Skip to content

Commit

Permalink
cleaned up definitions
Browse files Browse the repository at this point in the history
  • Loading branch information
@AmandaBirmingham
AmandaBirmingham committed Jun 14, 2024
1 parent da129e1 commit 383250f
Showing 1 changed file with 96 additions and 115 deletions.
211 changes: 96 additions & 115 deletions standards.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,27 +33,29 @@ host_type_specific_metadata:
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]))?)?)?)?)?$'
type: string
check_with: date_not_in_future
- allowed:
- not collected
- not provided
- restricted access
- not collected
- not provided
- restricted access
type: string
- regex: '^([0-9]{4})(?:-([0-1][0-2])(?:-([0-3][0-9])(?: ([0-2][0-9])(?::([0-5][0-9])(?::([0-5][0-9]))?)?)?)?)?$'
type: datetime
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]))?)?)?)?)?$'
type: string
check_with: date_not_in_future
- allowed:
- not collected
- not provided
- restricted access
- not collected
- not provided
- restricted access
type: string
- regex: '^([0-9]{4})(?:-([0-1][0-2])(?:-([0-3][0-9])(?: ([0-2][0-9])(?::([0-5][0-9])(?::([0-5][0-9]))?)?)?)?)?$'
type: datetime
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.
Expand All @@ -72,28 +74,25 @@ host_type_specific_metadata:
required: true
type: string
dna_extracted:
anyof:
- allowed:
- not collected
- not provided
type: string
- allowed:
- 'TRUE'
- 'FALSE'
type: string
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:
- allowed:
- not collected
- not provided
- restricted access
type: string
- 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
Expand Down Expand Up @@ -151,7 +150,6 @@ host_type_specific_metadata:
required: true
type: string
env_package:
anyof:
empty: false
field_desc: Environment where the sample was obtained.
is_phi: false
Expand All @@ -173,14 +171,14 @@ host_type_specific_metadata:
type: string
latitude:
anyof:
- allowed:
- not collected
- not provided
- restricted access
type: string
- 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.
Expand All @@ -197,14 +195,14 @@ host_type_specific_metadata:
type: string
longitude:
anyof:
- allowed:
- not collected
- not provided
- restricted access
type: string
- 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.
Expand All @@ -226,16 +224,13 @@ host_type_specific_metadata:
required: true
type: string
physical_specimen_remaining:
anyof:
- allowed:
- not collected
- not provided
- restricted access
type: string
- allowed:
- 'TRUE'
- 'FALSE'
type: string
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
Expand All @@ -252,12 +247,12 @@ host_type_specific_metadata:
type: string
taxon_id:
anyof:
- min: 1
type: integer
- allowed:
- not collected
- not provided
- not collected
- not provided
type: string
- min_exclusive: 0
type: integer
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
Expand Down Expand Up @@ -294,12 +289,12 @@ host_type_specific_metadata:
type: string
host_age:
anyof:
- allowed:
- not collected
- not provided
type: string
- min_exclusive: 0
type: number
- min_exclusive: 0
type: number
- allowed:
- not collected
- not provided
type: string
empty: false
field_desc: Host age in appropriate units
is_phi: false
Expand All @@ -324,25 +319,25 @@ host_type_specific_metadata:
type: string
host_taxid:
anyof:
- allowed:
- not applicable
- not collected
- not provided
type: string
- min_exclusive: 0
type: integer
- min: 1
type: integer
- allowed:
- not applicable
- not collected
- not provided
type: string
empty: false
field_desc: taxonomy id of host e.g. human is 9606
is_phi: false
required: true
host_weight:
anyof:
- allowed:
- not collected
- not provided
type: string
- min_exclusive: 0
type: number
- min_exclusive: 0
type: number
- allowed:
- not collected
- not provided
type: string
empty: false
field_desc: in kilograms preferred
is_phi: false
Expand All @@ -356,13 +351,13 @@ host_type_specific_metadata:
# is there any reason time_point has to be host associated??
time_point:
anyof:
- allowed:
- not applicable
- not collected
- not provided
- restricted access
type: string
- type: integer
- 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
Expand Down Expand Up @@ -408,37 +403,31 @@ host_type_specific_metadata:
required: true
type: string
host_life_stage:
anyof:
- allowed:
# 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
# TODO: Gail's writeup includes infant; should this?
# also, I see "child" there?
- allowed:
- adult
- juvenile
type: string
type: string
empty: false
field_desc: e.g. adult
is_phi: false
required: true
sex:
anyof:
- allowed:
- not applicable
- not collected
- not provided
- restricted access
type: string
- allowed:
allowed:
- female
- male
- neuter
- hermaphrodite
type: string
- not applicable
- not collected
- not provided
- restricted access
type: string
empty: false
is_phi: false
required: true
Expand Down Expand Up @@ -741,14 +730,14 @@ host_type_specific_metadata:
type: string
host_body_mass_index:
anyof:
- allowed:
- not applicable
- not collected
- not provided
- restricted access
type: string
- min_exclusive: 0
type: number
- 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
Expand All @@ -760,12 +749,12 @@ host_type_specific_metadata:
type: string
host_height:
anyof:
- allowed:
- not collected
- not provided
type: string
- 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
Expand Down Expand Up @@ -795,21 +784,13 @@ host_type_specific_metadata:
default: kg
type: string
irb_institute:
anyof:
- allowed:
- not provided
type: string
- type: string
type: string
empty: false
field_desc: the name of institute that approved the IRB (human studies)
is_phi: false
required: false
irb_protocol_id:
anyof:
- allowed:
- not provided
type: string
- type: string
type: string
empty: false
field_desc: the ID of the IRB protocol that covers the collection and analysis of
this sample (human studies)
Expand Down

0 comments on commit 383250f

Please sign in to comment.