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nmdc.yaml
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nmdc.yaml
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id: https://w3id.org/nmdc/nmdc
name: NMDC
title: NMDC Schema
notes:
- not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1
description: >-
Schema for National Microbiome Data Collaborative (NMDC).
This schema is organized into multiple modules, such as:
* a set of core types for representing data values
* a subset of the mixs schema
* an annotation schema
* the NMDC schema itself, into which the other modules are imported
license: https://creativecommons.org/publicdomain/zero/1.0/
version: 0.0.0
imports:
- annotation # also brings core and portal_*
- workflow_execution_activity
prefixes:
CATH: "https://bioregistry.io/cath:"
CHEBI: "http://purl.obolibrary.org/obo/CHEBI_"
CHEMBL.COMPOUND: "https://bioregistry.io/chembl.compound:" # https://bioregistry.io/chembl.compound:CHEMBL465070
CHMO: "http://purl.obolibrary.org/obo/CHMO_"
Contaminant: http://example.org/contaminant/ # present in MongoDB
DRUGBANK: "https://bioregistry.io/drugbank:" # https://bioregistry.io/drugbank:DB14938
EC: "https://bioregistry.io/eccode:" # https://bioregistry.io/eccode:1.1.1.1
EFO: http://www.ebi.ac.uk/efo/
EGGNOG: "https://bioregistry.io/eggnog:" # https://bioregistry.io/eggnog:veNOG12876
ENVO: "http://purl.obolibrary.org/obo/ENVO_"
FBcv: "http://purl.obolibrary.org/obo/FBcv_"
FMA: "http://purl.obolibrary.org/obo/FMA_"
GO: "http://purl.obolibrary.org/obo/GO_"
HMDB: "https://bioregistry.io/hmdb:" # https://bioregistry.io/hmdb:HMDB00001
ISA: http://example.org/isa/
KEGG.ORTHOLOGY: "https://bioregistry.io/kegg.orthology:" # https://github.com/prefixcommons/biocontext/blob/master/registry/idot_context.jsonld
MASSIVE: "https://bioregistry.io/reference/massive:"
MESH: "https://bioregistry.io/mesh:" # https://bioregistry.io/mesh:C063233
MS: "http://purl.obolibrary.org/obo/MS_"
MetaNetX: http://example.org/metanetx/
NCBITaxon: "http://purl.obolibrary.org/obo/NCBITaxon_"
NCBI: "http://example.com/ncbitaxon/" # temporary. see https://github.com/microbiomedata/issues/issues/893
NCIT: "http://purl.obolibrary.org/obo/NCIT_"
OBI: http://purl.obolibrary.org/obo/OBI_
ORCID: https://orcid.org/
PANTHER.FAMILY: "https://bioregistry.io/panther.family:" # https://bioregistry.io/panther.family:PTHR12345
PATO: "http://purl.obolibrary.org/obo/PATO_"
PFAM: "https://bioregistry.io/pfam:" # https://bioregistry.io/pfam:PF11779
PFAM.CLAN: "https://bioregistry.io/pfam.clan:" # https://bioregistry.io/pfam.clan:CL0192
PO: "http://purl.obolibrary.org/obo/PO_"
PR: "http://purl.obolibrary.org/obo/PR_"
PUBCHEM.COMPOUND: "https://bioregistry.io/pubchem.compound:"
RO: "http://purl.obolibrary.org/obo/RO_"
RetroRules: http://example.org/retrorules/
SO: "http://purl.obolibrary.org/obo/SO_"
SUPFAM: "https://bioregistry.io/supfam:" # https://bioregistry.io/supfam:SSF57615
TIGRFAM: "https://bioregistry.io/tigrfam:" # https://bioregistry.io/tigrfam:TIGR00010
UBERON: "http://purl.obolibrary.org/obo/UBERON_"
UO: "http://purl.obolibrary.org/obo/UO_"
bioproject: "https://identifiers.org/bioproject:"
biosample: "https://bioregistry.io/biosample:"
cas: "https://bioregistry.io/cas:"
doi: "https://bioregistry.io/doi:"
edam.data: "http://edamontology.org/data_"
emsl.project: "https://bioregistry.io/emsl.project:"
emsl: "http://example.org/emsl_in_mongodb/"
emsl_uuid_like: "http://example.org/emsl_uuid_like/"
generic: https://example.org/generic/
gnps.task: "https://bioregistry.io/gnps.task:"
gtpo: http://example.org/gtpo/
igsn: https://app.geosamples.org/sample/igsn/
img.taxon: "https://bioregistry.io/img.taxon:"
jgi.analysis: "https://data.jgi.doe.gov/search?q="
jgi.proposal: "https://bioregistry.io/jgi.proposal:"
jgi: http://example.org/jgi/
kegg: "https://bioregistry.io/kegg:" # https://bioregistry.io/kegg:hsa00190
linkml: https://w3id.org/linkml/
mgnify.proj: "https://bioregistry.io/mgnify.proj:"
my_emsl: "https://release.my.emsl.pnnl.gov/released_data/"
neon.identifier: http://example.org/neon/identifier/
neon.schema: http://example.org/neon/schema/
nmdc: https://w3id.org/nmdc/
prov: http://www.w3.org/ns/prov#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: http://www.w3.org/2000/01/rdf-schema#
skos: http://www.w3.org/2004/02/skos/core#
wikidata: "http://www.wikidata.org/entity/"
xsd: http://www.w3.org/2001/XMLSchema#
default_prefix: nmdc
default_range: string
emit_prefixes:
- KEGG.ORTHOLOGY
- MASSIVE
- biosample
- cas
- doi
- gnps.task
- gold
- img.taxon
- jgi.proposal
- kegg
- rdf
- rdfs
- skos
- xsd
settings:
id_nmdc_prefix: "^(nmdc)"
id_shoulder: "([0-9][a-z]{0,6}[0-9])"
id_blade: "([A-Za-z0-9]{1,})"
id_version: "(\\.[0-9]{1,})"
id_locus: "(_[A-Za-z0-9_\\.-]+)?$"
classes:
EukEval:
description: This class contains information pertaining to evaluating if a Metagenome-Assembled Genome (MAG) is eukaryotic.
comments:
- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information for this class.
slots:
- type
- completeness
- contamination
- ncbi_lineage_tax_ids
- ncbi_lineage
class_uri: nmdc:EukEval
NucleotideSequencing:
class_uri: nmdc:NucleotideSequencing
is_a: DataGeneration
description: A DataGeneration in which the sequence of DNA or RNA molecules is generated.
comments: For example data generated from an Illumina or Pacific Biosciences instrument.
slots:
- gold_sequencing_project_identifiers
- insdc_bioproject_identifiers
- insdc_experiment_identifiers
- ncbi_project_name
- target_gene
- target_subfragment
slot_usage:
id:
structured_pattern:
syntax: "{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$"
interpolated: true
MassSpectrometry:
class_uri: nmdc:MassSpectrometry
is_a: DataGeneration
description: Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.
exact_mappings:
- CHMO:0000470
slots:
- eluent_introduction_category
- has_calibration
- has_chromatography_configuration
- has_mass_spectrometry_configuration
slot_usage:
id:
structured_pattern:
syntax: "{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$"
interpolated: true
has_calibration:
structured_pattern:
syntax: "{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$"
interpolated: true
has_chromatography_configuration:
structured_pattern:
syntax: "{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$"
interpolated: true
has_mass_spectrometry_configuration:
structured_pattern:
syntax: "{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$"
interpolated: true
rules:
- title: has_calibration_required_if_gc
description: >-
If eluent_introduction_category is gas_chromatography, then has_calibration is required.
preconditions:
slot_conditions:
eluent_introduction_category:
equals_string: gas_chromatography
postconditions:
slot_conditions:
has_calibration:
required: true
- title: has_chromatography_configuration_required_if_lc_or_gc
description: >-
If eluent_introduction_category is liquid_chromatography or gas_chromatography, then has_chromatography_configuration is required.
preconditions:
slot_conditions:
eluent_introduction_category:
any_of:
- equals_string: liquid_chromatography
- equals_string: gas_chromatography
postconditions:
slot_conditions:
has_chromatography_configuration:
required: true
Configuration:
abstract: true
is_a: InformationObject
class_uri: nmdc:Configuration
description: A set of parameters that define the actions of a process and is shared among multiple instances of the process.
notes:
- This class is intended to represent the parameters within a method file (or similar) that control a process.
MassSpectrometryConfiguration:
is_a: Configuration
class_uri: nmdc:MassSpectrometryConfiguration
description: A set of parameters that define and control the actions of a mass spectrometry process.
notes:
- This class is intended to represent a mass spectrometry method file that controls a mass spectrometry process.
slots:
- mass_spectrometry_acquisition_strategy
- resolution_categories
- mass_analyzers
- ionization_source
- mass_spectrum_collection_modes
- polarity_mode
slot_usage:
name:
required: true
description:
required: true
id:
structured_pattern:
syntax: "{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$"
interpolated: true
ChromatographyConfiguration:
is_a: Configuration
class_uri: nmdc:ChromatographyConfiguration
description: A set of parameters that define and control the actions of a chromatography process.
notes:
- This class is intended to represent a chromatography method file associated with a mass spectrometry process.
slots:
- chromatographic_category
- ordered_mobile_phases
- stationary_phase
- temperature
slot_usage:
name:
required: true
description:
required: true
id:
structured_pattern:
syntax: "{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$"
interpolated: true
FunctionalAnnotationAggMember:
class_uri: nmdc:FunctionalAnnotationAggMember
slots:
- metagenome_annotation_id
- gene_function_id
- count
- type
slot_usage:
metagenome_annotation_id:
structured_pattern: # doesn't include act
syntax: "{id_nmdc_prefix}:(wfmgan|wfmtan)-{id_shoulder}-{id_blade}{id_version}$"
interpolated: true
Database:
class_uri: nmdc:Database
tree_root: true
aliases:
- NMDC metadata object
description:
An abstract holder for any set of metadata and data. It does not
need to correspond to an actual managed database top level holder class. When
translated to JSON-Schema this is the 'root' object. It should contain pointers
to other objects of interest. For MongoDB, the lists of objects that Database
slots point to correspond to **collections**.
slots:
- biosample_set
- calibration_set
- chemical_entity_set
- collecting_biosamples_from_site_set
- configuration_set
- data_generation_set
- data_object_set
- field_research_site_set
- functional_annotation_agg
- functional_annotation_set
- genome_feature_set
- instrument_set
- material_processing_set
- processed_sample_set
- protocol_execution_set
- storage_process_set
- study_set
- workflow_execution_set
Pooling:
class_uri: nmdc:Pooling
is_a: MaterialProcessing
description: physical combination of several instances of like material.
slots:
exact_mappings:
- OBI:0600016
slot_usage:
has_input:
minimum_cardinality: 2
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
required: true
minimum_cardinality: 1
maximum_cardinality: 1
structured_pattern:
syntax: "{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$"
interpolated: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$"
interpolated: true
Extraction:
class_uri: nmdc:Extraction
is_a: MaterialProcessing
description: A material separation in which a desired component of an input material is separated from the remainder.
exact_mappings:
- OBI:0302884
slots:
- substances_used
- extraction_targets
- input_mass
- volume
slot_usage:
has_input:
required: true
any_of:
- range: Biosample
- range: ProcessedSample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$"
interpolated: true
volume:
description: The volume of the solvent/solute being used, not the input.
LibraryPreparation:
class_uri: nmdc:LibraryPreparation
aliases:
- LibraryConstruction
is_a: MaterialProcessing
slots:
- is_stranded
- library_preparation_kit
- library_type
- nucl_acid_amp
- pcr_cond
- pcr_cycles
- pcr_primers
- stranded_orientation
close_mappings:
- OBI:0000711
comments:
- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)
slot_usage:
has_input:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$"
interpolated: true
pcr_cond:
description: Description of reaction conditions and components of polymerase chain reaction performed during library preparation
CollectingBiosamplesFromSite:
class_uri: nmdc:CollectingBiosamplesFromSite
is_a: PlannedProcess
title: Collecting Biosamples From Site
comments:
- "this illustrates implementing a Biosample relation with a process class"
close_mappings:
- OBI:0000744
slot_usage:
has_input:
range: Site
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
range: Biosample
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$"
interpolated: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$"
interpolated: true
ProtocolExecution:
class_uri: 'nmdc:ProtocolExecution'
is_a: PlannedProcess
description: A PlannedProces that has PlannedProcess parts. Can be used to represent the case of someone following a Protocol.
slots:
- has_process_parts
- protocol_execution_category
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$"
interpolated: true
has_input:
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
structured_pattern:
syntax: "{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_process_parts:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$"
interpolated: true
description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.
SubSamplingProcess:
class_uri: 'nmdc:SubSamplingProcess'
description: >
Separating a sample aliquot from the starting material for downstream activity.
related_mappings:
- OBI:0000744
notes:
- A subsample may be (a) a portion of the sample obtained by selection or division;
(b) an individual unit of the lot taken as part of the sample; (c) the final unit of multistage sampling.
The term 'subsample' is used either in the sense of a 'sample of a sample' or as a synonym for 'unit'.
In practice, the meaning is usually apparent from the context or is defined.
- TODO - Montana to visit slot descriptions
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-8683-0050 #Montana Smith
- ORCID:0000-0001-9076-6066 #Mark Miller
- ORCID:0009-0008-4013-7737 #James Tessmer
is_a: MaterialProcessing
slots:
- container_size
- contained_in
- temperature
- volume
- mass
- sampled_portion
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$"
interpolated: true
volume:
description: The output volume of the SubSampling Process.
mass:
description: The output mass of the SubSampling Process.
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
structured_pattern: # MAM 2024-05-22 isn't that inherited from a parent class?
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
range: ProcessedSample
description: The subsample.
structured_pattern: # MAM 2024-05-22 isn't that inherited from a parent class?
syntax: "{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
MixingProcess:
class_uri: 'nmdc:MixingProcess'
description: >
The combining of components, particles or layers into a more homogeneous state.
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-8683-0050 #Montana Smith
is_a: MaterialProcessing
comments:
- The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps
or by revolving or shaking the container.
- The process must not permit segregation of particles of different size or properties.
- Homogeneity may be considered to have been achieved in a practical sense when the sampling error
of the processed portion is negligible compared to the total error of the measurement system.
slots:
- duration
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$"
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
structured_pattern: # MAM 2024-05-22 isn't that inherited from a parent class?
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
range: ProcessedSample
description: The mixed sample.
structured_pattern:
syntax: "{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$"
interpolated: true
FiltrationProcess:
class_uri: 'nmdc:FiltrationProcess'
description: >-
The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.
related_mappings:
- CHMO:0001640
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-8683-0050 #Montana Smith
- ORCID:0000-0001-9076-6066 #Mark Miller
- ORCID:0009-0008-4013-7737 #James Tessmer
is_a: MaterialProcessing
slots:
- conditionings
- container_size
- filter_material
- filter_pore_size
- filtration_category
- is_pressurized
- separation_method
- volume
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$"
interpolated: true
volume:
description: The volume of sample filtered.
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
range: ProcessedSample
structured_pattern:
syntax: "{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$"
interpolated: true
StorageProcess:
class_uri: 'nmdc:StorageProcess'
description: >-
A planned process with the objective to preserve and protect material entities by placing them in an identified
location which may have a controlled environment.
is_a: PlannedProcess
related_mappings:
- OBI:0302893
slots:
- substances_used
- contained_in
- temperature
slot_usage:
substances_used:
description: The substance(s) that a processed sample is stored in.
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$"
interpolated: true
has_input:
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
structured_pattern:
syntax: "{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$"
interpolated: true
ChromatographicSeparationProcess:
class_uri: 'nmdc:ChromatographicSeparationProcess'
description:
The process of using a selective partitioning of the analyte or interferent between two immiscible phases.
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-1368-8217 #Yuri Corilo
is_a: MaterialProcessing
slots:
- chromatographic_category
- ordered_mobile_phases
- stationary_phase
- temperature
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$"
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
has_output:
range: ProcessedSample
structured_pattern:
syntax: "{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$"
interpolated: true
DissolvingProcess:
class_uri: 'nmdc:DissolvingProcess'
aliases:
- Solubilization
description: >
A mixing step where a soluble component is mixed with a liquid component.
exact_mappings:
- CHMO:0002773
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-1368-8217 #Yuri Corilo
is_a: MaterialProcessing
slots:
- duration
- temperature
- substances_used
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$"
interpolated: true
enums:
StrandedOrientationEnum:
description: This enumeration specifies information about stranded RNA library preparations.
permissible_values:
antisense orientation:
description: Orientation that is complementary (non-coding) to a sequence of messenger RNA.
comments:
- See https://www.genome.gov/genetics-glossary/antisense
exact_mappings:
- SO:0000077
sense orientation:
description: Orientation that corresponds to the coding sequence of messenger RNA.
MassSpectrometryAcquisitionStrategyEnum:
permissible_values:
data_independent_acquisition:
description:
- Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID.
aliases:
- DIA
- data independent acquisition from dissociation of full mass range
exact_mappings:
- MS:1003227
data_dependent_acquisition:
description:
Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run.
aliases:
-DDA
exact_mappings:
- MS:1003221
full_scan_only:
aliases:
- MS
description:
Mass spectrometer data acquisition method wherein only MS1 data are acquired.
ResolutionCategoryEnum:
permissible_values:
high:
description: higher than unit resolution
low:
description: at unit resolution
MassAnalyzerEnum:
permissible_values:
time_of_flight:
aliases:
- TOF
description:
Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy.
exact_mappings:
- MS:1000084
quadrupole:
aliases:
- Quad
- Q
description:
A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis.
exact_mappings:
- MS:1000081
Orbitrap:
aliases:
- Orbi
description:
An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer.
exact_mappings:
- MS:1000484
ion_cyclotron_resonance:
aliases:
- ICR
description:
A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z.
exact_mappings:
- MS:1000079
ion_trap:
aliases:
- LTQ
- Ion Trap
- Paul Trap
description:
A device for spatially confining ions using electric and magnetic fields alone or in combination.
exact_mappings:
- MS:1000264
IonizationSourceEnum:
permissible_values:
electrospray_ionization:
aliases:
- ESI
matrix_assisted_laser_desorption_ionization:
aliases:
- MALDI
atmospheric_pressure_photo_ionization:
aliases:
- APPI
atmospheric_pressure_chemical_ionization:
aliases:
- APCI
electron_ionization:
aliases:
- EI
MassSpectrumCollectionModeEnum:
permissible_values:
full_profile: { }
reduced_profile: { }
centroid: { }
PolarityModeEnum:
permissible_values:
positive: { }
negative: { }
EluentIntroductionCategoryEnum:
permissible_values:
liquid_chromatography:
aliases:
- LC
description: The processed sample is introduced into the mass spectrometer through a liquid chromatography process.
gas_chromatography:
aliases:
- GC
description: The processed sample is introduced into the mass spectrometer through a gas chromatography process.
direct_infusion_syringe:
description: The processed sample is introduced into the mass spectrometer through a direct infusion process using a syringe.
direct_infusion_autosampler:
description: The processed sample is introduced into the mass spectrometer through a direct infusion process using an autosampler.
LibraryTypeEnum:
permissible_values:
DNA: { }
RNA: { }
ContainerCategoryEnum:
description: The permitted types of containers used in processing metabolomic samples.
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-8683-0050 #Montana Smith
permissible_values:
v-bottom_conical_tube:
falcon_tube:
SeparationMethodEnum:
description: The tool/substance used to separate or filter a solution or mixture.
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-8683-0050 #Montana Smith
permissible_values:
ptfe_96_well_filter_plate:
syringe:
StationaryPhaseEnum:
description: The type of stationary phase used in a chromatography process.
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-4504-1039 #Katherine Heal
permissible_values:
BEH-HILIC:
C18:
C8:
C4:
C2:
C1:
C30:
C60:
CNT:
CN:
Diol:
HILIC:
NH2:
Phenyl:
Polysiloxane:
PS-DVB:
SAX:
SCX:
Silica:
WCX:
WAX:
ZIC-HILIC:
ZIC-pHILIC:
ZIC-cHILIC:
ProtocolCategoryEnum:
description: The possible protocols that may be followed for an assay.
permissible_values:
mplex:
derivatization:
filter_clean_up:
organic_matter_extraction:
solid_phase_extraction:
phosphorus_extraction:
ph_measurement:
respiration_measurement:
texture_measurement:
dna_extraction:
phenol_chloroform_extraction: { }
ChromatographicCategoryEnum:
permissible_values:
liquid_chromatography:
aliases:
- LC
gas_chromatography:
aliases:
- GC
solid_phase_extraction:
aliases:
- SPE
SamplePortionEnum:
permissible_values:
supernatant:
aliases:
- top_layer
pellet:
aliases:
- bottom_layer
organic_layer:
aqueous_layer:
non_polar_layer:
slots:
polarity_mode:
range: PolarityModeEnum
description: the polarity of which ions are generated and detected
mass_spectrum_collection_modes:
range: MassSpectrumCollectionModeEnum
description: Indicates whether mass spectra were collected in full profile, reduced profile, or centroid mode during acquisition.
multivalued: true
eukaryotic_evaluation:
range: EukEval
description: Contains results from evaluating if a Metagenome-Assembled Genome is of eukaryotic lineage.
ncbi_lineage_tax_ids:
range: string
pattern: '^\d+(-\d+)*$'
description: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)
comments:
- Example 1-131567-2759-2611352-33682-191814-2603949
ncbi_lineage:
range: string
description: Comma delimited ordered list of NCBI taxonomy names.
comments:
- Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae
has_failure_categorization:
range: FailureCategorization
multivalued: true
inlined_as_list: true
ionization_source:
range: IonizationSourceEnum
description: The ionization source used to introduce processed samples into a mass spectrometer
exact_mappings:
- MS:1000008
mass_analyzers:
range: MassAnalyzerEnum
description: The kind of mass analyzer(s) used during the spectra collection.
multivalued: true
exact_mappings:
- MS:1000443
resolution_categories:
range: ResolutionCategoryEnum
description: The relative resolution at which spectra were collected.
examples:
- value:
- high
- low
multivalued: true
mass_spectrometry_acquisition_strategy:
range: MassSpectrometryAcquisitionStrategyEnum
description: Mode of running a mass spectrometer method by which m/z ranges are selected and ions possibly fragment.
exact_mappings:
- MS:1003213
eluent_introduction_category:
range: EluentIntroductionCategoryEnum
description: A high-level categorization for how the processed sample is introduced into a mass spectrometer.
examples:
- value: liquid_chromatography
- value: direct_infusion_syringe
has_mass_spectrometry_configuration:
range: MassSpectrometryConfiguration
description: The identifier of the associated MassSpectrometryConfiguration.
has_chromatography_configuration:
range: ChromatographyConfiguration
description: The identifier of the associated ChromatographyConfiguration, providing information about how a sample was introduced into the mass spectrometer.
metagenome_annotation_id:
range: WorkflowExecution
description: The identifier for the analysis activity that generated the functional annotation results, where the analysis activity is an instance of the/an appropriate subclass of WorkflowExecution
required: true
any_of:
- range: MetagenomeAnnotation
- range: MetatranscriptomeAnnotation
gene_function_id:
range: uriorcurie
description: The identifier for the gene function.
examples:
- value: KEGG.ORTHOLOGY:K00627
required: true
count:
range: integer
required: true
functional_annotation_agg:
range: FunctionalAnnotationAggMember
multivalued: true
inlined: true
inlined_as_list: true
ecosystem_path_id:
range: string
description: A unique id representing the GOLD classifiers associated with a sample.
sample_collection_year:
range: integer
sample_collection_month:
library_preparation_kit:
range: string
## WHY ARE THESE COMMENTED OUT?
# exact_mappings:
# - GENEPIO:0001450
# processed_date: # can we move this or infer this from the date of some other process?
# # range: date
# range: string
# extraction_date: # replacing with start_ and end_date
# # range: date
# range: string