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nmdc.yaml
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nmdc.yaml
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id: https://microbiomedata/schema
name: NMDC
title: NMDC Schema
description: >-
Schema for National Microbiome Data Collaborative (NMDC).
This schem is organized into 3 separate modules:
This schema is organized into distinct modules:
* a set of core types for representing data values
* the mixs schema (auto-translated from mixs excel)
* annotation schema
* the NMDC schema itself
license: https://creativecommons.org/publicdomain/zero/1.0/
version: 2021.06.01rc1
prefixes:
nmdc: https://microbiomedata/meta/
GOLD: https://identifiers.org/gold/
mixs: https://w3id.org/gensc/
wgs: http://www.w3.org/2003/01/geo/wgs84_pos
qud: http://qudt.org/1.1/schema/qudt#
dcterms: http://purl.org/dc/terms/
linkml: https://w3id.org/linkml/
MS: http://purl.obolibrary.org/obo/MS_
OBI: http://purl.obolibrary.org/obo/OBI_
NCIT: http://purl.obolibrary.org/obo/NCIT_
igsn: https://app.geosamples.org/sample/igsn/
default_prefix: nmdc
default_range: string
default_curi_maps:
- obo_context
- idot_context
emit_prefixes:
- rdf
- rdfs
- xsd
- skos
# This file organizes the main NMDC schema.
# It brings in the mixs schema plus a schemaa
# of core types
imports:
- linkml:types
- mixs
- core
- prov
- workflow_execution_activity
- annotation
subsets:
sample subset:
description: >-
Subset consisting of entities linked to the processing of samples.
Currently, this subset consists of study, omics process, and biosample.
data object subset:
description: >-
Subset consisting of the data objects that either inputs or outputs of processes or workflows.
classes:
database:
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 databse
top level holder class. When translated to JSON-Schema this is the 'root' object.
It should contain pointers to other objects of interest
slots:
- biosample set
- study set
- data object set
- activity set
- mags activity set
- metabolomics analysis activity set
- metaproteomics analysis activity set
- metagenome annotation activity set
- metagenome assembly set
- read QC analysis activity set
- read based analysis activity set
- nom analysis activity set
- omics processing set
- functional annotation set
- genome feature set
slot_usage:
nmdc schema version:
description: >-
TODO
date created:
description: >-
TODO
etl software version:
description: >-
TODO
data object:
is_a: named thing
in_subset:
- data object subset
description: >-
An object that primarily consists of symbols that represent information.
Files, records, and omics data are examples of data objects.
slots:
- file size bytes
- md5 checksum
- data object type
- compression type
- was generated by
- url
- type # custom slot that specifies object type
id_prefixes:
- GOLD
biosample:
is_a: named thing
in_subset:
- sample subset
aliases: ['sample', 'material sample', 'specimen', 'biospecimen']
description: >-
A material sample. It may be environmental (encompassing many organisms) or isolate or tissue.
An environmental sample containing genetic material from multiple individuals is commonly referred to as a biosample.
slots:
- type # custom slot that specifies object type
# MIXS slots
- agrochem_addition
- alkalinity
- alkalinity_method
- alkyl_diethers
- alt
- al_sat
- al_sat_meth
- aminopept_act
- ammonium
- annual_precpt
- annual_temp
- bacteria_carb_prod
- bishomohopanol
- bromide
- calcium
- carb_nitro_ratio
- chem_administration
- chloride
- chlorophyll
- collection_date
- cur_land_use
- cur_vegetation
- cur_vegetation_meth
- crop_rotation
- density
- depth
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_inorg_phosp
- diss_org_carb
- diss_org_nitro
- diss_oxygen
- drainage_class
- elev
- env_package
- env_broad_scale
- env_local_scale
- env_medium
- extreme_event
- fao_class
- fire
- flooding
- geo_loc_name
- glucosidase_act
- heavy_metals
- heavy_metals_meth
- horizon
- horizon_meth
- lat_lon
- link_addit_analys
- link_class_info
- link_climate_info
- local_class
- local_class_meth
- magnesium
- mean_frict_vel
- mean_peak_frict_vel
- microbial_biomass
- microbial_biomass_meth
- misc_param
- n_alkanes
- nitrate
- nitrite
- org_matter
- org_nitro
- organism_count
- oxy_stat_samp
- part_org_carb
- perturbation
- petroleum_hydrocarb
- ph
- ph_meth
- phaeopigments
- phosplipid_fatt_acid
- pool_dna_extracts
- potassium
- pressure
- previous_land_use
- previous_land_use_meth
- profile_position
- redox_potential
- salinity
- salinity_meth
- samp_collect_device
- samp_store_dur
- samp_store_loc
- samp_store_temp
- samp_vol_we_dna_ext
- season_temp
- season_precpt
- sieving
- size_frac_low
- size_frac_up
- slope_gradient
- slope_aspect
- sodium
- soil_type
- soil_type_meth
- store_cond
- sulfate
- sulfide
- temp
- texture
- texture_meth
- tillage
- tidal_stage
- tot_carb
- tot_depth_water_col
- tot_diss_nitro
- tot_org_carb
- tot_org_c_meth
- tot_nitro_content
- tot_nitro_content_meth
- tot_phosp
- water_content
- water_content_soil_meth
# GOLD path fields
- ecosystem
- ecosystem_category
- ecosystem_type
- ecosystem_subtype
- specific_ecosystem
# GOLD specific fields
- add_date
- community
- habitat
- host_name
- identifier
- location
- mod_date
- ncbi_taxonomy_name
- proport_woa_temperature
- salinity_category # note: maps to gold:salinity
- sample_collection_site
- soluble_iron_micromol
- subsurface_depth
slot_usage:
lat_lon:
required: false
description: >-
This is currently a required field but it's not clear if this should be required for human hosts
part of:
required: false
range: study
description: >-
Relates the biosample to the study for which the sample was collected.
env_broad_scale:
required: true
env_local_scale:
required: true
env_medium:
required: true
id_prefixes:
- GOLD
exact_mappings:
- OBI:0000747
- NCIT:C43412
study:
is_a: named thing
in_subset:
- sample subset
aliases: ['proposal', 'research proposal', 'research study', 'investigation']
description: >-
A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
slots:
- ecosystem
- ecosystem_category
- ecosystem_type
- ecosystem_subtype
- specific_ecosystem
- principal investigator name
- doi
- type # custom slot that specifies object type
todos:
- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor
- project_name is redundant with name, so excluding it
biosample processing:
aliases:
- material processing
is_a: named thing
description: >-
A process that takes one or more biosamples as inputs and generates one or as outputs.
Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.
slots:
- has input
slot_usage:
has input:
range: biosample
broad_mappings:
- OBI:0000094 ## material processing: https://github.com/microbiomedata/nmdc-metadata/issues/171
omics processing:
aliases:
- omics assay
is_a: biosample processing
in_subset:
- sample subset
description: >-
The methods and processes used to generate omics data from a biosample or organism.
comments:
- The IDs for objects coming from GOLD will have prefixes gold:GpNNNN
slots:
- add_date
- mod_date
- has input
- has output
- instrument_name
- ncbi_project_name
- omics type
- part of
- principal investigator name
- processing_institution
- type # custom slot that specifies object type
broad_mappings:
- OBI:0000070 ## assay: https://github.com/microbiomedata/nmdc-metadata/issues/171
slots:
object set:
mixin: true
domain: database
multivalued: true
inlined: true
description:
Applies to a property that links a database object to a set of objects.
This is necessary in a json document to provide context for a list, and
to allow for a single json object that combines multiple object types
biosample set:
mixins: object set
domain: database
range: biosample
multivalued: true
inlined: true
description: >-
This property links a database object to the set of samples within it.
study set:
mixins: object set
domain: database
range: study
multivalued: true
inlined: true
description: >-
This property links a database object to the set of studies within it.
data object set:
mixins: object set
domain: database
range: data object
multivalued: true
inlined: true
description: >-
This property links a database object to the set of data objects within it.
genome feature set:
mixins: object set
domain: database
range: genome feature
multivalued: true
inlined: true
description: >-
This property links a database object to the set of all features
functional annotation set:
mixins: object set
domain: database
range: functional annotation
multivalued: true
inlined: true
description: >-
This property links a database object to the set of all functional annotations
activity set:
mixins: object set
domain: database
range: workflow execution activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of workflow activities.
mags activity set:
mixins: object set
domain: database
range: MAGs analysis activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of MAGs analysis activities.
metabolomics analysis activity set:
mixins: object set
domain: database
range: metabolomics analysis activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of metabolomics analysis activities.
metaproteomics analysis activity set:
mixins: object set
domain: database
range: metaproteomics analysis activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of metaproteomics analysis activities.
metagenome annotation activity set:
mixins: object set
domain: database
range: metagenome annotation activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of metaproteomics analysis activities.
metagenome assembly set:
mixins: object set
domain: database
range: metagenome assembly
multivalued: true
inlined: true
description: >-
This property links a database object to the set of metaproteomics analysis activities.
read QC analysis activity set:
mixins: object set
domain: database
range: read QC analysis activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of read QC analysis activities.
read based analysis activity set:
mixins: object set
domain: database
range: read based analysis activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of read based analysis activities.
nom analysis activity set:
mixins: object set
domain: database
range: nom analysis activity
multivalued: true
inlined: true
description: >-
This property links a database object to the set of natural organic matter (NOM) analysis activities.
omics processing set:
mixins: object set
domain: database
range: omics processing
multivalued: true
inlined: true
description: >-
This property links a database object to the set of omics processings within it.
omics type:
range: controlled term value
# range: string
description: >-
The type of omics data
examples:
- value: metatranscriptome
- value: metagenome
data object type:
range: controlled term value
description: >-
The type of data object
examples:
- value: metagenome_assembly
compression type:
range: string
description: >-
If provided, specifies the compression type
examples:
- value: gzip
todos:
- consider enum
instrument_name:
description: >-
The name of the instrument that was used for processing the sample.
## GOLD PATHS
gold_path_field:
is_a: attribute
range: string
abstract: true
description: >-
This is a grouping for any of the gold path fields
ecosystem:
is_a: gold_path_field
description: >-
TODO
ecosystem_category:
is_a: gold_path_field
description: >-
TODO
ecosystem_type:
is_a: gold_path_field
description: >-
TODO
ecosystem_subtype:
is_a: gold_path_field
description: >-
TODO
specific_ecosystem:
is_a: gold_path_field
description: >-
TODO
## GOLD DATABASE SPECFIC FIELDS
principal investigator name:
aliases:
- PI
- principal investigator
is_a: attribute
range: person value
description: >-
represents the PI
doi:
is_a: attribute
range: attribute value
add_date:
range: string
description: >-
The date on which the information was added to the database.
mod_date:
range: string
description: >-
The last date on which the database information was modified.
ecosystem_path_id:
range: string
description: >-
A unique id representing the GOLD classifers associated with a sample.
habitat:
range: string
location:
range: string
community:
range: string
ncbi_taxonomy_name:
range: string
ncbi_project_name:
range: string
sample_collection_site:
range: string
identifier:
range: string
sample_collection_year:
range: integer
sample_collection_month:
range: integer
sample_collection_day:
range: integer
sample_collection_hour:
range: integer
sample_collection_minute:
range: integer
salinity_category:
description: >-
Categorcial description of the sample's salinity.
Examples: halophile, halotolerant, hypersaline, huryhaline
range: string
see_also:
- https://github.com/microbiomedata/nmdc-metadata/pull/297
soluble_iron_micromol:
range: string
host_name:
range: string
subsurface_depth:
range: quantity value
proport_woa_temperature:
range: string
biogas_temperature:
range: string
soil_annual_season_temp:
range: string
biogas_retention_time:
range: string
processing_institution:
range: string
description: >-
The organization that processed the sample.
omics_type:
range: string
completion_date:
range: string