Sample¶

The sample information should provide all relevant facts about each sample and any controls/standards included in the study. There is ONE sample sheet per study.

Sample metadata should include a unique sample name, organism, organism part (for controls use eg. experimental blank and solvent) and sample type (ie. control, QC, experimental sample). Further sample descriptors should be included where available by selecting +Factor to add new columns (eg. Gender, Age, Treatment).

A group of samples can be added to the sample table using +Samples and pasting a list or selecting to import Raw data file names if appropriate. There is also the option to add as many new rows as required with +Rows and edit cells individually. Portal

Example of required information for different Sample types

Column Name	Description	Example 1	Example 2	Example 3	Example 4	Example 5	Example 6	Example 7
Source Name	Unique source identifier of the Sample or simply repeat 'Sample Name’	Single standard	Standard mix	Blank1	QC1	Sample1	QC2	Sample2
Characteristics[Organism]	A living entity	reference compound	reference compound	blank	Homo sapiens	Homo sapiens	Mus musculus	Mus musculus
Term Source REF	Selected ontology	BAO	BAO		NCBITaxon	NCBITaxon	NCBITaxon	NCBITaxon
Term Accession Number	Ontology term URL	http://www.bioassayontology.org/bao#BAO_0002092	http://www.bioassayontology.org/bao#BAO_0002092		http://purl.obolibrary.org/obo/NCBITaxon_9606	http://purl.obolibrary.org/obo/NCBITaxon_9606	http://purl.obolibrary.org/obo/NCBITaxon_10090	http://purl.obolibrary.org/obo/NCBITaxon_10090
Characteristics[Organism Part]	A portion of an organism	pure substance	mixture	solvent	blood plasma	blood plasma	blood plasma	blood plasma
Term Source REF	Selected ontology	CHEBI	CHEBI	CHEBI	BTO	BTO	BTO	BTO
Term Accession Number	Ontology term URL	http://purl.obolibrary.org/obo/CHEBI_60003	http://purl.obolibrary.org/obo/CHEBI_60004	http://purl.obolibrary.org/obo/CHEBI_46787	http://purl.obolibrary.org/obo/BTO_0000131	http://purl.obolibrary.org/obo/BTO_0000131	http://purl.obolibrary.org/obo/BTO_0000131	http://purl.obolibrary.org/obo/BTO_0000131
Characteristics[Variant]	Selected breed, strain, cultivar, etc (if available)						C57BL/6J	C57BL/6J
Term Source REF	Selected ontology						EFO	EFO
Term Accession Number	Ontology term URL						http://www.ebi.ac.uk//efo/EFO_0000606	http://www.ebi.ac.uk//efo/EFO_0000606
Characteristics[Sample type]	Sample role in the experiment	reference compound	reference compound mix	solvent blank	pooled quality control sample	experimental sample	pooled quality control sample	experimental sample
Term Source REF	Selected ontology	MSIO	MSIO	MSIO	MTBLS	CHMO	MTBLS	CHMO
Term Accession Number	Ontology term URL	http://purl.obolibrary.org/obo/MSIO_0000023	http://purl.obolibrary.org/obo/MSIO_0000024	http://purl.obolibrary.org/obo/MSIO_0000026	http://www.ebi.ac.uk/metabolights/ontology/MTBLS_001090	http://purl.obolibrary.org/obo/CHMO_0002746	http://www.ebi.ac.uk/metabolights/ontology/MTBLS_001090	http://purl.obolibrary.org/obo/CHMO_0002746
Protocol REF	Predetermined content: 'Sample Collection'. The example term MUST be present in all rows of this column	Sample collection	Sample collection	Sample collection	Sample collection	Sample collection	Sample collection	Sample collection
Sample Name	Unique identifier from a particular source. Usually associated with an output spectral data filename.	Leucin standard	Standard Mix	Blank1	QC1	Sample1	QC2	Sample2

Validation Rules:¶

Sample columns present in the sample file.
"Sample collection" column completely filled in.
No empty rows in sample file.
Organism and Organism Part characteristics and at least a Factor column are required
Organism name should be at least 5 characters long.
Organism cannot be 'human' or 'man', please choose the 'Homo sapiens' taxonomy term.
Organism cannot be one of the invalid terms.

Invalid organism term: cat, dog, mouse, horse, flower, man, fish, leave, root, mice, steam, bacteria, value, food, matrix, mus, rat, blood, urine, plasma, hair, fur, skin, saliva, fly, unknown.

Factors¶

The standard information captured in a sample sheet includes the organism and part of the organism studied. Each study will then vary in what sample information can be provided as eg. clinic samples may have gender, age and treatment information available and plant samples might have genetic variants and geological locations. This further information which helps to describe samples and to stratify the groups of interest for analysis and statistics is added to sample tables as factors.

Add factor in the sample sheet¶

From the sample section select +Add factor. Type the factor term and use the drop-down to select the most relevant ontology term. If there is no ontology term available, type your free text and press enter to accept (then OK to add to the factor). In the second step you can add a unit if the factor information you are adding includes numerical values, if not simply select add factor in this step.

A new column will then be added to the sample sheet so you can add the relevant information for each sample.

Example on how to add 'Treatment' Factor to Samples Portal

Delete factor column in sample sheet¶

To delete the factor, download the sample file and select to open with eg. Excel, then simply remove the factor related columns and re-upload the modified file. There will be 3-4 columns for each factor; Factor Value[factor_name], Unit (if added), Term source REF, Term accession number.

It is important not to remove the original columns or alter column headers when editing as the format is a fixed requirement.

View factor information¶

A list of all factors added to the study together with the ontology information can be found on the first tab of your study.

View summary of all Factors present in a study in the Descriptors section Portal