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nmdc_materialized_patterns.yaml
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name: NMDC
description: "Schema for National Microbiome Data Collaborative (NMDC).\nThis schema\
\ is organized into multiple modules, such as:\n\n * a set of core types for representing\
\ data values\n * a subset of the mixs schema\n * an annotation schema\n * the NMDC\
\ schema itself, into which the other modules are imported"
title: NMDC Schema
notes:
- not importing any MIxS terms where the relationship between the name (SCN) and the
id isn't 1:1
id: https://w3id.org/nmdc/nmdc
version: 0.0.0
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
CATH:
prefix_prefix: CATH
prefix_reference: 'https://bioregistry.io/cath:'
CHEBI:
prefix_prefix: CHEBI
prefix_reference: http://purl.obolibrary.org/obo/CHEBI_
CHEMBL.COMPOUND:
prefix_prefix: CHEMBL.COMPOUND
prefix_reference: 'https://bioregistry.io/chembl.compound:'
CHMO:
prefix_prefix: CHMO
prefix_reference: http://purl.obolibrary.org/obo/CHMO_
Contaminant:
prefix_prefix: Contaminant
prefix_reference: http://example.org/contaminant/
DRUGBANK:
prefix_prefix: DRUGBANK
prefix_reference: 'https://bioregistry.io/drugbank:'
EC:
prefix_prefix: EC
prefix_reference: 'https://bioregistry.io/eccode:'
EFO:
prefix_prefix: EFO
prefix_reference: http://www.ebi.ac.uk/efo/
EGGNOG:
prefix_prefix: EGGNOG
prefix_reference: 'https://bioregistry.io/eggnog:'
ENVO:
prefix_prefix: ENVO
prefix_reference: http://purl.obolibrary.org/obo/ENVO_
FBcv:
prefix_prefix: FBcv
prefix_reference: http://purl.obolibrary.org/obo/FBcv_
FMA:
prefix_prefix: FMA
prefix_reference: http://purl.obolibrary.org/obo/FMA_
GO:
prefix_prefix: GO
prefix_reference: http://purl.obolibrary.org/obo/GO_
HMDB:
prefix_prefix: HMDB
prefix_reference: 'https://bioregistry.io/hmdb:'
ISA:
prefix_prefix: ISA
prefix_reference: http://example.org/isa/
KEGG.ORTHOLOGY:
prefix_prefix: KEGG.ORTHOLOGY
prefix_reference: 'https://bioregistry.io/kegg.orthology:'
MASSIVE:
prefix_prefix: MASSIVE
prefix_reference: 'https://bioregistry.io/reference/massive:'
MESH:
prefix_prefix: MESH
prefix_reference: 'https://bioregistry.io/mesh:'
MS:
prefix_prefix: MS
prefix_reference: http://purl.obolibrary.org/obo/MS_
MetaNetX:
prefix_prefix: MetaNetX
prefix_reference: http://example.org/metanetx/
NCBITaxon:
prefix_prefix: NCBITaxon
prefix_reference: http://purl.obolibrary.org/obo/NCBITaxon_
NCBI:
prefix_prefix: NCBI
prefix_reference: http://example.com/ncbitaxon/
NCIT:
prefix_prefix: NCIT
prefix_reference: http://purl.obolibrary.org/obo/NCIT_
OBI:
prefix_prefix: OBI
prefix_reference: http://purl.obolibrary.org/obo/OBI_
ORCID:
prefix_prefix: ORCID
prefix_reference: https://orcid.org/
PANTHER.FAMILY:
prefix_prefix: PANTHER.FAMILY
prefix_reference: 'https://bioregistry.io/panther.family:'
PATO:
prefix_prefix: PATO
prefix_reference: http://purl.obolibrary.org/obo/PATO_
PFAM:
prefix_prefix: PFAM
prefix_reference: 'https://bioregistry.io/pfam:'
PFAM.CLAN:
prefix_prefix: PFAM.CLAN
prefix_reference: 'https://bioregistry.io/pfam.clan:'
PO:
prefix_prefix: PO
prefix_reference: http://purl.obolibrary.org/obo/PO_
PR:
prefix_prefix: PR
prefix_reference: http://purl.obolibrary.org/obo/PR_
PUBCHEM.COMPOUND:
prefix_prefix: PUBCHEM.COMPOUND
prefix_reference: 'https://bioregistry.io/pubchem.compound:'
RO:
prefix_prefix: RO
prefix_reference: http://purl.obolibrary.org/obo/RO_
RetroRules:
prefix_prefix: RetroRules
prefix_reference: http://example.org/retrorules/
SO:
prefix_prefix: SO
prefix_reference: http://purl.obolibrary.org/obo/SO_
SUPFAM:
prefix_prefix: SUPFAM
prefix_reference: 'https://bioregistry.io/supfam:'
TIGRFAM:
prefix_prefix: TIGRFAM
prefix_reference: 'https://bioregistry.io/tigrfam:'
UBERON:
prefix_prefix: UBERON
prefix_reference: http://purl.obolibrary.org/obo/UBERON_
UO:
prefix_prefix: UO
prefix_reference: http://purl.obolibrary.org/obo/UO_
bioproject:
prefix_prefix: bioproject
prefix_reference: 'https://identifiers.org/bioproject:'
biosample:
prefix_prefix: biosample
prefix_reference: 'https://bioregistry.io/biosample:'
cas:
prefix_prefix: cas
prefix_reference: 'https://bioregistry.io/cas:'
doi:
prefix_prefix: doi
prefix_reference: 'https://bioregistry.io/doi:'
edam.data:
prefix_prefix: edam.data
prefix_reference: http://edamontology.org/data_
emsl.project:
prefix_prefix: emsl.project
prefix_reference: 'https://bioregistry.io/emsl.project:'
emsl:
prefix_prefix: emsl
prefix_reference: http://example.org/emsl_in_mongodb/
emsl_uuid_like:
prefix_prefix: emsl_uuid_like
prefix_reference: http://example.org/emsl_uuid_like/
generic:
prefix_prefix: generic
prefix_reference: https://example.org/generic/
gnps.task:
prefix_prefix: gnps.task
prefix_reference: 'https://bioregistry.io/gnps.task:'
gtpo:
prefix_prefix: gtpo
prefix_reference: http://example.org/gtpo/
igsn:
prefix_prefix: igsn
prefix_reference: https://app.geosamples.org/sample/igsn/
img.taxon:
prefix_prefix: img.taxon
prefix_reference: 'https://bioregistry.io/img.taxon:'
jgi.analysis:
prefix_prefix: jgi.analysis
prefix_reference: https://data.jgi.doe.gov/search?q=
jgi.proposal:
prefix_prefix: jgi.proposal
prefix_reference: 'https://bioregistry.io/jgi.proposal:'
jgi:
prefix_prefix: jgi
prefix_reference: http://example.org/jgi/
kegg:
prefix_prefix: kegg
prefix_reference: 'https://bioregistry.io/kegg:'
KEGG.MODULE:
prefix_prefix: KEGG.MODULE
prefix_reference: 'https://bioregistry.io/kegg.module:'
linkml:
prefix_prefix: linkml
prefix_reference: https://w3id.org/linkml/
mgnify.proj:
prefix_prefix: mgnify.proj
prefix_reference: 'https://bioregistry.io/mgnify.proj:'
my_emsl:
prefix_prefix: my_emsl
prefix_reference: https://release.my.emsl.pnnl.gov/released_data/
neon.identifier:
prefix_prefix: neon.identifier
prefix_reference: http://example.org/neon/identifier/
neon.schema:
prefix_prefix: neon.schema
prefix_reference: http://example.org/neon/schema/
nmdc:
prefix_prefix: nmdc
prefix_reference: https://w3id.org/nmdc/
prov:
prefix_prefix: prov
prefix_reference: http://www.w3.org/ns/prov#
rdf:
prefix_prefix: rdf
prefix_reference: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs:
prefix_prefix: rdfs
prefix_reference: http://www.w3.org/2000/01/rdf-schema#
skos:
prefix_prefix: skos
prefix_reference: http://www.w3.org/2004/02/skos/core#
wikidata:
prefix_prefix: wikidata
prefix_reference: http://www.wikidata.org/entity/
xsd:
prefix_prefix: xsd
prefix_reference: http://www.w3.org/2001/XMLSchema#
KEGG.COMPOUND:
prefix_prefix: KEGG.COMPOUND
prefix_reference: 'https://bioregistry.io/kegg.compound:'
SIO:
prefix_prefix: SIO
prefix_reference: http://semanticscience.org/resource/SIO_
UniProtKB:
prefix_prefix: UniProtKB
prefix_reference: 'https://bioregistry.io/uniprot:'
biolink:
prefix_prefix: biolink
prefix_reference: https://w3id.org/biolink/vocab/
dcterms:
prefix_prefix: dcterms
prefix_reference: http://purl.org/dc/terms/
qud:
prefix_prefix: qud
prefix_reference: http://qudt.org/1.1/schema/qudt#
schema:
prefix_prefix: schema
prefix_reference: http://schema.org/
wgs84:
prefix_prefix: wgs84
prefix_reference: http://www.w3.org/2003/01/geo/wgs84_pos#
MISO:
prefix_prefix: MISO
prefix_reference: http://purl.obolibrary.org/obo/MISO_
COG:
prefix_prefix: COG
prefix_reference: 'https://bioregistry.io/cog:'
KEGG.REACTION:
prefix_prefix: KEGG.REACTION
prefix_reference: 'https://bioregistry.io/kegg.reaction:'
KEGG_PATHWAY:
prefix_prefix: KEGG_PATHWAY
prefix_reference: 'https://bioregistry.io/kegg.pathway:'
MetaCyc:
prefix_prefix: MetaCyc
prefix_reference: 'https://bioregistry.io/metacyc.compound:'
RHEA:
prefix_prefix: RHEA
prefix_reference: 'https://bioregistry.io/rhea:'
SEED:
prefix_prefix: SEED
prefix_reference: 'https://bioregistry.io/seed:'
gold:
prefix_prefix: gold
prefix_reference: 'https://bioregistry.io/gold:'
shex:
prefix_prefix: shex
prefix_reference: http://www.w3.org/ns/shex#
MIXS:
prefix_prefix: MIXS
prefix_reference: https://w3id.org/mixs/
MIXS_yaml:
prefix_prefix: MIXS_yaml
prefix_reference: https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/
BFO:
prefix_prefix: BFO
prefix_reference: http://purl.obolibrary.org/obo/BFO_
owl:
prefix_prefix: owl
prefix_reference: http://www.w3.org/2002/07/owl#
emit_prefixes:
- KEGG.ORTHOLOGY
- MASSIVE
- biosample
- cas
- doi
- gnps.task
- gold
- img.taxon
- jgi.proposal
- kegg
- rdf
- rdfs
- skos
- xsd
default_prefix: nmdc
default_range: string
types:
string:
name: string
description: A character string
notes:
- In RDF serializations, a slot with range of string is treated as a literal or
type xsd:string. If you are authoring schemas in LinkML YAML, the type is
referenced with the lower case "string".
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- schema:Text
base: str
uri: xsd:string
integer:
name: integer
description: An integer
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "integer".
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- schema:Integer
base: int
uri: xsd:integer
boolean:
name: boolean
description: A binary (true or false) value
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "boolean".
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- schema:Boolean
base: Bool
uri: xsd:boolean
repr: bool
float:
name: float
description: A real number that conforms to the xsd:float specification
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "float".
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- schema:Float
base: float
uri: xsd:float
double:
name: double
description: A real number that conforms to the xsd:double specification
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "double".
from_schema: https://w3id.org/nmdc/nmdc
close_mappings:
- schema:Float
base: float
uri: xsd:double
decimal:
name: decimal
description: A real number with arbitrary precision that conforms to the xsd:decimal
specification
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "decimal".
from_schema: https://w3id.org/nmdc/nmdc
broad_mappings:
- schema:Number
base: Decimal
uri: xsd:decimal
time:
name: time
description: A time object represents a (local) time of day, independent of any
particular day
notes:
- URI is dateTime because OWL reasoners do not work with straight date or time
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "time".
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- schema:Time
base: XSDTime
uri: xsd:time
repr: str
date:
name: date
description: a date (year, month and day) in an idealized calendar
notes:
- URI is dateTime because OWL reasoners don't work with straight date or time
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "date".
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- schema:Date
base: XSDDate
uri: xsd:date
repr: str
datetime:
name: datetime
description: The combination of a date and time
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "datetime".
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- schema:DateTime
base: XSDDateTime
uri: xsd:dateTime
repr: str
date_or_datetime:
name: date_or_datetime
description: Either a date or a datetime
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "date_or_datetime".
from_schema: https://w3id.org/nmdc/nmdc
base: str
uri: linkml:DateOrDatetime
repr: str
uriorcurie:
name: uriorcurie
description: a URI or a CURIE
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "uriorcurie".
from_schema: https://w3id.org/nmdc/nmdc
base: URIorCURIE
uri: xsd:anyURI
repr: str
curie:
name: curie
conforms_to: https://www.w3.org/TR/curie/
description: a compact URI
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "curie".
comments:
- in RDF serializations this MUST be expanded to a URI
- in non-RDF serializations MAY be serialized as the compact representation
from_schema: https://w3id.org/nmdc/nmdc
base: Curie
uri: xsd:string
repr: str
uri:
name: uri
conforms_to: https://www.ietf.org/rfc/rfc3987.txt
description: a complete URI
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "uri".
comments:
- in RDF serializations a slot with range of uri is treated as a literal or type
xsd:anyURI unless it is an identifier or a reference to an identifier, in which
case it is translated directly to a node
from_schema: https://w3id.org/nmdc/nmdc
close_mappings:
- schema:URL
base: URI
uri: xsd:anyURI
repr: str
ncname:
name: ncname
description: Prefix part of CURIE
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "ncname".
from_schema: https://w3id.org/nmdc/nmdc
base: NCName
uri: xsd:string
repr: str
objectidentifier:
name: objectidentifier
description: A URI or CURIE that represents an object in the model.
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "objectidentifier".
comments:
- Used for inheritance and type checking
from_schema: https://w3id.org/nmdc/nmdc
base: ElementIdentifier
uri: shex:iri
repr: str
nodeidentifier:
name: nodeidentifier
description: A URI, CURIE or BNODE that represents a node in a model.
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "nodeidentifier".
from_schema: https://w3id.org/nmdc/nmdc
base: NodeIdentifier
uri: shex:nonLiteral
repr: str
jsonpointer:
name: jsonpointer
conforms_to: https://datatracker.ietf.org/doc/html/rfc6901
description: A string encoding a JSON Pointer. The value of the string MUST conform
to JSON Point syntax and SHOULD dereference to a valid object within the current
instance document when encoded in tree form.
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "jsonpointer".
from_schema: https://w3id.org/nmdc/nmdc
base: str
uri: xsd:string
repr: str
jsonpath:
name: jsonpath
conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html
description: A string encoding a JSON Path. The value of the string MUST conform
to JSON Point syntax and SHOULD dereference to zero or more valid objects within
the current instance document when encoded in tree form.
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "jsonpath".
from_schema: https://w3id.org/nmdc/nmdc
base: str
uri: xsd:string
repr: str
sparqlpath:
name: sparqlpath
conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths
description: A string encoding a SPARQL Property Path. The value of the string
MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects
within the current instance document when encoded as RDF.
notes:
- If you are authoring schemas in LinkML YAML, the type is referenced with the
lower case "sparqlpath".
from_schema: https://w3id.org/nmdc/nmdc
base: str
uri: xsd:string
repr: str
external_identifier:
name: external_identifier
description: A CURIE representing an external identifier
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://microbiomedata.github.io/nmdc-schema/identifiers/
typeof: uriorcurie
uri: xsd:anyURI
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
bytes:
name: bytes
description: An integer value that corresponds to a size in bytes
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- UO:0000233
base: int
uri: xsd:long
decimal_degree:
name: decimal_degree
description: A decimal degree expresses latitude or longitude as decimal fractions.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://en.wikipedia.org/wiki/Decimal_degrees
base: float
uri: xsd:decimal
language_code:
name: language_code
description: A language code conforming to ISO_639-1
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://en.wikipedia.org/wiki/ISO_639-1
base: str
uri: xsd:language
unit:
name: unit
from_schema: https://w3id.org/nmdc/nmdc
mappings:
- qud:Unit
- UO:0000000
base: str
uri: xsd:string
enums:
CalibrationTargetEnum:
name: CalibrationTargetEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
mass_charge_ratio:
text: mass_charge_ratio
title: m/z
aliases:
- Mass
- m/z
retention_time:
text: retention_time
aliases:
- RT
retention_index:
text: retention_index
aliases:
- RI
CalibrationStandardEnum:
name: CalibrationStandardEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
fames:
text: fames
aliases:
- FAMES
alkanes:
text: alkanes
aliases:
- Alkanes
StrandedOrientationEnum:
name: StrandedOrientationEnum
description: This enumeration specifies information about stranded RNA library
preparations.
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
antisense orientation:
text: 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:
text: sense orientation
description: Orientation that corresponds to the coding sequence of messenger
RNA.
MassSpectrometryAcquisitionStrategyEnum:
name: MassSpectrometryAcquisitionStrategyEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
data_independent_acquisition:
text: 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:
text: 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:
text: full_scan_only
description: Mass spectrometer data acquisition method wherein only MS1 data
are acquired.
aliases:
- MS
ResolutionCategoryEnum:
name: ResolutionCategoryEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
high:
text: high
description: higher than unit resolution
low:
text: low
description: at unit resolution
MassAnalyzerEnum:
name: MassAnalyzerEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
time_of_flight:
text: time_of_flight
description: Instrument that separates ions by m/z in a field-free region
after acceleration to a fixed acceleration energy.
aliases:
- TOF
exact_mappings:
- MS:1000084
quadrupole:
text: quadrupole
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.
aliases:
- Quad
- Q
exact_mappings:
- MS:1000081
Orbitrap:
text: Orbitrap
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.
aliases:
- Orbi
exact_mappings:
- MS:1000484
ion_cyclotron_resonance:
text: ion_cyclotron_resonance
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.
aliases:
- ICR
exact_mappings:
- MS:1000079
ion_trap:
text: ion_trap
description: A device for spatially confining ions using electric and magnetic
fields alone or in combination.
aliases:
- LTQ
- Ion Trap
- Paul Trap
exact_mappings:
- MS:1000264
IonizationSourceEnum:
name: IonizationSourceEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
electrospray_ionization:
text: electrospray_ionization
aliases:
- ESI
matrix_assisted_laser_desorption_ionization:
text: matrix_assisted_laser_desorption_ionization
aliases:
- MALDI
atmospheric_pressure_photo_ionization:
text: atmospheric_pressure_photo_ionization
aliases:
- APPI
atmospheric_pressure_chemical_ionization:
text: atmospheric_pressure_chemical_ionization
aliases:
- APCI
electron_ionization:
text: electron_ionization
aliases:
- EI
MassSpectrumCollectionModeEnum:
name: MassSpectrumCollectionModeEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
full_profile:
text: full_profile
reduced_profile:
text: reduced_profile
centroid:
text: centroid
PolarityModeEnum:
name: PolarityModeEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
positive:
text: positive
negative:
text: negative
EluentIntroductionCategoryEnum:
name: EluentIntroductionCategoryEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
liquid_chromatography:
text: liquid_chromatography
description: The processed sample is introduced into the mass spectrometer
through a liquid chromatography process.
aliases:
- LC
gas_chromatography:
text: gas_chromatography
description: The processed sample is introduced into the mass spectrometer
through a gas chromatography process.
aliases:
- GC
direct_infusion_syringe:
text: direct_infusion_syringe
description: The processed sample is introduced into the mass spectrometer
through a direct infusion process using a syringe.
direct_infusion_autosampler:
text: direct_infusion_autosampler
description: The processed sample is introduced into the mass spectrometer
through a direct infusion process using an autosampler.
LibraryTypeEnum:
name: LibraryTypeEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
DNA:
text: DNA
RNA:
text: RNA
ContainerCategoryEnum:
name: ContainerCategoryEnum
description: The permitted types of containers used in processing metabolomic
samples.
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
permissible_values:
v-bottom_conical_tube:
text: v-bottom_conical_tube
falcon_tube:
text: falcon_tube
SeparationMethodEnum:
name: SeparationMethodEnum
description: The tool/substance used to separate or filter a solution or mixture.
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
permissible_values:
ptfe_96_well_filter_plate:
text: ptfe_96_well_filter_plate
syringe:
text: syringe
StationaryPhaseEnum:
name: StationaryPhaseEnum
description: The type of stationary phase used in a chromatography process.
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-4504-1039
permissible_values:
BEH-HILIC:
text: BEH-HILIC
C18:
text: C18
C8:
text: C8
C4:
text: C4
C2:
text: C2
C1:
text: C1
C30:
text: C30
C60:
text: C60
CNT:
text: CNT
CN:
text: CN
Diol:
text: Diol
HILIC:
text: HILIC
NH2:
text: NH2
Phenyl:
text: Phenyl
Polysiloxane:
text: Polysiloxane
PS-DVB:
text: PS-DVB
SAX:
text: SAX
SCX:
text: SCX
Silica:
text: Silica
WCX:
text: WCX
WAX:
text: WAX
ZIC-HILIC:
text: ZIC-HILIC
ZIC-pHILIC:
text: ZIC-pHILIC
ZIC-cHILIC:
text: ZIC-cHILIC
ProtocolCategoryEnum:
name: ProtocolCategoryEnum
description: The possible protocols that may be followed for an assay.
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
mplex:
text: mplex
derivatization:
text: derivatization
filter_clean_up:
text: filter_clean_up
organic_matter_extraction:
text: organic_matter_extraction
solid_phase_extraction:
text: solid_phase_extraction
phosphorus_extraction:
text: phosphorus_extraction
ph_measurement:
text: ph_measurement
respiration_measurement:
text: respiration_measurement
texture_measurement:
text: texture_measurement
dna_extraction:
text: dna_extraction
phenol_chloroform_extraction:
text: phenol_chloroform_extraction
ChromatographicCategoryEnum:
name: ChromatographicCategoryEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
liquid_chromatography:
text: liquid_chromatography
aliases:
- LC
gas_chromatography:
text: gas_chromatography
aliases:
- GC
solid_phase_extraction:
text: solid_phase_extraction
aliases:
- SPE
SamplePortionEnum:
name: SamplePortionEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
supernatant:
text: supernatant
aliases:
- top_layer
pellet:
text: pellet
aliases:
- bottom_layer
organic_layer:
text: organic_layer
aqueous_layer:
text: aqueous_layer
non_polar_layer:
text: non_polar_layer
BinQualityEnum:
name: BinQualityEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
HQ:
text: HQ
description: Metagenome-assembled genome is high quality based on MIMAG standards
(https://doi.org/10.1038/nbt.3893)
aliases:
- high quality
MQ:
text: MQ
description: Metagenome-assembled genome is medium quality based on MIMAG
standards (https://doi.org/10.1038/nbt.3893)
aliases:
- medium quality
LQ:
text: LQ
description: Metagenome-assembled genome is low quality based on MIMAG standards
(https://doi.org/10.1038/nbt.3893)
aliases:
- low quality
ChemicalConversionCategoryEnum:
name: ChemicalConversionCategoryEnum
from_schema: https://w3id.org/nmdc/nmdc
permissible_values:
addition:
text: addition
substitution:
text: substitution
acid_base:
text: acid_base
reduction_oxidation:
text: reduction_oxidation
combustion:
text: combustion
decomposition:
text: decomposition
protease_cleavage:
text: protease_cleavage
description: an enzymatic cleavage which relies on an enzyme with protease
activity to act on proteins and to produce polypeptides (protein fragments).
meaning: OBI:0600056
BiosampleCategoryEnum:
name: BiosampleCategoryEnum
description: Funding-based, sample location-based, or experimental method-based
defined categories
notes:
- Currently, these values can associated with biosamples via the biosample_categories
slot
- They might also be applicable to other classes
- They are intended to enable metadata search and or filtering, for example in
the NMDC data portal, https://data.microbiomedata.org/
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- category tag
permissible_values:
LTER:
text: LTER
meaning: https://lternet.edu/
title: National Science Foundation's Long Term Ecological Research Network
SIP:
text: SIP