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standards.yml
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ebi_null_vals_all: &ebi_null_vals_all
allowed:
- "not collected"
- "not provided"
- "restricted access"
- "not applicable"
type: string
taxon_id_formats: &taxon_id_formats
- regex: ^\d+$
type: string
- *ebi_null_vals_all
host_type_specific_metadata:
base:
metadata_fields:
sample_name:
empty: false
is_phi: false
regex: ^[a-zA-Z0-9\.]+$
required: true
type: string
unique: true
sample_type:
empty: false
is_phi: false
required: true
type: string
host_type_specific_metadata:
ebi_submittable:
"default": "not provided"
metadata_fields:
anonymized_name:
empty: true
is_phi: false
required: false
type: string
collection_device:
empty: false
is_phi: false
required: false
type: string
collection_method:
empty: false
is_phi: false
required: false
type: string
collection_timestamp:
anyof:
- regex: '^([0-9]{4})(?:-([0-1][0-9])(?:-([0-3][0-9])(?: ([0-2][0-9])(?::([0-5][0-9])(?::([0-5][0-9]))?)?)?)?)?$'
type: string
check_with: date_not_in_future
- *ebi_null_vals_all
empty: false
field_desc: The day and time of sampling as a single point in time expressed in
24-hour time format, e.g. 2016-11-22.
is_phi: false
required: true
collection_date:
anyof:
- regex: '^([0-9]{4})(?:-([0-1][0-9])(?:-([0-3][0-9])(?: ([0-2][0-9])(?::([0-5][0-9])(?::([0-5][0-9]))?)?)?)?)?$'
type: string
check_with: date_not_in_future
- *ebi_null_vals_all
empty: false
field_desc: The day and time of sampling as a single point in time expressed in
24-hour time format, e.g. 2016-11-22.
is_phi: false
required: true
country:
empty: false
is_phi: false
required: true
type: string
description:
empty: false
field_desc: A description of the sample that can include site, subject, and sample
material.
is_phi: false
required: true
type: string
dna_extracted:
allowed:
- 'TRUE'
- 'FALSE'
- not collected
- not provided
type: string
empty: false
field_desc: Whether the DNA been extracted from the sample.
is_phi: false
required: true
elevation:
anyof:
- min: -413.0
type: number
- allowed:
- not collected
- not provided
- restricted access
type: string
empty: false
field_desc: Height of land above sea level in meters at the sampling site
is_phi: false
required: true
units: elevation_units
elevation_units:
allowed:
- meters
# default: meters
empty: false
is_phi: false
required: false
type: string
empo_1:
empty: false
is_phi: false
required: true
type: string
empo_2:
empty: false
is_phi: false
required: true
type: string
empo_3:
empty: false
is_phi: false
required: true
type: string
empo_4:
# NOT putting the full list of options here: they should be
# resolved at the leaf levels
empty: false
is_phi: false
required: true
type: string
env_biome:
empty: false
field_desc: Classification of the location where the sample was obtained, from the
Environmental Ontology (ENVO).
is_phi: false
required: true
type: string
env_feature:
empty: false
field_desc: Classification of a specific feature in the biome, from the Environmental
Ontology (ENVO).
is_phi: false
required: true
type: string
env_material:
empty: false
field_desc: Classification of the material being sampled, from the Environmental
Ontology (ENVO).
is_phi: false
required: true
type: string
env_package:
empty: false
field_desc: Environment where the sample was obtained.
is_phi: false
required: true
type: string
geo_loc_name:
empty: false
field_desc: The geographical origin of the sample as defined by the country or location
as chosen from the GAZ ontology, e.g. USA:CA:San Diego .
is_phi: false
required: true
type: string
latitude:
anyof:
- max: 90.00
min: -90.00
type: number
- allowed:
- not collected
- not provided
- restricted access
type: string
empty: false
field_desc: Location of the sample site by latitude in decimal degrees, e.g. 32.72
for San Diego, USA.
is_phi: false
required: true
units: latitude_units
latitude_units:
allowed:
- Decimal degrees
# default: Decimal degrees
empty: false
is_phi: false
required: false
type: string
longitude:
anyof:
- max: 180.00
min: -180.00
type: number
- allowed:
- not collected
- not provided
- restricted access
type: string
empty: false
field_desc: Location of the sample site by longitude in decimal degrees, e.g. -117.16
for San Diego, USA.
is_phi: false
required: true
units: longitude_units
longitude_units:
allowed:
- Decimal degrees
# default: Decimal degrees
empty: false
is_phi: false
required: false
type: string
physical_specimen_location:
empty: false
field_desc: Where the sample is stored (if there is any left).
is_phi: false
required: true
type: string
physical_specimen_remaining:
allowed:
- 'TRUE'
- 'FALSE'
- not collected
- not provided
- restricted access
type: string
empty: false
field_desc: Whether there is any raw specimen left to sample.
is_phi: false
required: true
scientific_name:
empty: false
field_desc: The scientific name of the metagenome associated with this sample, as
defined in the NCBI Taxonomy. Be aware that this is NOT the scientific name of
the host! Note that this value must correspond to the taxon id entered in the
taxon_id field; for example, for a sample from the human gut, the scientific_name
should be human gut microbiome, corresponding to taxon id 408170.
is_phi: false
required: true
type: string
taxon_id:
anyof: *taxon_id_formats
empty: false
field_desc: The NCBI Taxonomy id of the metagenome associated with this sample.
Be aware that this is NOT the taxon id of the host! Note that this value must
correspond to the scientific name entered in the scientific_name field; for example,
for a sample from the human gut, the taxon_id should be 408170, corresponding
to the scientific name human gut metagenome.
is_phi: false
required: true
title:
empty: false
field_desc: Title of study.
is_phi: false
required: true
type: string
# TODO: Q: is this field actually required or no?
# tube_id:
# empty: false
# field_desc: The identification of the tube containing the sample.
# is_phi: false
# required: true
# type: string
host_type_specific_metadata:
host_associated:
metadata_fields:
empo_1:
allowed:
- Host-associated
default: Host-associated
type: string
env_package:
allowed:
- host-associated
default: host-associated
type: string
host_age:
anyof:
- min_exclusive: 0
type: number
- allowed:
- not collected
- not provided
type: string
empty: false
field_desc: Host age in appropriate units
is_phi: false
required: true
units: host_age_units
host_age_units:
empty: false
is_phi: false
required: true
type: string
host_common_name:
empty: false
field_desc: common usage term for host e.g. human
is_phi: false
required: true
type: string
host_scientific_name:
empty: false
field_desc: host scientific name e.g. Homo sapiens
is_phi: false
required: true
type: string
host_subject_id:
empty: false
field_desc: A label that applies to all samples belonging to one subject or one
sample
is_phi: false
required: true
type: string
host_taxid:
anyof: *taxon_id_formats
empty: false
field_desc: taxonomy id of host e.g. human is 9606
is_phi: false
required: true
host_weight:
anyof:
- min_exclusive: 0
type: number
- allowed:
- not collected
- not provided
type: string
empty: false
field_desc: in kilograms preferred
is_phi: false
required: true
units: host_weight_units
host_weight_units:
empty: false
is_phi: false
required: true
type: string
# is there any reason time_point has to be host associated??
time_point:
anyof:
- type: integer
- allowed:
- not applicable
- not collected
- not provided
- restricted access
type: string
empty: false
field_desc: A numeric ID to indicate order of linked samples
is_phi: false
required: false
host_type_specific_metadata:
host_associated_non_saline:
metadata_fields:
empo_2:
allowed:
- Host-associated (non-saline)
default: Host-associated (non-saline)
type: string
host_type_specific_metadata:
animal_non_saline:
metadata_fields:
empo_3:
allowed:
- Animal (non-saline)
default: Animal (non-saline)
type: string
env_feature:
allowed:
- animal-associated habitat
default: animal-associated habitat
type: string
# apparently uberon ontology is just for animal species..
host_body_habitat:
empty: false
field_desc: from UBERON e.g skin, gastrointestinal tract
is_phi: false
required: true
type: string
host_body_product:
empty: false
field_desc: from UBERON e.g. skin, feces
is_phi: false
required: true
type: string
host_body_site:
empty: false
field_desc: from UBERON e.g. skin of arm, colon
is_phi: false
required: true
type: string
host_life_stage:
# TODO: Gail's writeup includes infant and juvenile
# but NOT child ... but NPH uses child?
allowed:
- adult
- child
- not applicable
- not collected
- not provided
- restricted access
type: string
empty: false
field_desc: e.g. adult
is_phi: false
required: true
sex:
allowed:
- female
- male
- neuter
- hermaphrodite
- not applicable
- not collected
- not provided
- restricted access
type: string
empty: false
is_phi: false
required: true
host_type_specific_metadata:
vertebrate:
sample_type_specific_metadata:
colon content:
metadata_fields:
env_material:
allowed:
- intestine environment
default: intestine environment
type: string
host_body_habitat:
allowed:
- UBERON:gastrointestinal system
default: UBERON:gastrointestinal system
type: string
host_body_product:
allowed:
- UBERON:lumen of gut
default: UBERON:lumen of gut
type: string
host_body_site:
allowed:
- UBERON:colon
default: UBERON:colon
type: string
scientific_name:
allowed:
- gut metagenome
default: gut metagenome
type: string
taxon_id:
allowed:
- 749906
default: 749906
type: integer
colon mucosa:
metadata_fields:
env_material:
allowed:
- intestine environment
default: intestine environment
type: string
host_body_habitat:
allowed:
- UBERON:gastrointestinal system
default: UBERON:gastrointestinal system
type: string
host_body_product:
allowed:
- UBERON:colon mucosa
default: UBERON:colon mucosa
type: string
host_body_site:
allowed:
- UBERON:colon
default: UBERON:colon
type: string
scientific_name:
allowed:
- gut metagenome
default: gut metagenome
type: string
taxon_id:
allowed:
- 749906
default: 749906
type: integer
saliva:
metadata_fields:
empo_4:
allowed:
- Animal secretion (non-saline)
default: Animal secretion (non-saline)
type: string
env_material:
allowed:
- saliva material
default: saliva material
type: string
host_body_habitat:
allowed:
- UBERON:oral cavity
default: UBERON:oral cavity
type: string
host_body_product:
allowed:
- UBERON:saliva
default: UBERON:saliva
type: string
host_body_site:
allowed:
- UBERON:mouth
default: UBERON:mouth
type: string
scientific_name:
allowed:
- oral metagenome
default: oral metagenome
type: string
taxon_id:
allowed:
- 1227552
default: 1227552
type: integer
serum:
metadata_fields:
env_material:
allowed:
- blood
default: blood
type: string
host_body_habitat:
allowed:
- UBERON:blood
default: UBERON:blood
type: string
host_body_product:
allowed:
- UBERON:serum
default: UBERON:serum
type: string
host_body_site:
allowed:
- UBERON:blood plasma
default: UBERON:blood plasma
type: string
scientific_name:
allowed:
- blood metagenome
default: blood metagenome
type: string
taxon_id:
allowed:
- 1676987
default: 1676987
type: integer
skin:
metadata_fields:
empo_4:
allowed:
- Animal surface (non-saline)
default: Animal surface (non-saline)
type: string
env_material:
allowed:
- sebum material
default: sebum material
type: string
host_body_habitat:
allowed:
- UBERON:skin
default: UBERON:skin
type: string
host_body_product:
allowed:
- UBERON:sebum
default: UBERON:sebum
type: string
scientific_name:
allowed:
- skin metagenome
default: skin metagenome
type: string
taxon_id:
allowed:
- 1338477
default: 1338477
type: integer
sputum:
metadata_fields:
env_material:
allowed:
- bodily fluid material
default: bodily fluid material
type: string
host_body_habitat:
allowed:
- UBERON:respiratory system
default: UBERON:respiratory system
type: string
host_body_product:
allowed:
- UBERON:sputum
default: UBERON:sputum
type: string
host_body_site:
allowed:
- UBERON:lung
default: UBERON:lung
type: string
scientific_name:
allowed:
- lung metagenome
default: lung metagenome
type: string
taxon_id:
allowed:
- 1729361
default: 1729361
type: integer
# TODO: is this the correct level to introduce feces?
feces:
metadata_fields:
empo_4:
allowed:
- Animal distal gut (non-saline)
default: Animal distal gut (non-saline)
type: string
env_material:
allowed:
- fecal material
default: fecal material
type: string
host_body_habitat:
allowed:
- UBERON:feces
default: UBERON:feces
type: string
host_body_product:
allowed:
- UBERON:feces
default: UBERON:feces
type: string
host_body_site:
allowed:
- UBERON:feces
default: UBERON:feces
type: string
scientific_name:
allowed:
- feces metagenome
default: feces metagenome
type: string
taxon_id:
allowed:
- 1861841
default: 1861841
type: integer
tongue:
alias: saliva
urine:
metadata_fields:
env_material:
allowed:
- urine material
default: urine material
type: string
host_body_habitat:
allowed:
- UBERON:urine
default: UBERON:urine
type: string
host_body_product:
allowed:
- UBERON:urine
default: UBERON:urine
type: string
host_body_site:
allowed:
- UBERON:urine
default: UBERON:urine
scientific_name:
allowed:
- urine metagenome
default: urine metagenome
type: string
taxon_id:
allowed:
- 1346744
default: 1346744
type: integer
host_type_specific_metadata:
human:
metadata_fields:
env_biome:
# is urban really the only biome for humans?
allowed:
- urban biome
default: urban biome
type: string
env_feature:
allowed:
- human-associated habitat
default: human-associated habitat
type: string
env_package:
allowed:
- human-associated
default: human-associated
type: string
host_age_units:
allowed:
- years
default: years
type: string
host_body_mass_index:
anyof:
- min_exclusive: 0
type: number
- allowed:
- not applicable
- not collected
- not provided
- restricted access
type: string
empty: false
field_desc: Body mass index
is_phi: false
required: true
host_common_name:
allowed:
- human
default: human
type: string
host_height:
anyof:
- min_exclusive: 0
type: number
- allowed:
- not collected
- not provided
type: string
empty: false
field_desc: Height (or length) of host in cm preferred
is_phi: false
required: true
units: host_height_units
host_height_units:
allowed:
- cm
default: cm
empty: false
is_phi: false
required: true
type: string
host_scientific_name:
allowed:
- Homo sapiens
default: Homo sapiens
type: string
host_taxid:
allowed:
- '9606'
default: '9606'
type: string
host_weight_units:
allowed:
- kg
default: kg
type: string
irb_institute:
type: string
empty: false
field_desc: the name of institute that approved the IRB (human studies)
is_phi: false
required: false
irb_protocol_id:
type: string
empty: false
field_desc: the ID of the IRB protocol that covers the collection and analysis of
this sample (human studies)
is_phi: false
required: false
sample_type_specific_metadata:
antecubital crease:
alias: "antecubital fossa"
antecubital fossa:
# TODO: this is a duplicate of "skin of elbow"
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:elbow
default: UBERON:elbow
type: string
qiita_sample_type:
allowed:
- "skin of arm"
default: "skin of arm"
type: string
axilla skin:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:axilla
default: UBERON:axilla
type: string
qiita_sample_type:
allowed:
- "axilla skin"
default: "axilla skin"
type: string
back:
alias: "skin of back"
buccal mucosa:
base_type: "saliva"
metadata_fields:
host_body_site:
allowed:
- UBERON:buccal mucosa
default: UBERON:buccal mucosa
type: string
qiita_sample_type:
allowed:
- "buccal mucosa"
default: "buccal mucosa"
type: string
cheek:
alias: "skin of cheek"
# TODO: why is this a different item than (rather than an alias of) "skin of elbow"?
elbow skin:
alias: "skin of elbow"
external auditory canal:
alias: "skin of external ear canal"
face:
alias: "skin of face"
feces:
metadata_fields:
env_package:
allowed:
- human-gut
default: human-gut
type: string
scientific_name:
allowed:
- human gut metagenome
default: human gut metagenome
type: string
taxon_id:
allowed:
- 408170
default: 408170
type: integer
forehead:
alias: "skin of forehead"
glabella:
alias: "glabella skin"
glabella skin:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:glabella skin
default: UBERON:glabella skin
type: string
qiita_sample_type:
allowed:
- "skin of forehead"
default: "skin of forehead"
type: string
heel skin:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:heel
default: UBERON:heel
type: string
qiita_sample_type:
allowed:
- "skin of foot"
default: "skin of foot"
type: string
hypothenar palm:
alias: "skin of palm of manus"
inguinal crease:
alias: "skin of inguinal fold"
interdigit web:
alias: "manual digit skin"
manual digit skin:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:manual digit
default: UBERON:manual digit
type: string
qiita_sample_type:
allowed:
- "skin of hand"
default: "skin of hand"
type: string
manubrium:
alias: "skin of manubrium of sternum"
nail of pedal digit:
base_type: "skin"
metadata_fields:
env_material:
allowed:
- organic material
default: organic material
type: string
env_package:
allowed:
- human-associated
default: human-associated
type: string
host_body_site:
allowed:
- UBERON:pedal digit
default: UBERON:pedal digit
type: string
host_body_product:
allowed:
- UBERON:nail
default: UBERON:nail
type: string
qiita_sample_type:
allowed:
- "nail of pedal digit"
default: "nail of pedal digit"
type: string
nose:
alias: "nose skin"
nose skin:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- "UBERON:external nose"
default: "UBERON:external nose"
type: string
qiita_sample_type:
allowed:
- "skin of face"
default: "skin of face"
type: string
occiput:
alias: "skin of occiput"
oral mucosa:
alias: "buccal mucosa"
palm:
alias: "skin of palm of manus"
plantar heel:
alias: "heel skin"
pedal digit skin:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:pedal digit skin
default: UBERON:pedal digit skin
type: string
qiita_sample_type:
allowed:
- "skin of foot"
default: "skin of foot"
type: string
popliteal area:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:popliteal area
default: UBERON:popliteal area
type: string
qiita_sample_type:
allowed:
- "skin of knee"
default: "skin of knee"
type: string
popliteal crease:
alias: "popliteal area"
popliteal fossa:
alias: "popliteal area"
retroauricular crease:
alias: "retroauricular region"
retroauricular region:
base_type: "skin"
metadata_fields:
host_body_site:
allowed:
- UBERON:retroauricular area
default: UBERON:retroauricular area
type: string