Open turbomam opened 4 months ago
PREFIX FMA: <http://purl.obolibrary.org/obo/FMA_>
PREFIX nmdc: <https://w3id.org/nmdc/>
select
distinct ?bs
where {
?bs ?p ?node .
?node nmdc:term FMA:14541 .
}
https://api.microbiomedata.org/nmdcschema/ids/nmdc%3Absm-11-05fh0s26
PREFIX FMA: <http://purl.obolibrary.org/obo/FMA_>
PREFIX nmdc: <https://w3id.org/nmdc/>
select
distinct ?p
where {
?bs ?p ?node .
?node nmdc:term FMA:14541 .
}
{
"id": "nmdc:bsm-11-05fh0s26",
"name": "Mouse - antibiotic treatment, 5-ASA treatment, C17 treatment (HS177_41)",
"part_of": [
"nmdc:sty-11-hdd4bf83"
],
"env_broad_scale": {
"has_raw_value": "Animal-associated environment [ENVO:01001002]",
"term": {
"id": "ENVO:01001002",
"name": "Animal-associated environment"
}
},
"env_local_scale": {
"has_raw_value": "mouse cecal contents [FMA:14541]",
"term": {
"id": "FMA:14541",
"name": "mouse cecal contents"
}
},
"env_medium": {
"has_raw_value": "mouse cecal contents [FMA:14541]",
"term": {
"id": "FMA:14541",
"name": "mouse cecal contents"
}
},
"samp_name": "Mouse - antibiotic treatment, 5-ASA treatment, C17 treatment (HS177_41)",
"collection_date": {
"has_raw_value": "2021-11-05"
},
"depth": {
"has_raw_value": "0",
"has_numeric_value": 0
},
"elev": 23.1648,
"env_package": {
"has_raw_value": "Host-associated"
},
"experimental_factor": {
"has_raw_value": "antibiotic treatment, 5-ASA treatment, C17 treatment"
},
"geo_loc_name": {
"has_raw_value": "USA: California, Davis"
},
"gravidity": {
"has_raw_value": "no"
},
"host_age": {
"has_raw_value": "64 days",
"has_numeric_value": 64,
"has_unit": "days"
},
"host_body_habitat": {
"has_raw_value": "gastrointestinal tract"
},
"host_body_product": {
"has_raw_value": "cecal contents [FMA:14541]",
"term": {
"id": "FMA:14541",
"name": "cecal contents"
}
},
"host_body_site": {
"has_raw_value": "cecum [UBERON:0001153]",
"term": {
"id": "UBERON:0001153",
"name": "cecum"
}
},
"host_common_name": {
"has_raw_value": "Mouse"
},
"host_diet": [
{
"has_raw_value": "Teklad Diet #TD06415 high fat"
}
],
"host_genotype": {
"has_raw_value": "Swiss Webster"
},
"host_life_stage": {
"has_raw_value": "adult"
},
"host_sex": "female",
"lat_lon": {
"has_raw_value": "38.5382 -121.7617",
"latitude": 38.5382,
"longitude": -121.7617
},
"perturbation": [
{
"has_raw_value": "antibiotic-treated FMT, C17"
}
],
"source_mat_id": {
"has_raw_value": "UUID:047aacd5-857f-3e9e-b782-e70a0fc5a0ca"
},
"analysis_type": [
"metagenomics"
]
}
Add a taxon/species/strain identifier?
"host_body_site": {
"has_raw_value": "cecum [UBERON:0001153]",
"term": {
"id": "UBERON:0001153",
"name": "cecum"
}
}
Fix spelling, at least in name
PREFIX nmdc: <https://w3id.org/nmdc/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select ?p ?term ?label ?name (count(?s1) as ?count)
where {
graph <https://api.microbiomedata.org> {
?s1 ?p ?s2 .
?s2 nmdc:term ?term .
optional {
?term nmdc:name ?name
}
}
graph <http://purl.obolibrary.org/obo/nmdco.owl> {
optional {
?term rdfs:label ?label
}
}
}
group by ?p ?term ?label ?name
order by ?p ?term ?label ?name
term | label | name | count |
---|---|---|---|
CHEBI:00000 | cytopoint | 6 | |
CHEBI:00000 | maropitant | 6 | |
CHEBI:15414 | S-adenosyl-L-methionine | 4 | |
CHEBI:176843 | vitamin B12 | 2 | |
CHEBI:176915 | clindamycin | 3 | |
CHEBI:2676 | clavamox | 5 | |
CHEBI:28177 | theophylline | 2 | |
CHEBI:28971 | ampicillin | 1 | |
CHEBI:3011 | benazapril | 2 | |
CHEBI:32003 | pimobendan | 2 | |
CHEBI:3504 | simplicef | 1 | |
CHEBI:3534 | cephalexin | 1 | |
CHEBI:35720 | enrofloxacin | 2 | |
CHEBI:364453 | carprofen | 4 | |
CHEBI:4031 | cyclosporine | 2 | |
CHEBI:42797 | gabapentin | 2 | |
CHEBI:50270 | pantoprazole | 2 | |
CHEBI:50845 | doxycycline | 1 | |
CHEBI:6437 | levetiracetam | 2 | |
CHEBI:64482 | phosphatidylcholine | 4 | |
CHEBI:6775 | 5-ASA | 8 | |
CHEBI:6909 | metronidazole | 1 | |
CHEBI:7772 | omperazole | 2 | |
CHEBI:7773 | ondansetron | 6 | |
CHEBI:7959 | d-penicillamine | 2 | |
CHEBI:8378 | prednisolone | 4 | |
CHEBI:8382 | prednisone | 6 | |
CHEBI:9144 | silibinin | 4 | |
CHEBI:9241 | spironolactone | 2 | |
CHEBI:9321 | sulbactam | 1 | |
CHEBI:9654 | trazadone | 2 | |
CHEBI:9907 | ursodiol | 4 | |
ENVO:00000011 | garden | garden | 113 |
ENVO:00000011 | garden | garden | 113 |
ENVO:00000021 | freshwater lake | freshwater lake | 93 |
ENVO:00000022 | river | river | 452 |
ENVO:00000044 | peatland | 83 | |
ENVO:00000083 | hill | hill | 4 |
ENVO:00000086 | plain | plain | 4 |
ENVO:00000094 | volcanic feature | 4 | |
ENVO:00000100 | valley | valley | 12 |
ENVO:00000108 | meadow ecosystem | 53 | |
ENVO:00000114 | agricultural field | agricultural field | 12 |
ENVO:00000119 | planted forest | 4 | |
ENVO:00000120 | oil palm plantation | 6 | |
ENVO:00000128 | dry valley | dry valley | 2 |
ENVO:00000148 | riffle | riffle | 243 |
ENVO:00000161 | banana plantation | 3 | |
ENVO:00000170 | dune | 1 | |
ENVO:00000182 | plateau | plateau | 4 |
ENVO:00000291 | drainage basin | 10 | |
ENVO:00000292 | watershed | 53 | |
ENVO:00000305 | peninsula | peninsula | 4 |
ENVO:00000305 | peninsula | peninsula | 4 |
ENVO:00000376 | biosphere reserve | 60 | |
ENVO:00000384 | river bed | 33 | |
ENVO:00000444 | woodland clearing | woodland clearing | 4 |
ENVO:00000446 | terrestrial biome | terrestrial biome | 5606 |
ENVO:00000516 | hummock | hummock | 38 |
ENVO:00000548 | gravel field | 1 | |
ENVO:00000873 | freshwater biome | 38 | |
ENVO:00001998 | soil | soil | 5294 |
ENVO:00002000 | slope | slope | 14 |
ENVO:00002003 | fecal material | fecal material | 151 |
ENVO:00002003 | fecal material | feces material | 151 |
ENVO:00002007 | sediment | sediment | 165 |
ENVO:00002011 | fresh water | 1 | |
ENVO:00002042 | surface water | surface water | 287 |
ENVO:00002130 | hypolimnion | hypolimnion | 4 |
ENVO:00002131 | epilimnion | epilimnion | 398 |
ENVO:00002132 | metalimnion | metalimnion | 3 |
ENVO:00002194 | oil field production water | 17 | |
ENVO:00002204 | anthropogenic contamination feature | 10 | |
ENVO:00002258 | loam | 2 | |
ENVO:00002259 | agricultural soil | agricultural soil | 12 |
ENVO:00002261 | forest soil | forest soil | 22 |
ENVO:00002261 | forest soil | forest soil | 22 |
ENVO:00002269 | thermocline | thermocline | 10 |
ENVO:00003074 | manufactured product | 1 | |
ENVO:00003082 | enriched soil | 2 | |
ENVO:00005741 | alpine soil | 6 | |
ENVO:00005750 | grassland soil | grassland soil | 64 |
ENVO:00005760 | burned soil | burned soil | 2 |
ENVO:00005761 | meadow soil | meadow soil | 10 |
ENVO:00005773 | pasture soil | pasture soil | 2 |
ENVO:00005774 | peat soil | 118 | |
ENVO:00005778 | tropical soil | 105 | |
ENVO:00005784 | spruce forest soil | 17 | |
ENVO:00005800 | desert sand | 1 | |
ENVO:00005801 | rhizosphere | rhizosphere | 118 |
ENVO:00005802 | bulk soil | bulk soil | 172 |
ENVO:01000017 | sand | 52 | |
ENVO:01000018 | gravel | 1 | |
ENVO:01000174 | forest biome | 205 | |
ENVO:01000177 | grassland biome | 60 | |
ENVO:01000179 | desert biome | 6 | |
ENVO:01000183 | tropical desert biome | 2 | |
ENVO:01000185 | montane desert biome | 6 | |
ENVO:01000189 | temperate savanna biome | temperate savanna biome | 4 |
ENVO:01000211 | temperate coniferous forest biome | 6 | |
ENVO:01000215 | temperate shrubland biome | temperate shrubland biome | 8 |
ENVO:01000216 | montane shrubland biome | montane shrubland biome | 6 |
ENVO:01000219 | anthropogenic terrestrial biome | anthropogenic terrestrial biome | 107 |
ENVO:01000221 | temperate woodland biome | temperate woodland biome | 29 |
ENVO:01000221 | temperate woodland biome | temperate woodland biome | 29 |
ENVO:01000245 | cropland biome | 9 | |
ENVO:01000247 | rangeland biome | rangeland biome | 8 |
ENVO:01000249 | urban biome | urban biome | 15 |
ENVO:01000250 | subpolar coniferous forest biome | 31 | |
ENVO:01000252 | freshwater lake biome | freshwater lake biome | 560 |
ENVO:01000253 | freshwater river biome | freshwater river biome | 1040 |
ENVO:01000297 | freshwater river | freshwater river | 13 |
ENVO:01000349 | root matter | root matter | 101 |
ENVO:01000352 | field | field | 136 |
ENVO:01000355 | vegetation layer | 18 | |
ENVO:01000409 | freshwater littoral zone | freshwater littoral zone | 34 |
ENVO:01000599 | river water | river water | 13 |
ENVO:01000621 | microcosm | 17 | |
ENVO:01000687 | coast | 2 | |
ENVO:01000816 | area of deciduous forest | area of deciduous forest | 1069 |
ENVO:01000843 | area of evergreen forest | area of evergreen forest | 1268 |
ENVO:01000855 | area of mixed forest | area of mixed forest | 199 |
ENVO:01000861 | area of dwarf scrub | area of dwarf scrub | 295 |
ENVO:01000869 | area of scrub | area of scrub | 614 |
ENVO:01000887 | area of sedge- and forb-dominated herbaceous vegetation | area of sedge- and forb-dominated herbaceous vegetation | 123 |
ENVO:01000888 | area of gramanoid or herbaceous vegetation | area of gramanoid or herbaceous vegetation | 777 |
ENVO:01000891 | area of pastureland or hayfields | area of pastureland or hayfields | 169 |
ENVO:01000892 | area of cropland | area of cropland | 207 |
ENVO:01000893 | area of woody wetland | area of woody wetland | 245 |
ENVO:01000894 | area of emergent herbaceous wetland | area of emergent herbaceous wetland | 45 |
ENVO:01000941 | planetary subsurface zone | 17 | |
ENVO:01001001 | plant-associated environment | plant-associated biome | 192 |
ENVO:01001002 | animal-associated environment | Animal-associated environment | 156 |
ENVO:01001002 | animal-associated environment | animal-associated environment | 156 |
ENVO:01001057 | environment associated with a plant part or small plant | environment associated with a plant part or small plant | 199 |
ENVO:01001191 | water surface | water surface | 18 |
ENVO:01001209 | wetland ecosystem | 2 | |
ENVO:01001370 | tundra ecosystem | tundra ecosystem | 12 |
ENVO:01001442 | agriculture | agricultural biome | 384 |
ENVO:01001442 | agriculture | phyllosphere biome | 384 |
ENVO:01001616 | bare soil | bare soil | 10 |
ENVO:01001803 | tropical forest | 105 | |
ENVO:01001837 | subalpine biome | subalpine biome | 18 |
ENVO:01001841 | volcanic soil | 4 | |
ENVO:01001869 | fracking liquid | 2 | |
ENVO:02000059 | surface soil | 13 | |
ENVO:02500027 | anthropogenic environmental process | 2 | |
ENVO:03600094 | stream pool | stream pool | 95 |
ENVO:03600095 | stream run | stream run | 191 |
ENVO:03600096 | step pool | step pool | 31 |
ENVO:03605001 | epilithon | epilithon | 371 |
ENVO:03605002 | epipelon | epipelon | 27 |
ENVO:03605003 | epiphyton | epiphyton | 25 |
ENVO:03605004 | epipsammon | epipsammon | 100 |
ENVO:03605005 | epixylon | epixylon | 37 |
ENVO:03605006 | stream water | stream water | 104 |
ENVO:03605007 | freshwater stream | freshwater stream | 104 |
ENVO:03605008 | freshwater stream biome | freshwater stream biome | 104 |
ENVO:04000007 | lake water | lake water | 560 |
FMA:14541 | cecal contents | 99 | |
FMA:14541 | mouse cecal contents | 99 | |
NCBITaxon:1118232 | 101 | ||
NCBITaxon:1647806 | 471 | ||
NCBITaxon:1861841 | 94 | ||
NCBITaxon:256318 | metagenome | 87 | |
NCBITaxon:2809082 | 1 | ||
NCBITaxon:3689 | 306 | ||
NCBITaxon:410658 | soil metagenome | 363 | |
NCBITaxon:449393 | 245 | ||
NCBITaxon:556182 | 60 | ||
NCBITaxon:939928 | 108 | ||
NCBITaxon:9925 | 95 | ||
PO:0009007 | portion of plant tissue | 10 | |
PO:0025025 | root system | 10 | |
PO:0025034 | leaf | leaf | 98 |
UBERON:0000059 | large intestine | large intestine | 28 |
UBERON:0001153 | caecum | cecum | 33 |
UBERON:0001555 | digestive tract | digestive tract | 95 |
UBERON:0001988 | feces | Feces | 28 |
A changesheet has been submitted to use Uberon terms for the env_local_scale
and env_medium
for the Biosmaples relevant to this issue. The FMA host_body_product
assertions have been removed.
possible dupe issue from another repo?
Leave as is