minimum - Sample File Field Controls¶
Common¶
| Attribute | Value |
|---|---|
| Rule Name | default-sample-file-rule-01 |
| Rule Description | default |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | any-ontology-term |
| Recommended Ontologies [Ordered] | OBI, EFO, CHMO, NCBITaxon, NCIT, MS, BTO, CHEBI, UO, MESH, BAO, OMIT, GO, ENVO, MSIO, PO, MONDO, UBERON, SNOMED, CL, CLO, MI, EDAM, HP, MP |
| Allowed Placeholders | [MTBLS, http://www.ebi.ac.uk/metabolights/ontology/placeholder], [, ] |
| Allowed Other Sources | [MTBLS, http://www.ebi.ac.uk/metabolights/ontology/MTBLS_], [wikidata, https://www.wikidata.org/wiki/], [ILX, http://uri.interlex.org/base/ilx_] |
| Unexpected Terms | unknown, undefined, n/a, na, not applicable, not available, none, null, nill, not specified, not provided, -, --, ---, _, . |
| Unexpected Term Enforcement Level | required |
Factor Value (Common)¶
| Attribute | Value |
|---|---|
| Rule Name | default-sample-factor_value-rule-01 |
| Rule Description | default |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | any-ontology-term |
| Recommended Ontologies [Ordered] | OBI, EFO, CHMO, NCIT, NCBITaxon, MS, BTO, CHEBI, UO, MESH, BAO, OMIT, GO, ENVO, MSIO, PO, MONDO, UBERON, SNOMED, CL, CLO, MI, EDAM, HP, MP |
| Allowed Placeholders | [MTBLS, http://www.ebi.ac.uk/metabolights/ontology/placeholder] |
| Allowed Other Sources | [MTBLS, http://www.ebi.ac.uk/metabolights/ontology/MTBLS_], [wikidata, https://www.wikidata.org/wiki/], [ILX, http://uri.interlex.org/base/ilx_] |
Characteristic (Common)¶
| Attribute | Value |
|---|---|
| Rule Name | default-sample-characteristic-rule-01 |
| Rule Description | default |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | ontology-term-in-selected-ontologies |
| Ontologies [Ordered] | OBI, EFO, CHMO, NCBITaxon, NCIT, MS, BTO, CHEBI, UO, MESH, BAO, OMIT, GO, ENVO, MSIO, PO, MONDO, UBERON, SNOMED, CL, CLO, MI, EDAM, HP, MP |
| Allowed Placeholders | [MTBLS, http://www.ebi.ac.uk/metabolights/ontology/placeholder] |
| Allowed Other Sources | [wikidata, https://www.wikidata.org/wiki/], [ILX, http://uri.interlex.org/base/ilx_] |
Unit¶
| Attribute | Value |
|---|---|
| Rule Name | Sample-Unit-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | child-ontology-term |
| Allowed Parent Ontology Terms | [unit, UO, http://purl.obolibrary.org/obo/UO_0000000], [unit, EFO, http://purl.obolibrary.org/obo/UO_0000000], [Qualifier, NCIT, http://purl.obolibrary.org/obo/NCIT_C41009], [Unit of Measure, NCIT, http://purl.obolibrary.org/obo/NCIT_C25709] |
| Allowed Parent Ontology Term Exceptions | ^.unit$, ^.Unit of.*$ |
| Allowed Other Sources | [wikidata, https://www.wikidata.org/wiki/], [ILX, http://uri.interlex.org/base/ilx_] |
| Ontology Term Enforcement Level | recommended |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | kelvin | UO | http://purl.obolibrary.org/obo/UO_0000012 |
| 2 | tesla | UO | http://purl.obolibrary.org/obo/UO_0000228 |
| 3 | micrometer | UO | http://purl.obolibrary.org/obo/UO_0000017 |
| 4 | millimolar | UO | http://purl.obolibrary.org/obo/UO_0000063 |
| 5 | meter | UO | http://purl.obolibrary.org/obo/UO_0000008 |
| 6 | kilogram | UO | http://purl.obolibrary.org/obo/UO_0000009 |
| 7 | milligram per day | EFO | http://www.ebi.ac.uk/efo/EFO_0004419 |
| 8 | day | UO | http://purl.obolibrary.org/obo/UO_0000033 |
| 9 | hour | UO | http://purl.obolibrary.org/obo/UO_0000032 |
| 10 | minute | UO | http://purl.obolibrary.org/obo/UO_0000031 |
| 11 | degree Fahrenheit | UO | http://purl.obolibrary.org/obo/UO_0000195 |
| 12 | degree Celsius | UO | http://purl.obolibrary.org/obo/UO_0000027 |
Source Name¶
| Attribute | Value |
|---|---|
| Rule Name | Source Name-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | check-only-constraints |
| Pattern | ^[a-zA-Z0-9][a-zA-Z0-9-_ ]+[a-zA-Z0-9]$ |
| Pattern Message | Value must be at least 3 characters and contain only alphanumeric characters, space, - and _ characters |
| Pattern Enforcement Level | recommended |
Characteristics[Organism]¶
| Attribute | Value |
|---|---|
| Rule Name | Characteristics[Organism]-01 |
| Rule Description | |
| Applicable Study Categories | ms-mhd-enabled |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | ontology-term-in-selected-ontologies |
| Ontologies [Ordered] | NCBITaxon, ENVO, CHEBI |
| Allowed Other Sources | [wikidata, https://www.wikidata.org/wiki/], [ILX, http://uri.interlex.org/base/ilx_] |
| Unexpected Terms | cat, chicken, plant, sample, dog, mouse, horse, flower, fish, leave, root, mice, steam, bacteria, value, food, matrix, mus, rat, blood, urine, plasma, hair, fur, skin, saliva, fly, human, man, sheep |
| Unexpected Term Enforcement Level | required |
| Ontology Term Enforcement Level | required |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | Homo sapiens | NCBITaxon | http://purl.obolibrary.org/obo/NCBITaxon_9606 |
| 2 | Mus musculus | NCBITaxon | http://purl.obolibrary.org/obo/NCBITaxon_10090 |
| 3 | Rattus norvegicus | NCBITaxon | http://purl.obolibrary.org/obo/NCBITaxon_10116 |
| 4 | Arabidopsis thaliana | NCBITaxon | http://purl.obolibrary.org/obo/NCBITaxon_3702 |
| 5 | Vitis vinifera | NCBITaxon | http://purl.obolibrary.org/obo/NCBITaxon_29760 |
| 6 | Escherichia coli | NCBITaxon | http://purl.obolibrary.org/obo/NCBITaxon_562 |
| 7 | Trypanosoma brucei | NCBITaxon | http://purl.obolibrary.org/obo/NCBITaxon_5691 |
| 8 | sea water | ENVO | http://purl.obolibrary.org/obo/ENVO_00002149 |
Characteristics[Organism part]¶
| Attribute | Value |
|---|---|
| Rule Name | Characteristics[Organism part]-01 |
| Rule Description | |
| Applicable Study Categories | ms-mhd-enabled |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | ontology-term-in-selected-ontologies |
| Ontologies [Ordered] | UBERON, BTO, NCIT, MSIO, CHEBI |
| Allowed Other Sources | [wikidata, https://www.wikidata.org/wiki/], [ILX, http://uri.interlex.org/base/ilx_] |
| Ontology Term Enforcement Level | required |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | blood plasma | BTO | http://purl.obolibrary.org/obo/BTO_0000131 |
| 2 | blood serum | BTO | http://purl.obolibrary.org/obo/BTO_0000133 |
| 3 | urine | BTO | http://purl.obolibrary.org/obo/BTO_0001419 |
| 4 | feces | BTO | http://purl.obolibrary.org/obo/BTO_0000440 |
| 5 | leaf | BTO | http://purl.obolibrary.org/obo/BTO_0000713 |
| 6 | exocarp | BTO | http://purl.obolibrary.org/obo/BTO_0000733 |
| 7 | Whole Organism | NCIT | http://purl.obolibrary.org/obo/NCIT_C13413 |
| 8 | exometabolome | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000131 |
| 9 | endometabolome | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000125 |
| 10 | blank | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_002304 |
Characteristics[Sample type]¶
| Attribute | Value |
|---|---|
| Rule Name | Characteristics[Sample type]-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | ontology-term-in-selected-ontologies |
| Ontologies [Ordered] | CHMO, MSIO, MTBLS |
| Ontology Term Enforcement Level | recommended |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | experimental sample | CHMO | http://purl.obolibrary.org/obo/CHMO_0002746 |
| 2 | pooled quality control sample | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_001090 |
| 3 | experimental blank | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000218 |
| 4 | solvent blank | MSIO | http://purl.obolibrary.org/obo/MSIO_0000026 |
| 5 | sample preparation blank | MSIO | http://purl.obolibrary.org/obo/MSIO_0000025 |
| 6 | reference compound mix | MSIO | http://purl.obolibrary.org/obo/MSIO_0000024 |
| 7 | long term reference | MSIO | http://purl.obolibrary.org/obo/MSIO_0000019 |
Protocol REF¶
| Attribute | Value |
|---|---|
| Rule Name | Sample Protocol REF-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | selected-ontology-term |
| Allowed Placeholders | [MTBLS, http://www.ebi.ac.uk/metabolights/ontology/placeholder] |
| Allowed Other Sources | [MTBLS, http://www.ebi.ac.uk/metabolights/ontology/MTBLS_] |
| Ontology Term Enforcement Level | required |
Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | Sample collection |
Sample Name¶
| Attribute | Value |
|---|---|
| Rule Name | Sample Name-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | check-only-constraints |
| Pattern | ^[a-zA-Z0-9][a-zA-Z0-9-_ ]+[a-zA-Z0-9]$ |
| Pattern Message | Value must be at least 3 characters and contain only alphanumeric characters, space, - and _ characters |
| Pattern Enforcement Level | recommended |