This view has 230 main fields arranged in 10 sections (which themselves may contain subsections - only exception is the section references). Please see the table below for more details.
The result contains only fields with valid content. If a data field within BacDive is not filled with content this field is omitted in the response. This behavior resembles the setup of the BacDive's strain detail view in the portal. Thus the retrieved result may contain less fields than specified in the table of all data fields that are reachable by the web service.
The sections are shown always, even when empty. When a subsection is empty, it is also ommited. Most of the subsections (with some exceptions, for example the subsection strains) may contain one or more entries. Beyond the main fields, every entry in the subsections has a field ID_reference holding the ID of the reference. If the reference is text mined the subsection will contain a field text_mined with the value true (if the field text_mined has the value false, then it is ommited).
All references in the result are summed up in the section references.
| Legend for the table |
|---|
| section |
| subsection |
| field |
The table has three columns:
The subsections have no verbose names and no description. They are prefixed with the string 'subsection: '.
| Section ID | Section name | Description |
|---|---|---|
| taxonomy_name | Name and taxonomic classification | Information on the name and the taxonomic classification. |
| subsection: strains | ||
| domain | Domain | Domain name (taxonomic rank) |
| phylum | Phylum | Phylum name (taxonomic rank) |
| class | Class | Class name (taxonomic rank). |
| ordo | Order | name of order. taxonomic rank. |
| family | Family | Family name (taxonomic rank) |
| genus | Genus | Genus name (taxonomic rank) |
| species | Species | Species name, which includes genus, species and subspecies epithet (taxonomic rank) |
| species_epithet | Species epithet | Second part of species name |
| subspecies_epithet | Subspecies epithet | Third part of species name, where applicable |
| full_scientific_name | Full Scientific Name | Species name, author(s) and year of the valid publication of the species name. |
| designation | Strain Designation | Name of the strain as given in publications or public databases |
| variant | Variant | variations of a strain, e.g. serotype, biovar or isotype |
| is_type_strain | Type strain | Is this strain a type strain. |
| subsection: strains_synonyms_PNU | ||
| pnu_synonym | Synonym | species name / synonym name from PNU |
| subsection: strains_tax_PNU | ||
| species_epithet | Species epithet (LPSN) | Second part of species name |
| subspecies_epithet | Subspecies epithet | Third part of species name, where applicable |
| is_type_strain | Type strain | Is this strain a type strain. |
| domain_lpsn_url | domain_lpsn_url | The URL is a direct link to the corresponding LPSN page |
| phylum_lpsn_url | phylum_lpsn_url | The URL is a direct link to the corresponding LPSN page |
| class_lpsn_url | class_lpsn_url | The URL is a direct link to the corresponding LPSN page |
| ordo_lpsn_url | ordo_lpsn_url | The URL is a direct link to the corresponding LPSN page |
| family_lpsn_url | family_lpsn_url | The URL is a direct link to the corresponding LPSN page |
| genus_lpsn_url | genus_lpsn_url | The URL is a direct link to the corresponding LPSN page |
| species_lpsn_url | species_lpsn_url | The URL is a direct link to the corresponding LPSN page |
| domain | Domain | Domain name (taxonomic rank) according Prokaryotic Nomenclature Up-to-date |
| phylum | Phylum | Phylum name (taxonomic rank) according Prokaryotic Nomenclature |
| class | Class | Class name (taxonomic rank) according Prokaryotic Nomenclature . |
| ordo | Order | name of order. taxonomic rank according Prokaryotic Nomenclature Up-to-date. |
| family | Family | Family name (taxonomic rank) according Prokaryotic Nomenclature Up-to-date |
| genus | Genus | Genus name (taxonomic rank) |
| species | Species | Species name, which includes genus, species and subspecies epithet (taxonomic rank) according Prokaryotic Nomenclature Up-to-date |
| full_scientific_name | Full Scientific Name (LPSN) | Species name, author(s) and year of the valid publication of the species name. |
| Section ID | Section name | Description |
|---|---|---|
| morphology | Morphology | Information on morphological and physiological properties |
| subsection: cell_morphology | ||
| cell_len_unit | Cell length unit | Unit of length of the cell. |
| cell_width_unit | Cell width unit | Unit of width of the cell |
| gram_stain | Gram stain | Gram staining |
| cell_len | Cell length | Length of the cell. |
| cell_width | Cell width | Width of the cell |
| cell_shape | Cell shape | Description of the cell shape. |
| motility | Motility | ability of motility |
| flagellum_arrangement | Flagellum arrangement | The description of flagellum/flagella the bacterium is equipped with, in case of motility via flagellum/flagella. |
| confidence | Confidence in % | confidence |
| subsection: colony_morphology | ||
| colony_len_unit | Colony length unit | Unit of given length of the colony on distinct medium and temperature after a certain time of cultivation. |
| hemolysis_type | Type of hemolysis | alpha-, beta or gamma-hemolysis |
| hemolysis_ability | Hemolysis ability | positive (+) or negative (-) |
| colony_len | Colony size | Length of the colony on distinct medium and temperature after a certain time of cultivation. |
| colony_color | Colony color | Color of the colony on distinct medium and temperature after a certain time of cultivation. |
| colony_shape | Colony shape | Shape of the colony on distinct medium and temperature after a certain time of cultivation(form, elevation, margins, surface). |
| incubation_period | Incubation period | Incubation period in context with the description of colony morphology |
| medium_name | Cultivation medium used | Name of a medium for cultivation. |
| medium_composition | Cultivation medium composition | Composition of a medium for cultivation. |
| subsection: multicellular_morphology | ||
| multicell_size_unit | Multicellular complex size unit | Unit of given multicellular complex that is formed. |
| ability | Multicellular complex forming ability | Ability of forming multicellular complexes (aggregations). |
| multicell_name | Multicellular complex name | Names the kind of multicellular complex that is formed. |
| multicell_color | Multicellular complex color | Names the color of multicellular complex that is formed. |
| medium_name | Medium Name (multicellularity) | Name of the cultivation medium used for observing (potential) ability of multicellular complex formation. |
| multicell_size | Multicellular complex size | Average size of multicellular complex that is formed. |
| description | Multicellular complex further description | Detailed description of the multicellular complex that is formed. |
| subsection: pigmentation | ||
| pigment_production | Pigment production | Presence of pigmentation |
| pigment_color | Pigmentation color | Color of pigmentation. |
| pigment_name | Pigment name | Name of the pigment. |
| Section ID | Section name | Description |
|---|---|---|
| culture_growth_condition | Culture and growth conditions | Information on culture and growth conditions |
| subsection: culture_medium | ||
| medium_name | Culture medium | Name of the culture medium |
| medium_growth | Culture medium growth | if 1 growth, 0 no growth |
| media_link | Culture medium link | link to medium recipe |
| medium_composition | Culture medium composition | Components of the culture medium and recipe |
| subsection: culture_pH | ||
| ability | Testresult | positive/negative test result |
| test_type | Kind of pH | e.g. maximum, optimum or growth in general |
| pH | pH | tested pH values |
| ph_range | PH range | acidophile (growth positive <4), alkaliphile (growth positive >8.5) |
| confidence | Confidence in % | confidence |
| subsection: culture_temp | ||
| ability | Testresult | positive/negative test result |
| test_type | Kind of temperature | e.g. maximum, optimum or growth in general |
| temp | Temperature | temperature [°C] |
| temperature_range | Temperature range | psychrophilic (<25°C), mesophilic (25-39°C), thermophilic (40-79°C), hyperthermophilic (>80°C) |
| confidence | Confidence in % | confidence |
| Section ID | Section name | Description |
|---|---|---|
| physiology_metabolism | Physiology and metabolism | Information on physiology and metabolism |
| subsection: compound_production | ||
| compound_name | Name of produced compound | Name of produced compound (e.g. name of a secondary metabolite). |
| excreted | Is excreted product | Yes if produced compound is excreted. |
| subsection: ed_pathways | ||
| pathway | Pathway | EnzymeDetector pathway name e.g. Glycolysis |
| coverage | Enzyme coverage | EnzymeDetector coverage of this pathway in percent |
| subsection: enzymes | ||
| enzyme | Enzyme | enzyme e.g. catalase, urease, alkaline phosphatase |
| activity | Enzyme activity | Tested activity |
| ec_number | EC number | Corresponding EC number |
| subsection: FA_profile | ||
| FA_name | Fatty acid | e.g. C12:0 |
| FA_percent | Percentage | percentage |
| FA_STDV | SD | standard deviation if available |
| FA_ECL | ECL | Estimated chain length if available |
| subsection: halophily | ||
| halophily | Halophily / tolerance level | Tolerance level towards salinity (usually tested for NaCl). |
| salt | Salt | Kind of salt related to halophily information usually NaCl. |
| ability | Testresult | Ability of salt tolerance. |
| test_type | Tested relation | Kind of relation for a tested salt concentration |
| salt_concentration | Salt conc. | Tested salt concentration (usually in %) |
| salt_concentration_unit | salt concentration unit | e.g. %(w/v), % |
| confidence | Confidence in % | confidence |
| subsection: met_antibiogram | ||
| manual_annotation | Manually annotated | Is set true if manual annotation/curation has been conducted for a reference |
| Medium_antibiogram | Medium | Medium used for cultivation |
| Inc_temp_antibiogram | Incubation temperature [°C] | Incubation temperature in °C |
| Inc_time_antibiogram | Incubation time [d] | Incubation time in days |
| Inc_ox_antibiogram | Oxygen condition | e.g. aerobic, anaerobic |
| P_antibiogram | Penicillin G | 6 µg (disc) |
| OX_antibiogram | Oxacillin | 5 µg (disc) |
| AMP_antibiogram | Ampicillin | 10 µg (disc) |
| TIC_antibiogram | Ticarcillin | 75 µg (disc) |
| MEZ_antibiogram | Mezlocillin | 30 µg (disc) |
| KF_antibiogram | Cefalotin | 30 µg (disc) |
| KZ_antibiogram | Cefazolin | 30 µg (disc) |
| CTX_antibiogram | Cefotaxime | 30 µg (disc) |
| ATM_antibiogram | Aztreonam | 30 µg (disc) |
| IPM_antibiogram | Imipenem | 10 µg (disc) |
| TE_antibiogram | Tetracycline | 30 µg (disc) |
| C_antibiogram | Chloramphenicol | 30 µg (disc) |
| CN_antibiogram | Gentamycin | 10 µg (disc) |
| AK_antibiogram | Amikacin | 30 µg (disc) |
| VA_antibiogram | Vancomycin | 30 µg (disc) |
| E_antibiogram | Erythromycin | 15 µg (disc) |
| MY_antibiogram | Lincomycin | 15 µg (disc) |
| OFX_antibiogram | Ofloxacin | 5 µg (disc) |
| NOR_antibiogram | Norfloxacin | 10 µg (disc) |
| CT_antibiogram | Colistin | 10 µg (disc) |
| PIP_antibiogram | Pipemidic acid | 20 µg (disc) |
| F_antibiogram | Nitrofurantoin | 100 µg (disc) |
| B_antibiogram | Bacitracin | 10 Unit |
| PB_antibiogram | Polymyxin B | 300 Unit |
| K_antibiogram | Kanamycin | 30 µg (disc) |
| N_antibiogram | Neomycin | 30 µg (disc) |
| DO_antibiogram | Doxycycline | 30 µg (disc) |
| CRO_antibiogram | Ceftriaxone | 30 µg (disc) |
| DA_antibiogram | Clindamycin | 10 µg (disc) |
| FOS_antibiogram | Fosfomycin | 50 µg (disc) |
| MXF_antibiogram | Moxifloxacin | 5 µg (disc) |
| LZD_antibiogram | Linezolid | 10 µg (disc) |
| NS_antibiogram | Nystatin | 100 Unit |
| QD_antibiogram | Quinupristin/Dalfopristin | 15 µg (disc) |
| TEC_antibiogram | Teicoplanin | 30 µg (disc) |
| TZP_antibiogram | Piperacillin/Tazobactam | 30/10 µg (disc) |
| subsection: met_antibiotica | ||
| chebi_ID | Chebi ID | Identifier for Chebi |
| MET_group_ID | Group ID of combined antibiotics | Group of combined antibiotics |
| metabolite_antib | Metabolite | e.g. a substrate, an electron acceptor, a degraded metabolite |
| is_antibiotic | Antibiotic function | Yes if metabolite has an antibiotic function |
| ab_sensitive | Antibiotic sensitivity | General relation of an organism to an antibiotic substance |
| ab_sensitivity_conc | Concentration | Concentration in g/L |
| ab_sensitivity_unit | concentration unit | e.g. g/L, mM |
| ab_intermediate | Antibiotic intermediate | General relation of an organism to an antibiotic substance |
| ab_intermediate_conc | Concentration | Concentration in g/L |
| ab_intermediate_unit | concentration unit | e.g. g/L, mM |
| ab_resistant | Antibiotic resistance | General relation of an organism to an antibiotic substance |
| ab_resistance_conc | Concentration | Concentration in g/L |
| ab_resistance_unit | concentration unit | e.g. g/L, mM |
| subsection: met_production | ||
| chebi_ID | Chebi ID | Identifier for Chebi |
| metabolite_prod | Metabolite | e.g. a substrate, an electron acceptor, a degraded metabolite |
| production | Production | Yes if it is a metabolite production |
| excreted | Excretion | Yes if it is a metabolite excretion |
| subsection: met_test | ||
| chebi_ID | Chebi ID | Identifier for Chebi |
| metabolite_test | Metabolite | e.g. a substrate, an electron acceptor, a degraded metabolite |
| voges_proskauer | Voges-Proskauer-test | Test for acetoin production |
| methyl_red | Methylred-test | Test for mixed acid fermentation on glucose |
| indole_test | Indole test | Test for ability to convert tryptophan into indole |
| citrate_test | Citrate test | Test for the ability of using citrate as sole carbon source. |
| subsection: met_util | ||
| chebi_ID | Chebi ID | Identifier for Chebi |
| metabolite_util | Metabolite | e.g. a substrate, an electron acceptor, a degraded metabolite |
| ability | Utilization activity | Ability of metabolite utilization. |
| test_type | Kind of utilization tested | Type of applied utilization test. |
| subsection: murein | ||
| murein_short_index | Murein short key | To save space, a special system has been developed to characterize the different murein types. This key enables the user to link the abbreviations to the system proposed for the characterization and representation of peptidoglycan types proposed by Schleifer and Kandler 1972. An extension by an apostrophe e.g. A3 alpha' denotes that the L-Ala residue found normally in position 1 of the peptide subunit is replaced by Gly. |
| murein_types | Murein types | Characterization of the different murein types. |
| subsection: nutrition_type | ||
| nutrition_type | Nutrition type | eg. autotroph, heterotroph, phototrop, ... |
| subsection: observation | ||
| attribute | Observation | Known attribute or ability of the strain e.g. cellulose decompositon, yeast lysis |
| subsection: oxygen_tolerance | ||
| oxygen_tol | Oxygen tolerance | information depends on applied culture medium |
| confidence | Confidence in % | confidence |
| subsection: spore_formation | ||
| description | Spore description | Further description. |
| type | Type of spore | Type of spore |
| ability | Ability of spore formation | Ability of spore formation. |
| confidence | Confidence in % | confidence |
| subsection: tolerance | ||
| concentration_unit | Tolerated substance unit | Unit of tolerated compound/substance. |
| compound_name | Name of tolerated compound | Name of tolerated substances. |
| level_percent | Tolerance percentage | Tolerance level in percent towards substances. |
| concentration | Tolerated concentration | Tolerated substance - concentration tolerated. |
| Section ID | Section name | Description |
|---|---|---|
| environment_sampling_isolation_source | Isolation, sampling and environmental information | Information on isolation source, the sampling and environmental conditions |
| subsection: origin | ||
| sample_type | Sample type/isolated from | property of the sample the bacterium was isolated from. |
| Host_Species | Host species | The host species where a strain was isolated from |
| sample_date | Sampling date | The time of sampling. |
| geo_loc_name | Geographic location (country and/or sea, region) | The geographical origin of the sample as defined by the country or sea name followed by specific region name. |
| country | Country | country name: sample material/strain origin |
| iso_3 | Country ISO 3 Code | country name: sample material/strain origin |
| continent | Continent | continent name: sample material/strain origin |
| latitude | Geographic location (latitude) | The geographical origin of the sample as defined by latitude. |
| longitude | Geographic location (longitude) | The geographical origin of the sample as defined by longitude. |
| enrichment_cult_name | Enrichment culture | If derived/isolated from an enrichment culture medium is specified here. |
| enrichment_cult_composition | Enrichment culture composition | If derived/isolated from an enrichment culture medium is specified here. |
| enrichment_cult_duration | Enrichment culture duration | If derived/isolated from an enrichment culture duration is specified here. |
| enrichment_cult_temp | Enrichment culture temperature | If derived/isolated from an enrichment culture medium temperature is specified here. |
| isolation_date | Isolation date | See Bacterial and Fungal MINE: isolationDate is the last subfield |
| procedure_origin | Isolation/enrichment procedure | Further describtion on enrichment or isolation precedure |
| subsection: taxonmaps | ||
| file_name | File name | File name of the map preview |
| url | url | The URL is a direct link to the microbeatlas |
| LastTax | LastTax | LastTax |
| 16S_seq_accession | 16S_seq_accession | Known accession numbers of sequence databases can be entered. |
| SeqIdentity | SeqIdentity | SeqIdentity |
| Section ID | Section name | Description |
|---|---|---|
| safety_information | Safety information | Information on possible application of the strain and its possible interaction with e.g. potential hosts |
| subsection: risk_assessment | ||
| pathogenicity_human | Pathogenicity (human) | Ability of causing pathological conditions within the referring organism |
| pathogenicity_animal | Pathogenicity (animal) | Ability of causing pathological conditions within the referring organism |
| pathogenicity_plant | Pathogenicity (plant) | Ability of causing pathological conditions within the referring organism |
| biosafety_level | Biosafety level | Biosafety level defined for the strain |
| biosafety_level_comment | Biosafety level comment | Year/country/location when/where this biosafety level was defined |
| Section ID | Section name | Description |
|---|---|---|
| sequence_information | Sequence information | Information on genomic background e.g. entries in nucleic sequence databass |
| subsection: GC_content | ||
| GC_content | GC-content | Guanine-Cytosine content in mol % |
| GC_method | GC-content method | Method of guanine-cytosine content determination (e.g. high pressure liquid chromatography (HPLC),thermal denaturation, midpoint method (Tm),fluorimetric,Thermal denaturation, fluorometry,Buoyant density centrifugation (BD),capillary zone electrophoresis (CZE),real time PCR (RTD-PCR),sequence analysis,genome sequence analysis,paper chromatography) |
| subsection: sequence_16S | ||
| sequence_name | Sequence accession description | Given title of this accession number in the INSDC sequence database. |
| sequence_acc | Seq. accession number | Known accession numbers of sequence databases can be entered. |
| sequence_length | Sequence length | Length of the sequence |
| link_db | Sequence database | Name of the databse. |
| tax_id | Associated NCBI tax ID | NCBI tax ID Associated which is associated to the refering INSDC accession number. |
| subsection: sequence_genomes | ||
| sequence_name | Sequence accession description | Given title of this accession number in the corresponding database. |
| sequence_acc | Seq. accession number | Known accession numbers of sequence database. |
| assembly_lvl | Assembly level | Assembly level |
| source_db | Sequence database | Name of the databse. |
| tax_id | Associated NCBI tax ID | NCBI tax ID Associated which is associated to the refering INSDC accession number. |
| Section ID | Section name | Description |
|---|---|---|
| predictions | Genome-based predictions | Data predicted using genome information as a basis |
| subsection: predictions | ||
| trait | Trait | Trait |
| prediction | Prediction | |
| confidence | Confidence in % | confidence |
| training_data | In training data | |
| subsection: predictions_meta | ||
| sequence_acc | Seq. accession number | Known accession numbers of sequence database. |
| sequence_name | Sequence accession description | Given title of this accession number in the INSDC sequence database. |
| db | Sequence database | Name of the databse. |
| Section ID | Section name | Description |
|---|---|---|
| external_links | External links | Availability in culture collections |
| subsection: literature | ||
| topic | Topic | Topic of reference |
| pubmed_ID | Pubmed ID | Identification Number of the PubMed literature database |
| title | Title | Title of reference |
| authors | Authors | List of author(s) |
| journal | Journal | Journal Name of Reference |
| doi | DOI (Digital Object Identifier) | Reference identified via a Digital Object Identifier (DOI) |
| year | Year | Year of publication of the reference |
| subsection: straininfo_link | ||
| id_straininfo | Straininfo SI-ID | Straininfo SI-ID |
| culture_collections_html | Culture collections | Strain passport(s) associated to the strain at StrainInfo.net and its number(s) given by a public culture collection or bioresource center, where applicable more than one per strain |
| subsection: strains | ||
| strain_number | Culture collection no. | Accession number, i.e. the unique number given by a public culture collection or bioresource center to the strain, where applicable more than one per strain (e.g. DSM 2324, ATCC 6438, NCIB 2224) |
| Section ID | Section name | Description |
|---|---|---|
| references | References | References |
| subsection: references | ||
| ID_references | Reference ID | ID of the reference |
| reference | Reference | The complete reference |