metabolon - Investigation File Field Controls¶
Common¶
| Attribute | Value |
|---|---|
| Rule Name | default-investigation-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 | Investigation-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 |
Study Protocol Type¶
| Attribute | Value |
|---|---|
| Rule Name | Study Protocol 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] | EFO, NCIT, MTBLS, CHEBI, CHMO, MONDO, PRIDE, GO, MESH, MI, MS |
| 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 | recommended |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | sample collection protocol | EFO | http://www.ebi.ac.uk/efo/EFO_0005518 |
| 2 | sample preparation | MS | http://purl.obolibrary.org/obo/MS_1000831 |
| 3 | chromatography | CHMO | http://purl.obolibrary.org/obo/CHMO_0001000 |
| 4 | mass spectrometry | CHMO | http://purl.obolibrary.org/obo/CHMO_0000470 |
| 5 | data transformation | OBI | http://purl.obolibrary.org/obo/OBI_0200000 |
| 6 | metabolite identification | MI | http://purl.obolibrary.org/obo/MI_2131 |
| 7 | capillary electrophoresis | CHMO | http://purl.obolibrary.org/obo/CHMO_0001024 |
| 8 | flow injection analysis | MS | http://purl.obolibrary.org/obo/MS_1000058 |
| 9 | NMR sample | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_001110 |
| 10 | NMR spectroscopy | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_001111 |
| 11 | NMR assay | MTBLS | http://www.ebi.ac.uk/metabolights/ontology/MTBLS_001112 |
Study Design Type¶
| Attribute | Value |
|---|---|
| Rule Name | Study Design Type-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | any-ontology-term |
| Recommended Ontologies [Ordered] | EFO, MSIO, NCIT, MTBLS, CHEBI, CHMO, MONDO, PRIDE, GO, MESH |
| 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 | targeted metabolite profiling | MSIO | http://purl.obolibrary.org/obo/MSIO_0000100 |
| 2 | untargeted metabolite profiling | MSIO | http://purl.obolibrary.org/obo/MSIO_0000101 |
| 3 | nuclear magnetic resonance spectroscopy | CHMO | http://purl.obolibrary.org/obo/CHMO_0000591 |
| 4 | ultra-performance liquid chromatography-mass spectrometry | CHMO | http://purl.obolibrary.org/obo/CHMO_0000715 |
| 5 | gas chromatography-mass spectrometry | CHMO | http://purl.obolibrary.org/obo/CHMO_0000497 |
| 6 | tandem mass spectrometry | CHMO | http://purl.obolibrary.org/obo/CHMO_0000575 |
| 7 | Multi-omics study | PRIDE | http://purl.obolibrary.org/obo/PRIDE_0000461 |
| 8 | microbiome | EFO | http://www.ebi.ac.uk/efo/EFO_0004982 |
| 9 | Aging | NCIT | http://purl.obolibrary.org/obo/NCIT_C16269 |
| 10 | cancer | MONDO | http://purl.obolibrary.org/obo/MONDO_0004992 |
Study Person Roles¶
| Attribute | Value |
|---|---|
| Rule Name | Study Person Roles-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | child-ontology-term |
| Ontologies [Ordered] | NCIT |
| Allowed Parent Ontology Terms | [Personnel, NCIT, http://purl.obolibrary.org/obo/NCIT_C60758] |
| Ontology Term Enforcement Level | recommended |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | Principal Investigator | NCIT | http://purl.obolibrary.org/obo/NCIT_C19924 |
| 2 | Investigator | NCIT | http://purl.obolibrary.org/obo/NCIT_C25936 |
| 3 | Author | NCIT | http://purl.obolibrary.org/obo/NCIT_C42781 |
Study Assay Measurement Type¶
| Attribute | Value |
|---|---|
| Rule Name | Study Assay Measurement Type-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 | untargeted analysis | MS | http://purl.obolibrary.org/obo/MS_1003904 |
| 2 | targeted analysis | MS | http://purl.obolibrary.org/obo/MS_1003905 |
| 3 | semi-targeted analysis | MS | http://purl.obolibrary.org/obo/MS_1003906 |
Study Protocol Components Type¶
| Attribute | Value |
|---|---|
| Rule Name | Study Protocol Components Type-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | any-ontology-term |
| Recommended Ontologies [Ordered] | EFO, NCIT, MTBLS, CHEBI, CHMO, MONDO, PRIDE, GO, MESH |
| 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_] |
Study Protocol Parameter Name¶
| Attribute | Value |
|---|---|
| Rule Name | Study Protocol Parameter Name-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | any-ontology-term |
| Recommended Ontologies [Ordered] | MS, EFO, NCIT, MTBLS, CHMO, MONDO, PRIDE, GO, MESH, MI |
| 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 | recommended |
Recommended Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | Post Extraction | ||
| 2 | Derivatization | ||
| 3 | Chromatography Instrument | ||
| 4 | Autosampler model | ||
| 5 | Column model | ||
| 6 | Column type | ||
| 7 | Guard column | ||
| 8 | Scan polarity | ||
| 9 | Scan m/z range | ||
| 10 | Instrument | ||
| 11 | Ion source | ||
| 12 | Mass analyzer | ||
| 13 | DI Instrument | ||
| 14 | FIA Instrument | ||
| 15 | CE Instrument | ||
| 16 | SPE-IMS Instrument | ||
| 17 | Cartridge type | ||
| 18 | Column model 1 | ||
| 19 | Column type 1 | ||
| 20 | Column model 2 | ||
| 21 | Column type 2 | ||
| 22 | Detector | ||
| 23 | Signal range | ||
| 24 | Resolution | ||
| 25 | Temperature | ||
| 26 | Sample mounting | ||
| 27 | Sample preservation | ||
| 28 | Tissue modification | ||
| 29 | Sectioning instrument | ||
| 30 | Section thickness | ||
| 31 | Matrix | ||
| 32 | Matrix application | ||
| 33 | Stain | ||
| 34 | High-res image | ||
| 35 | Low-res image | ||
| 36 | Data Transformation software | ||
| 37 | Data Transformation software version | ||
| 38 | Instrument manufacturer | ||
| 39 | Solvent | ||
| 40 | Target material | ||
| 41 | Spatial resolution | ||
| 42 | Pixel size x | ||
| 43 | Pixel size y | ||
| 44 | Max count of pixel x | ||
| 45 | Max count of pixel y | ||
| 46 | Max dimension x | ||
| 47 | Max dimension y | ||
| 48 | Inlet type | ||
| 49 | Detector mode | ||
| 50 | Resolving power | ||
| 51 | Resolving power m/z | ||
| 52 | Native spectrum identifier format | ||
| 53 | Data file content | ||
| 54 | Spectrum representation | ||
| 55 | Raw data file format | ||
| 56 | Instrument software | ||
| 57 | Instrument software version | ||
| 58 | Line scan direction | ||
| 59 | Linescan sequence | ||
| 60 | Scan pattern | ||
| 61 | Number of scans | ||
| 62 | Scan type | ||
| 63 | Tomography | ||
| 64 | Field of view | ||
| 65 | Magnetic pulse sequence name | ||
| 66 | Voxel size | ||
| 67 | Localisation pulse sequence name | ||
| 68 | Number of transients | ||
| 69 | Water inhibition pulse sequence name | ||
| 70 | Magnetic field strength | ||
| 71 | Extration Method | ||
| 72 | NMR tube type | ||
| 73 | Sample pH | ||
| 74 | NMR Probe | ||
| 75 | Pulse sequence name |
Study Assay Technology Type¶
| Attribute | Value |
|---|---|
| Rule Name | Study Assay Technology Type-01 |
| Rule Description | |
| Applicable Study Categories | ms-mhd-enabled |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | selected-ontology-term |
| Ontology Term Enforcement Level | required |
Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | mass spectrometry assay | OBI | http://purl.obolibrary.org/obo/OBI_0000470 |
Study Factor Type¶
| Attribute | Value |
|---|---|
| Rule Name | Study Factor Type-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | any-ontology-term |
| Recommended Ontologies [Ordered] | EFO, MTBLS, ENVO, MESH, CHEBI, CHMO, NCIT, PO |
| 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 | disease | EFO | http://www.ebi.ac.uk/efo/EFO_0000408 |
| 2 | timepoint | EFO | http://www.ebi.ac.uk/efo/EFO_0000724 |
| 3 | treatment | EFO | http://www.ebi.ac.uk/efo/EFO_0000727 |
| 4 | genotype | EFO | http://www.ebi.ac.uk/efo/EFO_0000513 |
| 5 | age | EFO | http://www.ebi.ac.uk/efo/EFO_0000246 |
| 6 | diet | EFO | http://www.ebi.ac.uk/efo/EFO_0002755 |
| 7 | disease staging | EFO | http://www.ebi.ac.uk/efo/EFO_0000410 |
| 8 | exposure | EFO | http://www.ebi.ac.uk/efo/EFO_0000487 |
| 9 | biological replicate | EFO | http://www.ebi.ac.uk/efo/EFO_0002091 |
| 10 | technical replicate | EFO | http://www.ebi.ac.uk/efo/EFO_0002090 |
| 11 | Collection Date | NCIT | http://purl.obolibrary.org/obo/NCIT_C81286 |
Omics Type¶
| Attribute | Value |
|---|---|
| Rule Name | Omics Type-01 |
| Rule Description | |
| Applicable Study Categories | ms-mhd-enabled |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | selected-ontology-term |
| Ontology Term Enforcement Level | required |
Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | Metabolomics | EDAM | http://edamontology.org/topic_3172 |
| 2 | Lipidomics | EDAM | http://edamontology.org/topic_0153 |
| 3 | Exposomics | ||
| 4 | Fluxomics | EDAM | http://edamontology.org/topic_3955 |
Organization¶
| Attribute | Value |
|---|---|
| Rule Name | Organization-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | ontology-term-in-selected-ontologies |
| Ontologies [Ordered] | ROR |
| 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_] |
Study Publication Status¶
| Attribute | Value |
|---|---|
| Rule Name | Study Publication Status-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Applicable Only for The Studies | C, r, e, a, t, e, d, , a, t, , o, r, , a, f, t, e, r, :, , 2, 0, 2, 6, \, -, 0, 1, \, -, 0, 1, T, 0, 0, :, 0, 0, :, 0, 0 |
| Validation Type | selected-ontology-term |
| Ontology Term Enforcement Level | required |
Terms¶
| # | Term | Term Source | Term Accession |
|---|---|---|---|
| 1 | in preparation | EFO | http://www.ebi.ac.uk/efo/EFO_0001795 |
| 2 | submitted | EFO | http://www.ebi.ac.uk/efo/EFO_0001794 |
| 3 | preprint | EFO | http://www.ebi.ac.uk/efo/EFO_0010558 |
| 4 | published | EFO | http://www.ebi.ac.uk/efo/EFO_0001796 |
| 5 | Learning material | EDAM | http://edamontology.org/data_3669 |
Assay Acquisition Method¶
| Attribute | Value |
|---|---|
| Rule Name | Assay Acquisition Method-01 |
| Rule Description | |
| Applicable Study Categories | ms-mhd-enabled, ms-mhd-legacy |
| 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 | data-independent acquisition | MS | http://purl.obolibrary.org/obo/MS_1003215 |
| 2 | data-dependent acquisition | MS | http://purl.obolibrary.org/obo/MS_1003221 |
Software¶
| Attribute | Value |
|---|---|
| Rule Name | Software-01 |
| Rule Description | |
| Applicable Study Categories | All |
| Applicable Template Names | All |
| Applicable Template Versions | All |
| Validation Type | child-ontology-term |
| Ontologies [Ordered] | MS |
| Allowed Parent Ontology Terms | [software, MS, http://purl.obolibrary.org/obo/MS_1000531] |
| 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 | ProteoWizard msconvert | MS | http://purl.obolibrary.org/obo/MS_1002205 |
| 2 | ProteoWizard msaccess | MS | http://purl.obolibrary.org/obo/MS_1002208 |
| 3 | mzmine | MS | http://purl.obolibrary.org/obo/MS_1002342 |
| 4 | OpenMS | MS | http://purl.obolibrary.org/obo/MS_1003430 |