characteristic, Component or Factor. This MUST be followed by squared brackets containing a Term name ([term name]). An exception to this rule are so called featured building blocks which are handled just like descriptive building blocks. They have 3 or 4 columns and can be used for relationship-directed term search. An example would be Protocol Type.
• The columns of a building block MUST always be in the following order: main column, unit column (optional), Term Source REF (TSR), Term Accession Number (TAN).
• Unit column headers MUST start with Unit .
• The Term Source REF column header MUST start with TSR , followed by a bracket which MUST contain the short term identifier for the main column, if existing.
  • Example: Parameter [instrument model] is the main column, then TSR (MS:1000031) must be the Term Source REF.
  • Example free text input: If the main column was created with free text input, such as Characteristic [free text input], the Term Source REF MUST be created with an empty bracket TSR ().
• The Term Accession Number column header MUST follow the same rules as Term Source REF column headers, with the only difference to replace TSR with TAN .

• The table body for a main column with unit MUST have the unit as custom number format. This has to be done in the following format 0,00 "unit term name".
• Any building block MAY contain an ontology term as value or free text input.
• If a building block has a unit, the unit term name MUST be written in the unit column. In this case, unit term source ontology and the unit term identifier must be written in the TSR and TAN column.

• If a building block contains an existing ontology term, it MUST contain the source ontology name under TSR and the term identifier under TAN.

• In the case of any free text input the TSR and TAN columns will stay empty.

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

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

• 👀 This example shows free text input. If you cannot find any fitting ontology term for either/both building block or value you can simply insert free text input. The above table shows how such input would be inserted into an annotation table.

Component [instrument model]	TSR (MS:1000031)	TAN (MS:1000031)
SCIEX instrument model	MS	MS:1000121

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

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

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