MALDI-MS - Assay File Field Controls¶
Common¶
| Attribute | Value |
|---|---|
| Rule Name | default-assay-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, 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_] |
| Unexpected Terms | unknown, undefined, n/a, na, not applicable, not available, none, null, nill, not specified, not provided, -, --, --- |
| Unexpected Term Enforcement Level | required |
Unit¶
| Attribute | Value |
|---|---|
| Rule Name | Assay-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 |
Sample Name¶
| Attribute | Value |
|---|---|
| Rule Name | Assay-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 |
Parameter Value[Derivatization]¶
| Attribute | Value |
|---|---|
| Rule Name | Parameter Value[Derivatization]-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | check-only-constraints |
| Pattern | ^.*$ |
| Pattern Message | Define any value |
| Pattern Enforcement Level | recommended |
| Ontologies [Ordered] | MTBLS |
| Allowed Missing Terms | [none, , ] |
Parameter Value[Scan polarity]¶
| Attribute | Value |
|---|---|
| Rule Name | Parameter Value[Scan polarity]-01 |
| Rule Description | |
| Applicable Study Categories | ms-mhd-enabled |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | selected-ontology-term |
| Ontologies [Ordered] | MS |
| Ontology Term Enforcement Level | required |
Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | negative polarity acquisition | MS | http://purl.obolibrary.org/obo/MS_1000076 |
| 2 | positive polarity acquisition | MS | http://purl.obolibrary.org/obo/MS_1000077 |
| 3 | alternating polarity acquisition | MS | http://purl.obolibrary.org/obo/MS_1002833 |
| 4 | mixed polarity acquisition | MS | http://purl.obolibrary.org/obo/MS_1003774 |
Parameter Value[Mass analyzer]¶
| Attribute | Value |
|---|---|
| Rule Name | Parameter Value[Mass analyzer]-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | any-ontology-term |
| Recommended Ontologies [Ordered] | MS |
| 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_] |
| Ontology Term Enforcement Level | recommended |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | orbitrap | MS | http://purl.obolibrary.org/obo/MS_1000484 |
| 2 | triple quadrupole | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000698 |
| 3 | quadrupole time-of-flight | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000699 |
| 4 | time-of-flight | MS | http://purl.obolibrary.org/obo/MS_1000084 |
| 5 | hybrid triple quadrupole-linear ion trap | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000695 |
| 6 | ion cyclotron resonance cell | CHMO | http://purl.obolibrary.org/obo/CHMO_0000964 |
| 7 | ion trap | MS | http://purl.obolibrary.org/obo/MS_1000264 |
| 8 | ion trap time-of-flight | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_000700 |
| 9 | linear quadrupole ion trap mass-to-charge analyser | CHMO | http://purl.obolibrary.org/obo/CHMO_0000969 |
| 10 | quadrupole | MS | http://purl.obolibrary.org/obo/MS_1000081 |
| 11 | quadrupole ion trap | MS | http://purl.obolibrary.org/obo/MS_1000082 |
MS Assay Name¶
| Attribute | Value |
|---|---|
| Rule Name | MS Assay 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 |