Bacteria#
This is a example data for a bacterium. The data is artificial and should only demonstrate what the data in this schema look like.
Attention, this example data is outdated
{
"organism_type": "Bacteria",
"morph_type": null,
"unified_type_strain": true,
"unified_taxon": {
"name": "Eubacterium limosum",
"rank": "species",
"status": "validly published",
"identifier": [
{
"name": "LPSN",
"value": "https://lpsn.dsmz.de/species/eubacterium-limosum",
"property": "https://www.wikidata.org/wiki/Property:P1991",
"url": "https://lpsn.dsmz.de/species/eubacterium-limosum"
},
{
"name": "NCBI:txid",
"value": "1736",
"property": "https://www.wikidata.org/wiki/Property:P685",
"url": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1736"
}
],
"scientific": {
"name": "Eubacterium limosum",
"author": "(Eggerth 1935) Prévot 1938 (Approved Lists 1980)"
},
"alternate_name": [
"Butyribacterium limosum",
"Bacteroides limosus"
],
"parent": {
"name": "Eubacterium",
"rank": "genus",
"status": "validly published",
"identifier": [
{
"name": "LPSN",
"value": "https://lpsn.dsmz.de/genus/eubacterium",
"property": "https://www.wikidata.org/wiki/Property:P1991",
"url": "https://lpsn.dsmz.de/genus/eubacterium"
}
],
"scientific": {
"name": "Eubacterium",
"author": "Prévot 1938 (Approved Lists 1980)"
},
"alternate_name": [],
"parent": null,
"same_as": []
},
"same_as": [
"https://www.gbif.org/species/3226415/metrics"
]
},
"sample": [
{
"date": "/2011-09-12",
"country": null,
"description": "soil of landfill site",
"location": {
"name": "Pohang",
"description": null,
"geo": {
"latitude": 36.03901723905223,
"longitude": 129.365704500591,
"elevation": null,
"precision": null
}
},
"tags": [],
"source": "/sources/0"
}
],
"isolation": [
{
"date": null,
"isolator": {
"name": "Korea Research Institute of Bioscience and Biotechnology",
"identifier": [
{
"name": "ROR",
"value": "https://ror.org/03ep23f07",
"property": "https://www.wikidata.org/wiki/Property:P6782",
"url": null
}
],
"legal_name": null,
"address": null,
"url": null,
"email": null
},
"source": "/sources/0"
}
],
"legal": [
{
"dual_use": false,
"quarantine": null,
"nagoya": "No known restrictions under the Nagoya protocol",
"QPS": false,
"GRAS": false,
"gmo": false,
"gmo_information": null,
"source": "/sources/0"
}
],
"cell_shape": [
{
"cell_shape": "coccus",
"source": "/sources/0"
}
],
"oxygen": [
{
"relation": "anerobe",
"source": "/sources/0"
}
],
"multi_cell": [
{
"multi_cell": true,
"source": "/sources/0"
}
],
"cell_length": [
{
"min": 1.3,
"max": 2.2,
"unit": "µm",
"source": "/sources/0"
}
],
"cell_width": [
{
"min": 0.5,
"max": 0.8,
"unit": "µm",
"source": "/sources/0"
}
],
"cell_motility": [
{
"motile": true,
"flagellum": true,
"flag_arr": null,
"gliding": false,
"source": "/sources/0"
}
],
"colony": [],
"spore": [
{
"building": true,
"type": "endospore",
"ejection": null,
"source": "/sources/0"
}
],
"temperature": [
{
"optimal": 37.0,
"minimal": null,
"maximal": null,
"unit": "C",
"tests": [
{
"minimal": 30.0,
"maximal": 39.0,
"unit": "C",
"growth": true
},
{
"minimal": 45.0,
"maximal": 43.0,
"unit": "C",
"growth": false
}
],
"source": "/sources/0"
}
],
"ph": [
{
"optimal": 7.0,
"minimal": null,
"maximal": null,
"unit": "pH",
"tests": [
{
"minimal": 6.0,
"maximal": 9.0,
"unit": "pH",
"growth": true
}
],
"source": "/sources/0"
}
],
"identifier": [
{
"name": "CCNO",
"value": "DSM 20543",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "ATCC 8486",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "NCIB 9763",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "CCUG 16793",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "JCM 6421",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "BCRC 14401",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "CIP 104169",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "JCM 9978",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "KCTC 3266",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "CCNO",
"value": "NCIMB 9763",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "Designation",
"value": "STAFF 1027",
"property": null,
"url": null,
"source": "/sources/0"
},
{
"name": "BacDiveID",
"value": "5432",
"property": "https://www.wikidata.org/wiki/Property:P2946",
"url": "https://bacdive.dsmz.de/strain/5432",
"source": "/sources/0"
},
{
"name": "SI-ID",
"value": "34969",
"property": null,
"url": "https://straininfo.dsmz.de/strain/34969",
"source": "/sources/0"
}
],
"connected_persons": [
{
"name": "J.-W. Bae",
"identifier": [
{
"name": "ORCiD",
"value": "https://orcid.org/0000-0001-6433-5270",
"property": "https://www.wikidata.org/wiki/Property:P496",
"url": null
}
],
"role": "isolator",
"source": "/sources/0"
}
],
"pathogenicity": [
{
"host": "human",
"pathogen": "opportunistic",
"classification": "German classification",
"source": "/sources/0"
},
{
"host": "animal",
"pathogen": "no pathogen",
"classification": "German classification",
"source": "/sources/0"
},
{
"host": "plant",
"pathogen": "no pathogen",
"classification": "German classification",
"source": "/sources/0"
}
],
"bio_safety": [
{
"group": "1",
"classification": "German classification",
"url": "https://www.baua.de/EN/Service/Legislative-texts-and-technical-rules/Rules/TRBA/TRBA-466.html",
"source": "/sources/0"
},
{
"group": "1",
"classification": "Japan classification",
"url": null,
"source": "/sources/0"
}
],
"sequences": [
{
"type": "nucleotide",
"level": "identifier sequence",
"accession": "LC019782",
"description": "Eubacterium limosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 9978",
"length": "1425",
"url": [
"https://www.ncbi.nlm.nih.gov/nuccore/LC019782",
"https://www.ebi.ac.uk/ena/browser/view/LC019782"
],
"source": "/sources/0"
},
{
"type": "nucleotide",
"level": "identifier sequence",
"accession": "M59120",
"description": "Eubacterium limosum strain ATCC 8486 16S ribosomal RNA gene, partial sequence",
"length": "1525",
"url": [
"https://www.ncbi.nlm.nih.gov/nuccore/M59120",
"https://www.ebi.ac.uk/ena/browser/view/M59120",
"https://www.arb-silva.de/browser/ssu/M59120"
],
"source": "/sources/0"
},
{
"type": "nucleotide",
"level": "identifier sequence",
"accession": "AB595134",
"description": "Eubacterium limosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 6421",
"length": "1484",
"url": [
"https://www.ncbi.nlm.nih.gov/nuccore/AB595134",
"https://www.ebi.ac.uk/ena/browser/view/AB595134",
"https://www.arb-silva.de/browser/ssu/AB595134"
],
"source": "/sources/0"
},
{
"type": "nucleotide",
"level": "genome",
"accession": "GCA_000807675",
"description": "Eubacterium limosum ATCC 8486",
"length": null,
"url": [
"https://www.ncbi.nlm.nih.gov/assembly/GCA_000807675",
"https://www.ebi.ac.uk/ena/browser/view/GCA_000807675"
],
"source": "/sources/0"
},
{
"type": "nucleotide",
"level": "gene",
"accession": "1736.3",
"description": "Eubacterium limosum ATCC 8480",
"length": null,
"url": [
"https://www.patricbrc.org/view/Genome/1736.3"
],
"source": "/sources/0"
},
{
"type": "nucleotide",
"level": "genome",
"accession": "2814123220",
"description": "Eubacterium limosum ATCC 8486",
"length": null,
"url": [
"https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2814123220"
],
"source": "/sources/0"
}
],
"gc": [
{
"method": "thermal denaturion, midpoint method (Tm)",
"value": 47.8,
"source": "/sources/0"
}
],
"literature": [
{
"name": "Something",
"url": "https://doi.org/10.1128/JB.30.3.277-299.1935",
"date": null,
"author": [],
"publisher": [],
"source": "/sources/0"
},
{
"name": "Something different",
"url": "https://doi.org/10.1128/AEM.62.4.1242-1247.1996",
"date": null,
"author": [],
"publisher": [],
"source": "/sources/0"
},
{
"name": "Something completely different",
"url": "https://doi.org/10.1099/00207713-44-4-787",
"date": null,
"author": [],
"publisher": [],
"source": "/sources/0"
}
],
"cell_wall": [
{
"name": "B04",
"identifier": [],
"alternate_name": [
"B2alpha {L-Ser} [L-Orn] D-Glu-D-Lys(D-Orn)"
],
"percent": null,
"source": "/sources/0"
}
],
"fatty_acid_profiles": [
{
"profile": [
{
"name": "C15:0 ISO",
"identifier": [],
"alternate_name": [],
"percent": 31.9,
"ecl": "14.621"
},
{
"name": "C16:0",
"identifier": [],
"alternate_name": [],
"percent": 14.0,
"ecl": "16"
},
{
"name": "C17:1 ISO I/C16:0 DMA",
"identifier": [],
"alternate_name": [],
"percent": 9.7,
"ecl": "16.481"
},
{
"name": "C15:0 ANTEISO",
"identifier": [],
"alternate_name": [],
"percent": 6.7,
"ecl": "14.711"
},
{
"name": "C18:2 ω6,9c/C18:0 ANTE",
"identifier": [],
"alternate_name": [],
"percent": 5.4,
"ecl": "17.724"
},
{
"name": "C14:0 ISO 3OH",
"identifier": [],
"alternate_name": [],
"percent": 5.3,
"ecl": "15.117"
},
{
"name": "C14:0",
"identifier": [],
"alternate_name": [],
"percent": 4.2,
"ecl": "14"
},
{
"name": "unknown 14.966",
"identifier": [],
"alternate_name": [],
"percent": 3.9,
"ecl": "14.966"
},
{
"name": "unknown 18.177",
"identifier": [],
"alternate_name": [],
"percent": 3.3,
"ecl": "18.177"
}
],
"temperature": 37,
"medium": "blood Agar",
"library": "BHIBLA",
"software": "Sherlock 6.1",
"source": "/sources/0"
}
],
"stainings": [
{
"name": "Gram stain",
"value": "negative",
"source": "/sources/0"
}
],
"hemolysis": [
{
"blood": "sheep",
"hemolysis": "alpha",
"source": "/sources/0"
},
{
"blood": "horse",
"hemolysis": "beta",
"source": "/sources/0"
}
],
"cultivation_media": [
{
"name": "PYG MEDIUM (MODIFIED) (DSMZ Medium 104)",
"url": "https://mediadive.dsmz.de/medium/104?bacdive=5432",
"reagents": [
"Yeast extract",
"Peptone",
"Glucose",
"Trypticase peptone",
"Beef extract",
"L-Cysteine HCl x H2O",
"NaHCO3",
"NaCl",
"KH2PO4",
"K2HPO4",
"MgSO4 x 7 H2O",
"CaCl2 x 2 H2O",
"Hemin",
"Ethanol",
"Resazurin",
"Tween 80",
"Vitamin K1",
"NaOH",
"Distilled water"
],
"source": "/sources/0"
},
{
"name": "CIP Medium 187",
"url": "https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=187",
"reagents": [],
"source": "/sources/0"
}
],
"halophily": [
{
"name": "Sodium Chloride",
"identifier": [
{
"name": "PubChem",
"value": "5234",
"property": "https://wikidata.org/wiki/Property:P662",
"url": "https://pubchem.ncbi.nlm.nih.gov/compound/5234"
},
{
"name": "ChEBI",
"value": "CHEBI:26710",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:26710"
}
],
"alternate_name": [
"Table salt",
"sodium chloride",
"ClNa"
],
"optimal": 0.0,
"minimal": null,
"maximal": null,
"unit": "g/g%",
"tests": [
{
"minimal": 0.0,
"maximal": 1.0,
"unit": "g/g%",
"growth": true
}
],
"source": "/sources/0"
}
],
"tolerances": [
{
"name": "amikacin",
"identifier": [
{
"name": "ChEBI",
"value": "CHEBI:2637",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:2637"
}
],
"alternate_name": [
"1-N-(L(−)-γ-amino-α-hydroxybutyryl)kanamycin A",
"Amikacin",
"O-3-amino-3-deoxy-α-D-glucopyranosyl-(1→4)-O-(6-amino-6-deoxy-α-D-glucopyranosyl-(1→6))-N3-(4-amino-L-2-hydroxybutyryl)-2-deoxy-L-streptamine"
],
"reaction": null,
"mic": null,
"unit": null,
"tests": [
{
"reaction": "sensitive",
"concentration": "30",
"unit": "g/L"
}
],
"source": "/sources/0"
},
{
"name": "ampicillin",
"identifier": [
{
"name": "ChEBI",
"value": "CHEBI:28971",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28971"
}
],
"alternate_name": [
"AP",
"AMP",
"ABPC",
"Ampicillin",
"ampicillin acid",
"ampicillin anhydrous"
],
"reaction": null,
"mic": null,
"unit": null,
"tests": [
{
"reaction": "resistant",
"concentration": "10",
"unit": "g/L"
}
],
"source": "/sources/0"
},
{
"name": "cefuroxime",
"identifier": [
{
"name": "ChEBI",
"value": "CHEBI:3515",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:3515"
}
],
"alternate_name": [
"Sharox",
"Zinacef Danmark",
"Cefuroxim",
"Cefuroxime",
"Cephuroxime"
],
"reaction": null,
"mic": null,
"unit": null,
"tests": [
{
"reaction": "intermediate",
"concentration": "30",
"unit": "g/L"
}
],
"source": "/sources/0"
}
],
"enzymes": [
{
"name": "acid phosphatase",
"ec_num": "3.1.3.2",
"url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.3.2",
"alternate_name": [
"acid phosphatase",
"tartrate-resistant acid phosphatase",
"prostatic acid phosphatase",
"tracp",
"acpase",
"uteroferrin",
"tracp 5b",
"phosphatidic acid phosphatase",
"tracp5b"
],
"active": true,
"source": "/sources/0"
},
{
"name": "alkaline phosphatase",
"ec_num": "3.1.3.1",
"url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.3.1",
"alternate_name": [
"ap",
"alkaline phosphatase",
"bone alkaline phosphatase",
"placental alkaline phosphatase",
"alpase",
"apase",
"intestinal alkaline phosphatase",
"tnsalp",
"phosphomonoesterase",
"secreted alkaline phosphatase"
],
"active": true,
"source": "/sources/0"
},
{
"name": "alpha-chymotrypsin",
"ec_num": "3.4.21.1",
"url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.4.21.1",
"alternate_name": [
"chymotrypsin",
"alpha-chymotrypsin",
"bovine alpha-chymotrypsin",
"chymotrypsin a",
"alpha-ct",
"chymotrypsin b",
"chtp",
"alpha chymotrypsin",
"alpha-chymotrypsin a",
"chymotrypsin ii"
],
"active": false,
"source": "/sources/0"
},
{
"name": "alpha-fucosidase",
"ec_num": "3.2.1.51",
"url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.51",
"alternate_name": [
"alpha-l-fucosidase",
"acid hydrolase",
"fuca1",
"serum alpha-l-fucosidase",
"serum afu",
"alpha-fuc",
"fuca2",
"alf1_wf",
"alpha-l-fucosidase i",
"alphafuc"
],
"active": false,
"source": "/sources/0"
},
{
"name": "arginine dihydrolase",
"ec_num": "3.5.3.6",
"url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.5.3.6",
"alternate_name": [
"arginine deiminase",
"arginine dihydrolase",
"ppadi",
"arginine-degrading enzyme",
"l-arginine deiminase",
"arca-1",
"lymphocyte blastogenesis inhibitory factor",
"paadi",
"streptococcal acid glycoprotein"
],
"active": false,
"source": "/sources/0"
},
{
"name": "beta-galactosidase",
"ec_num": "3.2.1.23",
"url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.23",
"alternate_name": [
"beta-galactosidase",
"beta-gal",
"beta-d-galactosidase",
"senescence-associated beta-galactosidase",
"endo-beta-galactosidase",
"bglap",
"sa-beta-gal",
"acid beta-galactosidase",
"beta galactosidase",
"betagal"
],
"active": true,
"source": "/sources/0"
}
],
"metabolites": [
{
"name": "alanine",
"identifier": [
{
"name": "ChEBI",
"value": " CHEBI:16449",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16449"
},
{
"name": "PubChem",
"value": "5950",
"property": "https://wikidata.org/wiki/Property:P662",
"url": "https://pubchem.ncbi.nlm.nih.gov/compound/5950"
}
],
"alternate_name": [
"L-alanine",
"Alinine",
"2-Aminopropanoic acid",
"2-aminopropanoic acid",
"Alanine"
],
"tests": [
{
"type": "utilization",
"active": true,
"protocol": null,
"utilization": null
}
],
"source": "/sources/0"
},
{
"name": "asparagine",
"identifier": [
{
"name": "ChEBI",
"value": " CHEBI:22653",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:22653"
},
{
"name": "PubChem",
"value": "6267",
"property": "https://wikidata.org/wiki/Property:P662",
"url": "https://pubchem.ncbi.nlm.nih.gov/compound/6267"
}
],
"alternate_name": [
"L-asparagine",
"asparagine"
],
"tests": [
{
"type": "production",
"active": true,
"protocol": null,
"utilization": null
},
{
"type": "utilization",
"active": true,
"protocol": null,
"utilization": null
}
],
"source": "/sources/0"
},
{
"name": "aspartate",
"identifier": [
{
"name": "ChEBI",
"value": " CHEBI:35391",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35391"
},
{
"name": "PubChem",
"value": "5460542",
"property": "https://wikidata.org/wiki/Property:P662",
"url": "https://pubchem.ncbi.nlm.nih.gov/compound/5460542"
}
],
"alternate_name": [
"aspartate(1-)",
"hydrogen aspartate",
"2-ammoniosuccinate",
"2-ammoniobutanedioate",
"aspartic acid monoanion",
"CHEBI:35391",
"FT-0653860",
"FT-0657391"
],
"tests": [
{
"type": "utilization",
"active": true,
"protocol": null,
"utilization": null
}
],
"source": "/sources/0"
},
{
"name": "formate",
"identifier": [
{
"name": "ChEBI",
"value": " CHEBI:15740",
"property": "https://wikidata.org/wiki/Property:P683",
"url": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15740"
}
],
"alternate_name": [
"aminate",
"formate",
"formiate",
"formic acid, ion(1−)",
"formylate",
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