Building Block Types

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

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

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

Source Name	Parameter [...]	Data File Name
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.
  • In the abstract case we have for example Parameter and Factor with the same Term, only the reference columns would not be unique, in this case we add a id to the reference columns, as excel does not allow non-unique column headers: Add the #number to all reference column headers, such as: Component [instrument model], Term Source REF (MS:1000031#2), Term Accession Number (MS:1000031#2). #number must be an positive integer.
• The columns of a building block MUST always be in the following order: main column, unit column (optional), Term Source REF, Term Accession Number.
• Unit column headers MUST start with Unit and be made unique with a (#number), such as Unit, Unit (#1), Unit (#2), Unit (#42). They MAY use ascending numbers. #number must be an positive integer.
• The Term Source REF column header MUST start with Term Source REF , 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 Term Source REF (MS:1000031) must be the Term Source REF.
  • Example free text input. If the main column was created with free text input, such as Characteristics [free text input], the Term Source REF MUST be created with an empty bracket Term Source REF (). In this case, headers MUST be made unique, by adding #number in the empty brackets. For example Parameter [free text input], Term Source REF (), .. and Parameter [another one], Term Source REF (#2), .. .
• The Term Accession Number column header MUST follow the same rules as Term Source REF column headers, with the only difference to replace Term Source REF with Term Accession Number .

• 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 a Term as value or free text input.
• If a building block has an unit, the unit term name MUST be written in the unit column. In this case unit term source ontology and purl.obolibrary.org link must be written in Term Source REF and Term Accession Number.

• If a building block contains an existing Term it MUST contain the source ontology name under Term Source REF and a purl.obolibrary.org link under Term Accession Number. The link must be created, such as http://purl.obolibrary.org/obo/{ontology identifier}, where {ontology identifier} MUST be replaced with the term unique identifier, with an underscore instead of a colon.
  • Example: SCIEX instrument model (MS:1000121) would result in http://purl.obolibrary.org/obo/MS_1000121
  • Full example:

• In the case of any free text input all missing information MUST be filled with user-specific. Example:

• Example with unit free text input:

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

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

• 👀 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.
• If you use Add Building Block or/and Term search to insert your free text input, Swate will handle all formatting for you.

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

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

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

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