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trait_condensed.yaml
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trait_condensed.yaml
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id: https://w3id.org/bacteria-archaea-traits
name: bacteria-archaea-traits
description: bacteria-archaea-traits
imports:
- biolinkml:types
prefixes:
biolinkml: https://w3id.org/biolink/biolinkml/
bacteria-archaea-traits: https://w3id.org/bacteria-archaea-traits
default_prefix: bacteria-archaea-traits
types: {}
classes:
bacteria-archaea-traits:
slots:
- tax_id
- species_tax_id
- data_source
- org_name
- species
- genus
- family
- order
- class
- phylum
- superkingdom
- gram_stain
- metabolism
- pathways
- carbon_substrates
- sporulation
- motility
- range_tmp
- range_salinity
- cell_shape
- isolation_source
- d1_lo
- d1_up
- d2_lo
- d2_up
- doubling_h
- genome_size
- gc_content
- coding_genes
- optimum_tmp
- optimum_ph
- growth_tmp
- rRNA16S_genes
- tRNA_genes
- ref_id
slots:
tax_id:
range: integer
examples:
value: '542'
species_tax_id:
range: integer
examples:
value: '542'
data_source:
range: data_source_enum
examples:
value: silva
org_name:
range: string
examples:
value: Zymomonas mobilis
species:
range: string
examples:
value: Zymomonas mobilis
genus:
range: string
examples:
value: Zymomonas
family:
range: string
examples:
value: Sphingomonadaceae
order:
range: string
examples:
value: Sphingomonadales
class:
range: string
examples:
value: Alphaproteobacteria
phylum:
range: string
examples:
value: Proteobacteria
superkingdom:
range: superkingdom_enum
examples:
value: Bacteria
gram_stain:
range: gram_stain_enum
examples:
value: NA
metabolism:
range: metabolism_enum
examples:
value: NA
pathways:
## TODO map to GO. See https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/5
range: string
examples:
value: NA
carbon_substrates:
range: string
examples:
value: NA
sporulation:
range: sporulation_enum
examples:
value: NA
motility:
range: motility_enum
examples:
value: NA
range_tmp:
range: range_tmp_enum
examples:
value: NA
range_salinity:
range: range_salinity_enum
examples:
value: NA
cell_shape:
range: cell_shape_enum
examples:
value: NA
isolation_source:
range: string
examples:
value: NA
d1_lo:
range: string
examples:
value: NA
d1_up:
range: string
examples:
value: NA
d2_lo:
range: string
examples:
value: NA
d2_up:
range: string
examples:
value: NA
doubling_h:
range: string
examples:
value: '1.7'
genome_size:
range: string
examples:
value: NA
gc_content:
range: string
examples:
value: NA
coding_genes:
range: string
examples:
value: NA
optimum_tmp:
range: string
examples:
value: NA
optimum_ph:
range: string
examples:
value: NA
growth_tmp:
range: string
examples:
value: '30'
rRNA16S_genes:
range: rRNA16S_genes_enum
examples:
value: NA
tRNA_genes:
range: string
examples:
value: NA
ref_id:
range: string
examples:
value: '20237'
enums:
data_source_enum:
## TODO: the mappings below are automated
permissible_values:
methanogen:
description: methanogen
meaning: http://purl.obolibrary.org/obo/NCBITaxon_206131
bacdive-microa:
description: bacdive-microa
amend-shock:
description: amend-shock
meaning: http://purl.obolibrary.org/obo/OMIT_0013662
faprotax:
description: faprotax
protraits:
description: protraits
edwards:
description: edwards
meaning: http://purl.obolibrary.org/obo/GSSO_007098
engqvist:
description: engqvist
kremer:
description: kremer
mediadb:
description: mediadb
gold:
description: gold
meaning: http://purl.obolibrary.org/obo/NCIT_C2392
schulz-jorgensen:
description: schulz-jorgensen
meaning: http://purl.obolibrary.org/obo/GAZ_00137373
corkrey:
description: corkrey
jemma-refseq:
description: jemma-refseq
meaning: http://purl.obolibrary.org/obo/MI_0481
nielsensl:
description: nielsensl
genbank:
description: genbank
meaning: http://purl.obolibrary.org/obo/NCIT_C43818
kegg:
description: kegg
meaning: http://purl.obolibrary.org/obo/FOBI_040235
fierer:
description: fierer
prochlorococcus:
description: prochlorococcus
meaning: http://purl.obolibrary.org/obo/NCBITaxon_1218
rrndb:
description: rrndb
campedelli:
description: campedelli
patric:
description: patric
silva:
description: silva
meaning: http://purl.obolibrary.org/obo/GAZ_00556354
pasteur:
description: pasteur
meaning: http://purl.obolibrary.org/obo/GAZ_00390372
roden-jin:
description: roden-jin
meaning: http://purl.obolibrary.org/obo/GAZ_00599142
masonmm:
description: masonmm
microbe-directory:
description: microbe-directory
meaning: http://purl.obolibrary.org/obo/NCIT_C49057
superkingdom_enum:
## TODO: the mappings below are automated
permissible_values:
Archaea:
description: Archaea
meaning: http://purl.obolibrary.org/obo/NCIT_C61092
Bacteria:
description: Bacteria
meaning: http://purl.obolibrary.org/obo/NCBITaxon_2
gram_stain_enum:
## TODO: the mappings below are automated
permissible_values:
negative:
description: negative
meaning: http://www.ebi.ac.uk/efo/EFO_0009949
positive:
description: positive
meaning: http://purl.obolibrary.org/obo/CL_0000084
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895
metabolism_enum:
## TODO: the mappings below are automated
permissible_values:
anaerobic:
description: anaerobic
meaning: http://purl.obolibrary.org/obo/NCIT_C103137
strictly anaerobic:
description: strictly anaerobic
meaning: http://identifiers.org/teddy/TEDDY_0000007
obligate aerobic:
description: obligate aerobic
meaning: http://purl.obolibrary.org/obo/NCIT_C28341
aerobic:
description: aerobic
meaning: http://purl.obolibrary.org/obo/EO_0007024
facultative:
description: facultative
meaning: http://purl.obolibrary.org/obo/OMP_0000087
microaerophilic:
description: microaerophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0000515
obligate anaerobic:
description: obligate anaerobic
meaning: http://purl.obolibrary.org/obo/NCIT_C103137
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895
sporulation_enum:
## TODO: the mappings below are automated
permissible_values:
'yes':
description: 'yes'
meaning: http://www.ebi.ac.uk/efo/EFO_0004238
'no':
description: 'no'
meaning: http://identifiers.org/medgen/CN239215
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895
motility_enum:
## TODO: the mappings below are automated
permissible_values:
'yes':
description: 'yes'
meaning: http://www.ebi.ac.uk/efo/EFO_0004238
'no':
description: 'no'
meaning: http://identifiers.org/medgen/CN239215
gliding:
description: gliding
meaning: http://purl.obolibrary.org/obo/IDOMAL_0002121
flagella:
description: flagella
meaning: http://purl.obolibrary.org/obo/OMIT_0006618
axial filament:
description: axial filament
meaning: http://www.orpha.net/ORDO/Orphanet_98904
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895
range_tmp_enum:
## TODO: the mappings below are automated
permissible_values:
mesophilic:
description: mesophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0000111
facultative psychrophilic:
description: facultative psychrophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0001306
extreme thermophilic:
description: extreme thermophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0000118
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895
thermophilic:
description: thermophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0000118
psychrotolerant:
description: psychrotolerant
meaning: http://purl.obolibrary.org/obo/MICRO_0001310
thermotolerant:
description: thermotolerant
meaning: http://purl.obolibrary.org/obo/MICRO_0001286
psychrophilic:
description: psychrophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0001306
range_salinity_enum:
## TODO: the mappings below are automated
permissible_values:
halotolerant:
description: halotolerant
meaning: http://purl.obolibrary.org/obo/MICRO_0001316
extreme-halophilic:
description: extreme-halophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0001314
euryhaline:
description: euryhaline
halophilic:
description: halophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0001314
moderate-halophilic:
description: moderate-halophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0001314
stenohaline:
description: stenohaline
non-halophilic:
description: non-halophilic
meaning: http://purl.obolibrary.org/obo/MICRO_0001314
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895
cell_shape_enum:
## TODO: the mappings below are automated
## https://github.com/Knowledge-Graph-Hub/kg-microbe/issues/4
permissible_values:
'disc ':
description: 'disc '
meaning: http://purl.obolibrary.org/obo/FBbt_00001768
ring:
description: ring
meaning: http://www.ebi.ac.uk/cmpo/CMPO_0000302
flask:
description: flask
meaning: http://purl.obolibrary.org/obo/NCIT_C96144
star:
description: star
meaning: http://www.orpha.net/ORDO/Orphanet_140952
bacillus:
description: bacillus
meaning: http://purl.obolibrary.org/obo/NCBITaxon_1471
spirochete:
description: spirochete
meaning: http://purl.obolibrary.org/obo/OMP_0000125
coccus:
description: coccus
meaning: http://purl.obolibrary.org/obo/MICRO_0000402
coccobacillus:
description: coccobacillus
meaning: http://purl.obolibrary.org/obo/MICRO_0000366
filament:
description: filament
meaning: http://www.orpha.net/ORDO/Orphanet_98904
square:
description: square
meaning: http://www.ebi.ac.uk/efo/EFO_0007843
fusiform:
description: fusiform
meaning: http://www.ebi.ac.uk/efo/EFO_0010305
triangular:
description: triangular
meaning: http://purl.obolibrary.org/obo/HP_0000325
spindle:
description: spindle
meaning: http://identifiers.org/medgen/C1968782
irregular:
description: irregular
meaning: http://identifiers.org/medgen/C0156404
spiral:
description: spiral
meaning: http://purl.obolibrary.org/obo/UBERON_0002227
tailed:
description: tailed
meaning: http://purl.obolibrary.org/obo/UBERON_0002533
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895
branched:
description: branched
pleomorphic:
description: pleomorphic
meaning: http://www.ebi.ac.uk/efo/EFO_1001972
vibrio:
description: vibrio
meaning: http://purl.obolibrary.org/obo/NCBITaxon_55601
rRNA16S_genes_enum:
## TODO: the mappings below are automated
permissible_values:
'16':
description: '16'
meaning: http://www.ebi.ac.uk/efo/EFO_0002344
'15':
description: '15'
meaning: http://www.ebi.ac.uk/efo/EFO_0006482
'6':
description: '6'
meaning: http://www.ebi.ac.uk/efo/EFO_0002845
'11':
description: '11'
meaning: http://www.ebi.ac.uk/efo/EFO_0006368
'9':
description: '9'
meaning: http://www.ebi.ac.uk/efo/EFO_0002847
'14':
description: '14'
meaning: http://www.ebi.ac.uk/efo/EFO_0002844
'10':
description: '10'
meaning: http://www.ebi.ac.uk/efo/EFO_0002181
'12':
description: '12'
meaning: http://www.ebi.ac.uk/efo/EFO_0006282
'8':
description: '8'
meaning: http://www.ebi.ac.uk/efo/EFO_0006737
'4':
description: '4'
meaning: http://www.ebi.ac.uk/efo/EFO_0002798
'1':
description: '1'
meaning: http://www.ebi.ac.uk/efo/EFO_0006645
'2':
description: '2'
meaning: http://www.ebi.ac.uk/efo/EFO_0005158
'13':
description: '13'
meaning: http://www.ebi.ac.uk/efo/EFO_0003797
'5':
description: '5'
meaning: http://www.ebi.ac.uk/efo/EFO_0002861
'3':
description: '3'
meaning: http://www.ebi.ac.uk/efo/EFO_0006622
'7':
description: '7'
meaning: http://www.ebi.ac.uk/efo/EFO_0002846
'17':
description: '17'
meaning: http://www.ebi.ac.uk/efo/EFO_0003758
NA:
description: NA
meaning: http://purl.obolibrary.org/obo/CL_0000895