MicrO.owl
type: Ontology
creator: Lead Creator: Carrine E. Blank, University of Montana, fall 2013 through spring 2016. Co-contributors and advisors: Hong Cui (University of Arizona), Lisa Moore (University of Southern Maine), and Ramona Walls (University of Arizona).
version info: MicrO (An Ontology of Prokaryotic Phenotypic and Metabolic Characters). Version 1.5.1 released 6/14/2018. Includes terms and term synonyms extracted from > 3000 prokaryotic taxonomic descriptions, collected from a large number of taxonomic descriptions from Archaea, Cyanobacteria, Bacteroidetes, Firmicutes and Mollicutes. The ontology and the synonym lists were developed to facilitate the automated extraction of phenotypic data and character states from prokaryotic taxonomic descriptions using a natural language processing algorithm (MicroPIE). MicroPIE was developed by Hong Cui, Elvis Hsin-Hui Wu, and Jin Mao (University of Arizona) in collaboration with Carrine E. Blank (University of Montana) and Lisa R. Moore (University of Southern Maine). Descriptions and links to MicroPIE can be found at http://avatol.org/ngp/nlp/overview-2/. https://github.com/biosemantics/micropie2 The most current version of MicrO can be downloaded from https://github.com/carrineblank/MicrO.
comment: Many thanks to Chris Mungall (LBNL), Elvis Hsin-Hui Wu (University of Arizona), Gail Gasparich (Towson University), and Gordon Burleigh (University of Florida) for comments and/or assistance with ontology construction and compilation of taxonomic descriptions and term definitions. Thanks to Oliver He (University of Michigan) for technical assistance with OntoBee and OntoFox, and Gareth Owen (ChEBI project leader, head curator) and other curators at ChEBI for assistance in the incorporation of microbial-specific chemical terms and synonyms into ChEBI. Thanks also to the instructors (Melissa Haendel, Matt Yoder, Jim Baihoff) and students of the 2013 NESCent Ontologies for Evolutionary Biology workshop, and to Karen Cranston (NESCent director) and the support staff at NESCent. This work was supported by a grant from the National Science Foundation Assembling the Tree of Life Program (DBI-1208534), and by a travel grant to attend the 2013 NESCent Ontologies for Evolutionary Biology workshop.
imports: BFO imports.owl
imports: BSPO imports.owl
imports: CHMO imports.owl
imports: CL imports.owl
imports: ChEBI imports.owl
imports: DRON imports.owl
imports: ENVO imports.owl
imports: FMA imports.owl
imports: GO imports.owl
imports: IAO imports.owl
imports: IDO imports.owl
imports: NCBITax imports.owl
imports: NDF-RT imports.owl
imports: OBI imports.owl
imports: PATO imports.owl
imports: PO imports.owl
imports: PR imports.owl
imports: REO imports.owl
imports: RO imports.owl
imports: Uberon imports.owl

is an assay using the culture medium
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between an assay (x) and a microbiological culture medium (y), where the medium is needed to carry out the assay.
created by: Carrine Blank
range: microbiological culture medium
sub property of: is an assay using the material entity
domain: OBI_0000070

has shape
type: ObjectProperty
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a shape (y).
created by: Carrine Blank
sub property of: has morphology
range: PATO_0000052
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has position
type: ObjectProperty
created by: Carrine Blank
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a position quality (y).
sub property of: has physical quality
range: PATO_0000140
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has structure
type: ObjectProperty
created by: Carrine Blank
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a structure (y).
sub property of: has morphology
range: PATO_0000141
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has morphology
type: ObjectProperty
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a morphology (y).
created by: Carrine Blank
sub property of: has physical object quality
range: PATO_0000051
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has angle
type: ObjectProperty
type: FunctionalProperty
definition: Relationship between two connected entities that are connected and have a spatial relationship defined by an angle that exists between the two connected entities.
created by: Carrine Blank
sub property of: BFO_0000051

is an assay using the chemical reagent
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between an assay (x) and a chemical entity (y), where the chemical entity is used as a chemical reagent or substance used to carry out the assay.
created by: Carrine Blank
range: CHEBI_24431
sub property of: is an assay using the material entity
domain: OBI_0000070

has size
type: ObjectProperty
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a size (y).
created by: Carrine Blank
sub property of: has morphology
range: PATO_0000117
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has physical quality
type: ObjectProperty
created by: Carrine Blank
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a physical quality (y).
sub property of: has physical object quality
range: PATO_0001018
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has texture
type: ObjectProperty
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a texture (y).
created by: Carrine Blank
sub property of: has morphology
range: PATO_0000150
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has organismal quality
type: ObjectProperty
created by: Carrine Blank
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and an organismal quality (y).
sub property of: has physical object quality
range: PATO_0001995
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has physical object quality
type: ObjectProperty
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a physical object quality (y).
created by: Carrine Blank
range: PATO_0001241
sub property of: RO_0000086
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

is an enzymatic hydrolytic extract derived from
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed via the process of enzymatic hydrolysis.
created by: Carrine Blank
range: BFO_0000040
domain: microbiological medium ingredient, derived from enzymatic hydrolysis of protein
sub property of: is an extract derived from

is an acid hydrolytic extract derived from
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed via the process of acid hydrolysis.
range: BFO_0000040
domain: undefined organic chemical mixture
sub property of: is an extract derived from

is the quality assayed by
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a quality (x) and an assay (y).
created by: Carrine Blank
inverse of: is an assay for the quality
sub property of: is assayed by
range: OBI_0000070
domain: PATO_0000001

is culture medium used by
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a microbiological culture medium (x) and a cellular organism (y) where the culture medium is used to support the growth of cellular organism y.
created by: Carrine Blank
domain: microbiological culture medium
range: NCBITaxon_131567
sub property of: topObjectProperty

is an extract derived from
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical or physical extraction procedure.
range: BFO_0000040
domain: undefined organic chemical mixture
sub property of: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.

MICRO_0000474
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
sub property of: working-temp obj props

is an oleaginous extract derived from
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between an oleoginous (oily) material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed from material derived from the organism.
range: BFO_0000040
domain: microbiological medium ingredient, derived from oil
sub property of: is an extract derived from

MICRO_0000476
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
sub property of: working-temp obj props

is an aqueous extract derived from
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed via the process of an aqueous extraction (an extraction with water).
range: BFO_0000040
sub property of: is an extract derived from
domain: MICRO_0001370

MICRO_0000478
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
sub property of: working-temp obj props

is an assay for the quality
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between an assay (x) and a quality (y).
sub property of: is an assay for
domain: OBI_0000070
range: PATO_0000001

uses chemical entity
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y).
created by: Carrine Blank
range: CHEBI_24431
sub property of: topObjectProperty
domain: Class
  union of: prokaryotic metabolic process
  union of: MICRO_0001444

is an assay for the enzymatic substrate
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between an assay (x) and a chemical entity (y), where the chemical entity used is a chemical enzymatic reactant in the designated process (namely a chemical reaction catalyzed by an enzyme).
range: CHEBI_24431
sub property of: is an assay for the metabolic substrate
domain: OBI_0000070

is an assay for the enzymatic product
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a chemical enzymatic product of the designated process (namely a chemical reaction catalyzed by an enzyme).
range: CHEBI_24431
sub property of: is an assay for the metabolic product
domain: OBI_0000070

is an assay for the metabolic substrate
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a metabolic substrate used in the designated process (generally a metabolic process deriving from a combination of enzymatic processes).
range: CHEBI_24431
sub property of: is an assay using the chemical reagent
domain: OBI_0000070

is an assay for the metabolic product
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a metabolic product in the designated process (generally a metabolic process deriving from a combination of enzymatic processes).
range: CHEBI_24431
inverse of: is metabolic product assayed by
domain: OBI_0000070
sub property of: OBI_0000299

is metabolic substrate assayed by
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a metabolic substrate (generally a metabolic process deriving from a combination of enzymatic processes) assayed by the diagnostic assay.
domain: CHEBI_24431
inverse of: is an assay for the metabolic substrate
range: OBI_0000070
sub property of: OBI_0000295

is enzymatic substrate assayed by
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a chemical enzymatic reactant (namely a chemical reaction catalyzed by an enzyme) being assayed in the diagnostic assay.
created by: Carrine Blank
domain: CHEBI_24431
inverse of: is an assay for the enzymatic substrate
sub property of: is metabolic substrate assayed by
range: OBI_0000070

is metabolic product assayed by
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a metabolic product of the process (a metabolic process deriving from a combination of enzymatic processes) which is being assayed by the diagnostic assay.
created by: Carrine Blank
domain: CHEBI_24431
range: OBI_0000070
sub property of: OBI_0000312

is enzymatic product assayed by
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a chemical enzymatic product of the enzymatic process (a chemical reaction catalyzed by an enzyme) assayed by the diagnostic assay.
created by: Carrine Blank
domain: CHEBI_24431
inverse of: is an assay for the enzymatic product
sub property of: is metabolic product assayed by
range: OBI_0000070

is the enzymatic activity assayed by
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between a molecular function (x), namely the enzymatic activity being tested and an assay (y), namely an analytical investigation/test for the presence of an enzymatic activity.
domain: GO_0003674
sub property of: is assayed by
range: OBI_0000070

is an assay for the enzymatic activity of
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between an assay (x), namely an analytical investigation/test for the presence of an enzymatic activity, and a molecular function (y), namely the enzymatic activity being tested.
range: GO_0003674
inverse of: is the enzymatic activity assayed by
sub property of: is an assay for
domain: OBI_0000070

is an assay for the fermentation substrate
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between an assay (x) and a chemical entity (y), where the chemical entity used is a fermentation substrate in the designated process (generally a metabolic fermentation process deriving from a combination of enzymatic processes).
created by: Carrine Blank
range: CHEBI_24431
sub property of: is an assay for the metabolic substrate
inverse of: is fermentation substrate assayed by
domain: OBI_0000070

is fermentation product assayed by
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a fermentation product (generally a metabolic fermentation process deriving from a combination of enzymatic processes) assayed by the diagnostic assay.
created by: Carrine Blank
domain: CHEBI_24431
sub property of: is metabolic product assayed by
range: OBI_0000070

is fermentation substrate assayed by
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a fermentation substrate (generally a metabolic fermentation process deriving from a combination of enzymatic processes) being assayed by the diagnostic assay.
created by: Carrine Blank
domain: CHEBI_24431
sub property of: is metabolic substrate assayed by
range: OBI_0000070

is assayed by
type: ObjectProperty
type: TransitiveProperty
definition: A relationship between a process, quality, cellular component, molecular function, or a chemical entity (x) and an assay (y).
created by: Carrine Blank
range: OBI_0000070

is an assay for
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between a microbiological diagnostic test (x) and a biological process, quality, cellular component, molecular function, or a chemical entity (y).
inverse of: is assayed by
domain: OBI_0000070

is an assay for the biological process of
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between an assay (x), namely an analytical investigation/test for the presence of a physical biological process, and a biological process (y).
range: GO_0008150
sub property of: is an assay for
domain: OBI_0000070

is the biological process assayed by
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between a biological process (x), and an assay (y) which is an analytical investigation/test for the presence of a physical biological process.
domain: GO_0008150
sub property of: is assayed by
inverse of: is an assay for the biological process of
range: OBI_0000070

is an assay for the biosynthetic production of
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between a n assay (x), namely an analytical investigation/test for the presence of a metabolic product, and a chemical entity (y).
range: CHEBI_24431
domain: OBI_0000070
sub property of: OBI_0000299

biosynthetic production is assayed by
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between a chemical entity (x), which is a biosynthetic product, that is assayed by an assay (y). Differentiated from 'is metabolic production of' which has the same domain and ranges, but is where an assay is used to detect a product of metabolism (i.e. energy generation).
domain: CHEBI_24431
inverse of: is an assay for the biosynthetic production of
range: OBI_0000070
sub property of: OBI_0000312

is prokaryotic physiological quality of
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between a prokaryotic physiological quality (x) and a prokaryotic physiologically differentiated cell (y).
domain: prokaryotic physiological quality
range: MICRO_0001541
sub property of: topObjectProperty

MICRO_0001220
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
sub property of: working-temp obj props

is an assay for the cellular component
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between an assay (x), namely an analytical investigation/test for the presence of a physical cellular component, and a cellular component (y).
range: GO_0005575
sub property of: is an assay for
domain: OBI_0000070

is the cellular component assayed by
type: ObjectProperty
type: TransitiveProperty
definition: A relationship between a cellular component (x), and an assay (y) which is an analytical investigation/test for the presence of a cellular component.
created by: Carrine Blank
domain: GO_0005575
sub property of: is assayed by
inverse of: is an assay for the cellular component
range: OBI_0000070

has ingredient
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a material entity (x), which is a man-made material entity such as a chemical solution or a culture medium, and a chemical entity (y), where the chemical entity forms part of a mixture of chemicals that make up the material entity.
created by: Carrine Blank
IAO_0000119: Wikipedia:ingredient An ingredient is a substance that forms part of a mixture (in a general sense). For example, in cooking, recipes specify which ingredients are used to prepare a specific dish. Many commercial products contain a secret ingredient that is purported to make them better than competing products. In the pharmaceutical industry, an active ingredient is that part of a formulation that yields the effect required by the customer. National laws usually require prepared food products to display a list of ingredients, and specifically require that certain additives be listed. In most developed countries, the law requires that ingredients be listed according to their relative weight[1] in the product. If an ingredient itself consists of more than one ingredient (such as the cookie pieces which are a part of "cookies and cream" flavor ice cream), then that ingredient is listed by what percentage of the total product it occupies, with its own ingredients displayed next to it in brackets. The term constituent is often chosen when referring to the substances that constitute the tissue of living beings such as plants and people, because the word ingredient in many minds connotes a sense of human agency (that is, something that a person combines with other substances), whereas the natural products present in living beings were not added by any human agency but rather occurred naturally ("a plant doesn't have ingredients"). Thus all ingredients are constituents, but not all constituents are ingredients.
range: CHEBI_24431
sub property of: has chemical composition
domain: Class
  union of: CHEBI_60004
  union of: OBI_0000079
  union of: OBI_0302729

is an ingredient of
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a chemical entity (x) and a mixture, culture medium, or chemical solution (y), where y is artificial created by human activity.
created by: Carrine Blank
sub property of: BFO_0000050
domain: CHEBI_24431
inverse of: has ingredient
range: Class
  union of: CHEBI_60004
  union of: OBI_0000079
  union of: OBI_0302729

has susceptibility towards the chemical
type: ObjectProperty
created by: Carrine Blank
definition: Relationship between a prokaryotic cell or cellular component (x) and a chemical solution or chemical entity (y).
range: Class
  union of: CHEBI_24431
  union of: OBI_0302729
domain: Class
  union of: CL_0000520
  union of: GO_0005575

develops into
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between an independent continuant (x) and another independent continuant (y), where x develops (or transforms) into y through a developmental process.
created by: Carrine Blank
range: BFO_0000004
domain: BFO_0000004
inverse of: RO_0002202

has salinity
type: ObjectProperty
type: FunctionalProperty
created by: Carrine Blank
definition: Relationship between a microbiological culture medium (x) and a salinity quality (y).
domain: microbiological culture medium
range: MICRO_0001289
sub property of: culture medium has quality

has pH
type: ObjectProperty
type: FunctionalProperty
created by: Carrine Blank
definition: Relationship between a microbiological culture medium (x) and a pH quality (y).
domain: microbiological culture medium
sub property of: culture medium has quality
range: MICRO_0001380

has redox
type: ObjectProperty
type: FunctionalProperty
created by: Carrine Blank
definition: Relationship between a microbiological culture medium (x) and a redox quality (y).
domain: microbiological culture medium
sub property of: culture medium has quality
range: MICRO_0001397

MICRO_0001304
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
sub property of: working-temp obj props

culture medium has quality
type: ObjectProperty
created by: Carrine Blank
definition: Relationship between a microbiological culture medium (x) and a quality (y).
domain: microbiological culture medium
inverse of: is quality of the culture medium
range: PATO_0000001
sub property of: RO_0000086

has chemical composition
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a material entity (x) and a material entity (y), where the material entity is a natural substance (such as a chemical entity) that has a mixture of chemical substances in it.
created by: Carrine Blank
range: BFO_0000040
domain: BFO_0000040
sub property of: BFO_0000051

is an assay using the material entity
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between an assay (x) and a material entity (y), where the material entity is needed to carry out the assay.
created by: Carrine Blank
range: BFO_0000040
domain: OBI_0000070
sub property of: OBI_0000293

is quality of the culture medium
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a quality (x), such as a pH quality, redox quality, or salinity quality, and a microbiological culture medium (y) which is an independent continuant.
range: microbiological culture medium
domain: PATO_0000001
sub property of: RO_0000080

Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
type: ObjectProperty
label: is chemical entity derived from
created by: Carrine Blank
range: BFO_0000040
domain: CHEBI_24431
sub property of: topObjectProperty

has cell wall
type: ObjectProperty
type: FunctionalProperty
created by: Carrine Blank
definition: Relationship between a particular cellular organism (x) and an external encapuslating structure (y).
sub property of: BFO_0000051
range: GO_0030312
domain: NCBITaxon_131567

is an assay using the cellular organism
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between an assay (x) and cellular organisms (y), where the organism(s) is needed to carry out the assay.
created by: Carrine Blank
sub property of: is an assay using the material entity
range: NCBITaxon_131567
domain: OBI_0000070

uses carbon source
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is a carbon source.
range: CHEBI_24431
sub property of: uses chemical entity
domain: Class
  union of: prokaryotic metabolic process
  union of: MICRO_0001444

uses energy source
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity or sunlight (y), where the chemical entity or sunlight is a energy source.
created by: Carrine Blank
sub property of: topObjectProperty
domain: Class
  union of: prokaryotic metabolic process
  union of: MICRO_0001444
range: Class
  union of: CHEBI_24431
  union of: MICRO_0001441

uses electron donor
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is a electron donor.
created by: Carrine Blank
range: CHEBI_24431
sub property of: uses chemical entity
domain: Class
  union of: prokaryotic metabolic process
  union of: MICRO_0001444

uses electron acceptor
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is an electron acceptor.
range: CHEBI_24431
sub property of: uses chemical entity
domain: Class
  union of: prokaryotic metabolic process
  union of: MICRO_0001444

working-temp obj props
type: ObjectProperty
created by: Carrine Blank
sub property of: topObjectProperty

has symmetry
type: ObjectProperty
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a symmetry quality (y).
created by: Carrine Blank
sub property of: has spatial pattern
range: PATO_0000965
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

has spatial pattern
type: ObjectProperty
definition: Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a spatial position quality (y).
created by: Carrine Blank
sub property of: has position
range: PATO_0000060
domain: Class
  union of: CL_0000520
  union of: GO_0005575
  union of: MICRO_0002468

contains prokaryotic metabolic process
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a prokaryotic metabolically differentiated cell (x) and a prokaryotic metabolic process (y).
range: prokaryotic metabolic process
domain: MICRO_0001444
inverse of: is prokaryotic metabolic process occuring in
sub property of: contains biological process

has prokaryotic physiological quality
type: ObjectProperty
type: TransitiveProperty
definition: A relationship between a prokaryotic physiologically differentiated cell (x) and a prokaryotic physiological quality (y).
created by: Carrine Blank
range: prokaryotic physiological quality
domain: MICRO_0001541
sub property of: RO_0000086

has measurement
type: ObjectProperty
created by: Carrine Blank
definition: xxxx

is prokaryotic metabolic process carried out in the presence of
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: A relationship between a prokaryotic metabolic process (x) and an inorganic molecular entity, an organic molecular entity or sunlight (y).
sub property of: BFO_0000066
domain: prokaryotic metabolic process
range: Class
  union of: CHEBI_24835
  union of: CHEBI_50860
  union of: MICRO_0001441

is prokaryotic metabolic process occuring in
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a prokaryotic metabolic process (x) and a prokaryotic metabolically differentiated cell (y).
created by: Carrine Blank
sub property of: BFO_0000066
domain: prokaryotic metabolic process
range: MICRO_0001444

has prokaryotic metabolic quality
type: ObjectProperty
created by: Carrine Blank
definition: Relationship between a prokaryotic metabolically differentiated cell (x) and a prokaryotic metabolic quality (y).
domain: MICRO_0001444
range: MICRO_0001488
inverse of: is prokaryotic metabolic quality of
sub property of: RO_0000086

is prokaryotic metabolic quality of
type: ObjectProperty
type: TransitiveProperty
definition: Relationship between a prokaryotic metabolic quality (x) and a prokaryotic metabolically differentiated cell (y) which is an independent continuant.
created by: Carrine Blank
range: MICRO_0001444
domain: MICRO_0001488
sub property of: RO_0000080

is prokaryotic metabolic quality of a cell carrying out the process
type: ObjectProperty
type: TransitiveProperty
definition: A relationship between a prokaryotic metabolic quality (x) and a prokaryotic metabolic process (y).
created by: Carrine Blank
range: prokaryotic metabolic process
domain: MICRO_0001488

is prokaryotic metabolic process which makes a cell
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between a prokaryotic metabolic process (x) and a prokaryotic metabolic quality (y).
domain: prokaryotic metabolic process
range: MICRO_0001488
inverse of: is prokaryotic metabolic quality of a cell carrying out the process

has colony margin symmetry
type: ObjectProperty
definition: Relationship between a prokaryotic colony (x) and a symmetry quality (y), pertaining specifically to the symmetry of the prokaryotic colony margin.
created by: Carrine Blank
sub property of: has symmetry
range: PATO_0000965
domain: MICRO_0002468

contains biological process
type: ObjectProperty
definition: A relationship between a prokaryotic differentiated cell (x) and a biological process (y).
created by: Carrine Blank
sub property of: BFO_0000067
range: GO_0008150
domain: prokaryotic differentiated cell

is an assay for the fermentation product
type: ObjectProperty
type: TransitiveProperty
created by: Carrine Blank
definition: Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a fermentation product in the designated process (generally a metabolic fermentation process deriving from a combination of enzymatic processes).
range: CHEBI_24431
sub property of: is an assay for the metabolic product
inverse of: is fermentation product assayed by
domain: OBI_0000070

has sodium chloride percentage of
type: DatatypeProperty
created by: Carrine Blank
definition: Describes the percentage of sodium chloride concentration in which an organism is capable of growth.

has cell width
type: DatatypeProperty

has pH value
type: DatatypeProperty
type: FunctionalProperty
created by: Carrine Blank
definition: Describes the pH (hydrogen ion concentration) in which an organism is capable of growth.

GO_0019414
type: Class
IAO_0000232: zzzz Note that there is an error with this class (sulfate can't be used as an electron donor)

flagellar quality
type: Class
equivalent class: Class
  intersection of: prokaryotic cell quality
  intersection of: Restriction
    on property: RO_0000080
    some values from: flagellated cell
definition: Prokaryotic cell quality where a cell has either a bacterial-type flagellum (or flagella) or a periplasmic flagellum.
created by: Carrine Blank

branch perpendicular to trichome
type: Class
equivalent class: Class
  intersection of: MICRO_0000639
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: cell filament
      intersection of: Restriction
        on property: BFO_0000051
        some values from: Class
disjoint with: MICRO_0000640
definition: Filament branch angle, where the angle between the cylindrical cells of the branching filament and the cylindrical cells of the main trichome is perpendicular.
has related synonym: lateral branches
has exact synonym: branches perpendicular to trichome
created by: Carrine Blank
has related synonym: branches lateral
has exact synonym: branches perpendicular to the long trichome axis

filament branch size
type: Class
equivalent class: Class
  intersection of: morphologically differentiated branches
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000117
subclass of: morphologically differentiated branches
subclass of: Restriction
  on property: has size
  some values from: PATO_0000117
created by: Carrine Blank
has broad synonym: branch length
definition: Filament branch morphological quality relating to the size (length, and hence the number of cells in the branch, and thickness) of a filament branch, relative to the size of the main trichome.
has broad synonym: branch size

morphologically differentiated branches
type: Class
equivalent class: Class
  intersection of: differentiated filament branching
  intersection of: Restriction
    on property: has morphology
    some values from: PATO_0000051
created by: Carrine Blank
has exact synonym: branching morphology
definition: Filament branch physical object quality defining the morphology (shape, size, length) of branches in relationship to the main filament.

straight filament branch
type: Class
equivalent class: Class
  intersection of: MICRO_0000635
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002180
subclass of: MICRO_0000635
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002180
disjoint with: arcuate filament branch
has exact synonym: filament branch straight
created by: Carrine Blank
has exact synonym: branches straight
definition: The nature of branches in a microbial filament to be straight (i.e. not curved).

arcuate filament branch
type: Class
equivalent class: Class
  intersection of: MICRO_0000635
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000406
subclass of: MICRO_0000635
subclass of: Restriction
  on property: has shape
  some values from: PATO_0000406
has broad synonym: branches later curve to the direction of the original trichome
created by: Carrine Blank
has broad synonym: branches arcuate
has exact synonym: filament branch arcuate
definition: The nature of branches in a microbial filament to be arcuate (curved).

solitary branches
type: Class
equivalent class: Class
  intersection of: MICRO_0000638
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      union of: true branch
      union of: false branch
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002436
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000616
subclass of: MICRO_0000638
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    union of: true branch
    union of: false branch
subclass of: Restriction
  on property: has position
  some values from: PATO_0002436
subclass of: Restriction
  on property: has symmetry
  some values from: PATO_0000616
disjoint with: paired branches
has exact synonym: irregularly branched
has exact synonym: branches solitary
definition: Filament branch spatial pattern where the filament exhibits branching (either false or true branching). Filaments occur singularly (solitary), and do not occur in pairs (are offset from one another).
created by: Carrine Blank
has exact synonym: filaments irregularly branched

paired branches
type: Class
equivalent class: Class
  intersection of: MICRO_0000638
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      union of: true branch
      union of: false branch
  intersection of: Restriction
    on property: has position
    some values from: PATO_0001933
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000632
subclass of: MICRO_0000638
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    union of: true branch
    union of: false branch
subclass of: Restriction
  on property: has position
  some values from: PATO_0001933
subclass of: Restriction
  on property: has symmetry
  some values from: PATO_0000632
created by: Carrine Blank
has exact synonym: branches paired
definition: Filament branch spatial pattern where the filament exhibits branching (either false or true branching). Filaments occur paired, opposite from one another.

heterocyte position relative to branches
type: Class
equivalent class: Class
  intersection of: differentiated filament branching
  intersection of: Class
    union of: Restriction
      on property: has position
      some values from: PATO_0000140
    union of: Restriction
      on property: RO_0001025
      some values from: BSPO_0000070
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: heterocyte
      intersection of: Restriction
        on property: BFO_0000051
        some values from: Class
subclass of: differentiated filament branching
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: heterocyte
    intersection of: Restriction
      on property: BFO_0000051
      some values from: Class
        intersection of: cell filament
        intersection of: Restriction
subclass of: Class
  union of: Restriction
    on property: has position
    some values from: PATO_0000140
  union of: Restriction
    on property: RO_0001025
    some values from: BSPO_0000070
created by: Carrine Blank
definition: Differentiated filament branching relating the distribution of heterocytes in the filament and their spatial relationship to the branches.

branches thinner than main filament
type: Class
equivalent class: Class
  intersection of: MICRO_0000636
  intersection of: Restriction
    on property: has size
    some values from: PATO_0001715
subclass of: MICRO_0000636
subclass of: Restriction
  on property: has size
  some values from: PATO_0001715
disjoint with: MICRO_0000637
has exact synonym: branches thinner
has exact synonym: secondary filaments thinner
has exact synonym: secondary lateral branches generally thinner
has exact synonym: thinner branches
definition: Filament branch size where the diameter of cylindrical cells in the filament branches are thicker than the diameter of cylindrical cells in the main trichome.
created by: Carrine Blank
has exact synonym: branches usually slightly thinner

heterocytes basal in branches
type: Class
equivalent class: Class
  intersection of: heterocytes in branches
  intersection of: Restriction
    on property: RO_0001025
    some values from: BSPO_0000074
subclass of: heterocytes in branches
subclass of: Restriction
  on property: RO_0001025
  some values from: BSPO_0000074
definition: The physical relationship of branches in a microbial filament to heterocytes, being physically adjacent to heterocytes wherein branches initiate at the heterocytes.
has exact synonym: branches initiating at the heterocytes
has broad synonym: branches initiate at heterocytes
created by: Carrine Blank
has narrow synonym: lateral branches initiating at the heterocytes
has narrow synonym: branches initiate usually at originally intercalary heterocytes

heterocytes apical in branches
type: Class
equivalent class: Class
  intersection of: heterocytes in branches
  intersection of: Restriction
    on property: RO_0001025
    some values from: BSPO_0000073
subclass of: heterocytes in branches
subclass of: Restriction
  on property: RO_0001025
  some values from: BSPO_0000073
has broad synonym: branches terminated by heterocytes
definition: The physical relationship of branches in a microbial filament to heterocytes, where heterocytes are located at the end of branches.
created by: Carrine Blank

heterocytes not in branches
type: Class
equivalent class: Class
  intersection of: heterocyte position relative to branches
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: heterocyte
      intersection of: Restriction
        on property: RO_0001025
        some values from: Class
subclass of: heterocyte position relative to branches
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: heterocyte
    intersection of: Restriction
      on property: RO_0001025
      some values from: Class
        intersection of: cell filament
        intersection of: Restriction
has exact synonym: branches distant from heterocytes
has broad synonym: branches distant from heterocytes
has broad synonym: distant from the heterocytes
definition: Heterocyte position where the heterocyte is not located in the filament branch.
created by: Carrine Blank

heterocytes in branches
type: Class
equivalent class: Class
  intersection of: heterocyte position relative to branches
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: heterocyte
      intersection of: Restriction
        on property: RO_0001025
        some values from: Class
subclass of: heterocyte position relative to branches
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: heterocyte
    intersection of: Restriction
      on property: RO_0001025
      some values from: Class
        intersection of: filament branch
        intersection of: Restriction
created by: Carrine Blank
definition: Heterocyte position where the heterocyte is located in the filament branch. Heterocyte location within the filament branch has apical-basal polarity.

paired false branching
type: Class
equivalent class: Class
  intersection of: paired branches
  intersection of: Restriction
    on property: BFO_0000051
    some values from: false branch
subclass of: paired branches
subclass of: Restriction
  on property: BFO_0000051
  some values from: false branch
has exact synonym: binary false branched
created by: Carrine Blank
has exact synonym: double false branching
definition: Paired filament branches where the filament exhibits false branching.

paired true branching
type: Class
equivalent class: Class
  intersection of: paired branches
  intersection of: Restriction
    on property: BFO_0000051
    some values from: true branch
subclass of: paired branches
subclass of: Restriction
  on property: BFO_0000051
  some values from: true branch
has exact synonym: paired true branching
definition: Paired filament branches where the filament exhibits true branching.
created by: Carrine Blank

solitary false branching
type: Class
equivalent class: Class
  intersection of: solitary branches
  intersection of: Restriction
    on property: BFO_0000051
    some values from: false branch
subclass of: solitary branches
subclass of: Restriction
  on property: BFO_0000051
  some values from: false branch
definition: Solitary filament branches where the filament exhibits false branching.
has exact synonym: single false branching
created by: Carrine Blank

solitary true branching
type: Class
equivalent class: Class
  intersection of: solitary branches
  intersection of: Restriction
    on property: BFO_0000051
    some values from: true branch
subclass of: solitary branches
subclass of: Restriction
  on property: BFO_0000051
  some values from: true branch
created by: Carrine Blank
definition: Solitary filament branches where the filament exhibits true branching.

differentiated apical cell
type: Class
equivalent class: Class
  intersection of: differentiated cyanobacterial filament part
  intersection of: Restriction
    on property: BFO_0000051
    some values from: apical cell
subclass of: differentiated cyanobacterial filament part
subclass of: Restriction
  on property: BFO_0000051
  some values from: apical cell
definition: Filament differentiation quality, relating to the morphology and differentiation of the apical cell in the filament.
created by: Carrine Blank

sub-apical cell
type: Class
equivalent class: Class
  intersection of: MICRO_0001285
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002475
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002099
  intersection of: Restriction
    on property: RO_0001025
    some values from: BSPO_0000057
subclass of: MICRO_0001285
subclass of: Restriction
  on property: has position
  some values from: PATO_0002475
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002099
subclass of: Restriction
  on property: RO_0001025
  some values from: BSPO_0000057
definition: A trichome cell that is located subterminally in a trichome, and which has undergone differentation. Found in trichomes with apical-basal polarity.
created by: Carrine Blank

short filament branch
type: Class
equivalent class: Class
  intersection of: filament branch size
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000574
subclass of: filament branch size
subclass of: Restriction
  on property: has size
  some values from: PATO_0000574
disjoint with: long filament branch
created by: Carrine Blank
has exact synonym: branches short
definition: Filament branch length where the branches are short and contain few cells (relative to the length and number of cells in the main filament).

long filament branch
type: Class
equivalent class: Class
  intersection of: filament branch size
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000573
subclass of: filament branch size
subclass of: Restriction
  on property: has size
  some values from: PATO_0000573
created by: Carrine Blank
definition: Filament branch length where the branches are long and contain many cells (relative to the length and number of cells in the main filament).
has exact synonym: branches many-celled
has exact synonym: branches long

prokaryotic nucleobase quality
type: Class
equivalent class: Class
  intersection of: prokaryotic cell part quality
  intersection of: Restriction
    on property: RO_0000080
    some values from: CHEBI_16991
definition: The molar percentage of nucleobases in the DNA of a prokaryotic chromosome and/or plasmid.
created by: Carrine Blank

bacilloid cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001873
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001873
created by: Carrine Blank
has exact synonym: bacilloid
definition: A prokaryotic cell that is bacillus-like (some variation of cylindrical).

amphilophotrichous cell
type: Class
equivalent class: Class
  intersection of: multiply flagellated
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002476
  intersection of: Restriction
    on property: has structure
    some values from: PATO_0001861
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0001324
  intersection of: Restriction
    on property: RO_0002180
    on class: GO_0009288
    min qualified cardinality: 2
has exact synonym: bipolar polytrichous flagella
has exact synonym: tufts of polar flagella
definition: Flagellated cell where the cell has multiple flagella, located in two tufts at both ends (poles) of the cell.
created by: Carrine Blank
has exact synonym: polar tufts of flagella

prokaryotic acidic environment
type: Class
equivalent class: Class
  intersection of: ENVO_01000315
  intersection of: Restriction
    on property: RO_0001015
    some values from: Class
      union of: CL_0000520
      union of: NCBITaxon_131567
subclass of: ENVO_01000315
subclass of: Restriction
  on property: RO_0001015
  some values from: Class
    union of: CL_0000520
    union of: NCBITaxon_131567
disjoint with: prokaryotic alkaline environment
has broad synonym: acidic
created by: Carrine Blank
definition: An acidic environment that is the environment inhabited by a prokaryotic cell.

prokaryotic alkaline environment
type: Class
equivalent class: Class
  intersection of: ENVO_01000316
  intersection of: Restriction
    on property: RO_0001015
    some values from: Class
      union of: CL_0000520
      union of: NCBITaxon_131567
subclass of: ENVO_01000316
subclass of: Restriction
  on property: RO_0001015
  some values from: Class
    union of: CL_0000520
    union of: NCBITaxon_131567
definition: An alkaline environment that is the environment inhabited by a prokaryotic cell.
created by: Carrine Blank
has exact synonym: alkaline

optical quality assay
type: Class
subclass of: OBI_0000070
subclass of: Restriction
  on property: is an assay using the material entity
  some values from: MICRO_0001591
subclass of: Restriction
  on property: is an assay for the quality
  some values from: PATO_0000001
has broad synonym: An assay to determine macroscopic or microscopic optical quality of a prokaryotic cell, or aggregation of prokaryotic cells.
created by: Carrine Blank

fermentation product
type: Class
subclass of: prokaryotic metabolite
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: Class
      union of: CHEBI_15366
      union of: CHEBI_15378
      union of: CHEBI_16236
      union of: CHEBI_30768
      union of: CHEBI_30772
      union of: CHEBI_32816
    intersection of: Restriction
      on property: is metabolic product assayed by
      some values from: GO_0006113
definition: Prokaryotic metabolite where fermentation produces are produced as a result of fermentation.

cyanobacterial filament
type: Class
subclass of: cell filament
subclass of: Restriction
  on property: BFO_0000050
  some values from: NCBITaxon 1117
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: trichome
    intersection of: Restriction
      on property: BFO_0000051
      some values from: extracellular sheath
definition: A type of filament only found in some filamentous cyanobacterial taxa. Is comprised by a trichome and an extracellular sheath. May or may not have branches.
created by: Carrine Blank

isopolar symmetric
type: Class
equivalent class: Class
  intersection of: differentiated isopolar trichome
  intersection of: Restriction
    on property: BFO_0000051
    some values from: terminal heterocyte
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000632
subclass of: differentiated isopolar trichome
subclass of: Restriction
  on property: has symmetry
  some values from: PATO_0000632
subclass of: Restriction
  on property: BFO_0000051
  some values from: terminal heterocyte
definition: An isopolar trichome morphology quality where heterocysts are only present at the poles, or terminals, of the trichome such that the trichome morphology is symmetric.
created by: Carrine Blank

isopolar metameric
type: Class
equivalent class: Class
  intersection of: differentiated isopolar trichome
  intersection of: Restriction
    on property: BFO_0000051
    some values from: intercalary heterocyte
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000632
subclass of: differentiated isopolar trichome
subclass of: Restriction
  on property: has symmetry
  some values from: PATO_0000632
subclass of: Restriction
  on property: BFO_0000051
  some values from: intercalary heterocyte
definition: An isopolar trichome morphology quality where heterocysts are regularly dispersed along the length of the trichome such that the trichome morphology is symmetric.
created by: Carrine Blank

differentiated isopolar trichome
type: Class
equivalent class: Class
  intersection of: differentiated cyanobacterial filament part
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: isopolar trichome
      intersection of: Restriction
        on property: BFO_0000051
        some values from: Class
created by: Carrine Blank
definition: Trichome differentiation quality of isopolar trichomes with respect to the location of heterocytes and the symmetrical arrangement of the heterocytes.

meristematic zone
type: Class
equivalent class: Class
  intersection of: trichome part
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1182
      union of: NCBITaxon 1185
      union of: NCBITaxon_119859
  intersection of: Restriction
    on property: has position
    some values from: Class
      union of: PATO_0002475
      union of: PATO_0002476
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0051301
definition: A part of a trichome where rapid cell division occurs. Meristematic zones, which arise terminally or subterminally, are found in the trichomes of Scytonemataceae, Rivulariaceae, and Microchaetaceae. Zone involves several cells along the trichome.
created by: Carrine Blank

diffluent sheath
type: Class
equivalent class: Class
  intersection of: sheath having distinctive spatial pattern
  intersection of: Restriction
    on property: has spatial pattern
    some values from: PATO_0000635
subclass of: sheath having distinctive spatial pattern
subclass of: Restriction
  on property: has spatial pattern
  some values from: PATO_0000635
definition: A sheath that is easily dissolving and indistinct (unlocalized).
created by: Carrine Blank

casein agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: ENVO_00003907
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
IAO_0000119: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/CaseinAgar.html FORMULA Ingredients per liter of deionized water:* Dry Milk, Instant Nonfat 50.0gm Pancreatic Digest of Casein 5.0gm Yeast Extract 2.5gm Glucose 1.0gm Agar 12.5gm Final pH 6.8 +/- 0.3 at 25 degrees C.
definition: An organic-rich, solid microbiological culture medium that contains nonfat dry milk, pancreatic digest of casein (casitone), yeast extract, glucose, and agar. Used for the differentiation of prokaryotes based on their ability to degrade casein.
created by: Carrine Blank

cell filament
type: Class
equivalent class: Class
  intersection of: multicellular prokaryote
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001360
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002023
has broad synonym: trichomous
has broad synonym: filaments
has exact synonym: filament
definition: A group of prokaryotic cells where the cells are attached to one another end-to-end, forming long threads. Formed when cell division occurs in a single plane (at right angles to the filament axis) and when cells do not detach from one another.
created by: Carrine Blank
has broad synonym: chains
has broad synonym: filamentous
has broad synonym: mycelium-like
has broad synonym: filament-forming

true branch
type: Class
equivalent class: Class
  intersection of: filament branch
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1189
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001296
created by: Carrine Blank
definition: A trichome part formed when there is transient cell division in another plane other than crosswise to the length of the trichome axis. This results in the formation of a branch at right angles to the axis of the length of the trichome. Found only in the Stigonematales (Cyanobacteria).

false branch
type: Class
equivalent class: Class
  intersection of: filament branch
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1150
      union of: NCBITaxon 1161
      union of: NCBITaxon 1189
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001295
definition: A trichome part formed when there is interruption of the axis of a trichome. Are initiated when necritic cells form, breaking the trichome. Or are initiated at heterocytes. At first both ends of the interrupted trichome grow aside one another, later on the two new trichome ends grow in different directions. Occurs in the Oscillatoriales, Nostocales, and Stigonematales (Cyanobacteria).
created by: Carrine Blank

filament branch
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament part
  intersection of: Restriction
    on property: BFO_0000051
    some values from: extracellular sheath
  intersection of: Restriction
    on property: has morphology
    some values from: PATO_0000402
subclass of: cyanobacterial filament part
subclass of: Restriction
  on property: BFO_0000051
  some values from: extracellular sheath
subclass of: Restriction
  on property: has morphology
  some values from: PATO_0000402
definition: A filament part formed when a new trichome begins to grow at an angle to the axis of the original length of the filament, also enclosed in sheath.
created by: Carrine Blank

firm sheath
type: Class
equivalent class: Class
  intersection of: sheath having distinctive spatial pattern
  intersection of: Restriction
    on property: has spatial pattern
    some values from: PATO_0000627
subclass of: sheath having distinctive spatial pattern
subclass of: Restriction
  on property: has spatial pattern
  some values from: PATO_0000627
definition: A sheath that is firm and distinct (localized, not easily dissolving and not indistinct).
created by: Carrine Blank

sheath having distinctive spatial pattern
type: Class
equivalent class: Class
  intersection of: MICRO_0000800
  intersection of: Restriction
    on property: has spatial pattern
    some values from: PATO_0000060
subclass of: MICRO_0000800
subclass of: Restriction
  on property: has spatial pattern
  some values from: PATO_0000060
created by: Carrine Blank
definition: Morphologically differentiated filament part, where the sheath has a distinctive spatial pattern.

thylakoid-containing cell
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: BFO_0000051
    some values from: cyanobacterial thylakoid
created by: Carrine Blank
definition: A prokaryotic cell containing thylakoids membranes.

epilithic environment
type: Class
equivalent class: Class
  intersection of: ENVO_01000254
  intersection of: Restriction
    on property: RO_0002220
    some values from: ENVO_00001995
subclass of: ENVO_01000254
subclass of: Restriction
  on property: RO_0002220
  some values from: ENVO_00001995
created by: Carrine Blank
definition: An environment that exists on the surface of a rock (or a rocky substrate).
has broad synonym: epilithic

epipelic environment
type: Class
equivalent class: Class
  intersection of: ENVO_01000254
  intersection of: Restriction
    on property: RO_0002219
    some values from: ENVO_00002006
  intersection of: Restriction
    on property: RO_0002220
    some values from: Class
      union of: ENVO_00002007
      union of: ENVO_00002982
      union of: ENVO_01000016
      union of: ENVO_01000017
subclass of: ENVO_01000254
subclass of: Restriction
  on property: RO_0002219
  some values from: ENVO_00002006
subclass of: Restriction
  on property: RO_0002220
  some values from: Class
    union of: ENVO_00002007
    union of: ENVO_00002982
    union of: ENVO_01000016
    union of: ENVO_01000017
has broad synonym: epipelic
created by: Carrine Blank
definition: A submerged environment consisting of a rocky substrate comprised of sediments, clays, or silt, colonized by a microorganisms or a microbial community.
has broad synonym: submerged stones

epiphytic environment
type: Class
equivalent class: Class
  intersection of: ENVO_01000254
  intersection of: Restriction
    on property: RO_0002220
    some values from: NCBITaxon 3193
subclass of: ENVO_01000254
subclass of: Restriction
  on property: RO_0002220
  some values from: NCBITaxon 3193
IAO_0000119: Wikipedia: Epiphyte An epiphyte is a plant that grows harmlessly upon another plant (such as a tree) and derives its moisture and nutrients from the air, rain, and sometimes from debris accumulating around it. Epiphytes differ from parasites in that epiphytes grow on other plants for physical support and do not necessarily negatively affect the host. An epiphytic organism that is not a plant is called an epibiont.[1] Epiphytes are usually found in the temperate zone (e.g., many mosses, liverworts, lichens, and algae) or in the tropics (e.g., many ferns, cacti, orchids, and bromeliads).[2] Many houseplants are epiphyte species due to their minimal water and soil requirements. Epiphytes provide a rich and diverse habitat for other organisms including animals, fungi, bacteria, and myxomycetes.[3]
created by: Carrine Blank
definition: An environment that exists on a terrestrial plant (Embryophyte).
has broad synonym: epiphytic

endophytic environment
type: Class
equivalent class: Class
  intersection of: ENVO_01000254
  intersection of: Restriction
    on property: RO_0002219
    some values from: NCBITaxon 3193
subclass of: ENVO_01000254
subclass of: Restriction
  on property: RO_0002219
  some values from: NCBITaxon 3193
definition: An environment that exists within a plant (Embryophyte).
created by: Carrine Blank
has broad synonym: endophytic
IAO_0000119: Wikipedia: Endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease.[1][2][3][4] Endophytes are ubiquitous and have been found in all species of plants studied to date; however, most of these endophyte/plant relationships are not well understood.[5][6] Endophytes are also known to occur within lichens[7] and algae. Many economically important grasses (e.g., Festuca spp. and Lolium spp. ) carry fungal endophytes in genus Epichloë,[8] some of which may enhance host growth[9] and may improve the plant's ability to tolerate abiotic stresses, such as drought, and enhance resistance to insects, plant pathogens and mammalian herbivores.[10][11][12][13]
has broad synonym: lives inside a plant

periphytic environment
type: Class
equivalent class: Class
  intersection of: ENVO_01000254
  intersection of: Restriction
    on property: RO_0002219
    some values from: ENVO_00002006
  intersection of: Restriction
    on property: RO_0002220
    some values from: Class
      union of: ENVO_00001995
      union of: NCBITaxon 3193
      union of: NCBITaxon_33208
subclass of: ENVO_01000254
subclass of: Restriction
  on property: RO_0002219
  some values from: ENVO_00002006
subclass of: Restriction
  on property: RO_0002220
  some values from: Class
    union of: ENVO_00001995
    union of: NCBITaxon 3193
    union of: NCBITaxon_33208
has broad synonym: periphytic
created by: Carrine Blank
has broad synonym: periphytically
definition: An environmental system that is submerged, and attached to submerged rocks, plants, animals, or other objects.

calyptra
type: Class
equivalent class: Class
  intersection of: apical cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1150
      union of: NCBITaxon 1161
  intersection of: Restriction
    on property: has morphology
    some values from: Class
      intersection of: PATO_0000591
      intersection of: Restriction
        on property: has morphology
        some values from: PATO_0000600
definition: Modified apical cell, having a thickened or enlarged morphology. Has a hood-like, lid-like, or cap-like form. Little is known about the role, although presence is environmentally influenced. Not all trichomes in a natural population will exhibit a calyptra. Found in the Oscillatoriales and Nostocales.
created by: Carrine Blank
has broad synonym: end cells aways with calyptra
IAO_0000119: http://huey.colorado.edu/cyanobacteria/taxa/calyptra.php Definition of Calyptra Thickened or enlarged tip of a cyanobacterial filament, a hoodlike, lidlike, or caplike structure.

morphologically distinct colony
type: Class
equivalent class: Class
  intersection of: MICRO_0002468
  intersection of: Restriction
    on property: has morphology
    some values from: PATO_0000051
definition: A prokaryotic colony that has a distinct morphology (size, shape, texture, or structure).
created by: Carrine Blank

tapered by apical and basal widening
type: Class
equivalent class: Class
  intersection of: tapered trichome
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002239
subclass of: tapered trichome
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002239
has broad synonym: trichomes narrowed in the middle part and clearly widened at the ends
created by: Carrine Blank
has broad synonym: branches dilated terminal portions
definition: Tapered trichome quality where the trichome is wider at the apical and basal ends, and narrower toward the center of the trichome (hour-glass shaped).

prokaryotic cell part quality
type: Class
equivalent class: Class
  intersection of: prokaryotic quality
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      union of: GO_0005575
      union of: GO_0044464
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0000001
subclass of: prokaryotic quality
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0000001
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    union of: GO_0005575
    union of: GO_0044464
definition: Prokaryotic quality (morphology, symmetry, position) relating to a cell part or cellular component.
created by: Carrine Blank

tapered by apical and basal narrowing
type: Class
equivalent class: Class
  intersection of: tapered trichome
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002400
subclass of: tapered trichome
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002400
has broad synonym: attenuated trichome ends
has broad synonym: trichomes attenuated towards the ends
has broad synonym: trichomes attenuated toward both ends
has broad synonym: continually attenuated to the ends
has broad synonym: trichomes attenuated at the ends of developed trichomes
created by: Carrine Blank
has broad synonym: tapering to the ends
has broad synonym: cells narrowed at both ends
has broad synonym: trichomes narrowed to the ends
has broad synonym: attenuated toward the ends
definition: Tapered trichome quality where the trichome is narrower at the apical and basal ends, and widened toward the center of the trichome (fusiform-shaped).
has broad synonym: trichomes narrows towards the ends
has broad synonym: trichomes attenuated to the ends

widened spaces between thylakoids
type: Class
equivalent class: Class
  intersection of: thylakoid-containing cell
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0000374
created by: Carrine Blank
has broad synonym: intrathylakoidal spaces
definition: Thylakoid-containing cell where there are widened spaces between the thylakoid membranes. Function is not clear and are likely influenced by environmental factors. Frequency and location are taxa-specific.

susceptibility to lysis by detergent
type: Class
equivalent class: Class
  intersection of: prokaryotic cell wall lysis susceptibility
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005618
      intersection of: Restriction
        on property: RO_0000053
        some values from: Class
created by: Carrine Blank
definition: Prokaryotic cell wall lysis susceptibility that defines how susceptible the cell wall is to lysis when the cell is placed in the presence of an environment with an altered chemical composition (detergent).

Berkefeld N filter
type: Class
subclass of: Berkefeld filter candle
definition: A gravity-driven water filter made by the British Berkefeld® company, with an intermediate pore size N (for Normal). Pore sizes average 0.43 microns in diameter.
created by: Carrine Blank

216L marine medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32954
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53258
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63038
  intersection of: Restriction
    on property: has ingredient
    some values from: ENVO_00002149
  intersection of: Restriction
    on property: has ingredient
    some values from: tryptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: An organic rich, liquid marine microbiological culture medium containing acetate, tryptone, yeast extract, citrate, ammonium nitrate, with a seawater base. Used for the cultivation of Marispirillum.
IAO_0000119: From: Lai, Q., Yuan, J., Gu, L. & Shao, Z. (2009). Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment. Int J Syst Evol Microbiol 59, 1278–1281. Recipe: sodium acetate, 1.0 g Tryptone, 10.0 g yeast extract, 2.0 g sodium citrate, 0.5 g NH4NO3, 0.2 g seawater, 1L pH 7.5
created by: Carrine Blank
has broad synonym: 216L
has exact synonym: 216L broth

216L marine agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32954
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53258
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63038
  intersection of: Restriction
    on property: has ingredient
    some values from: ENVO_00002149
  intersection of: Restriction
    on property: has ingredient
    some values from: tryptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Lai, Q., Yuan, J., Gu, L. & Shao, Z. (2009). Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment. Int J Syst Evol Microbiol 59, 1278–1281. Recipe: sodium acetate, 1.0 g Tryptone, 10.0 g yeast extract, 2.0 g sodium citrate, 0.5 g NH4NO3, 0.2 g seawater, 1L pH 7.5 Agar is added to the medium to solidify.
created by: Carrine Blank
has exact synonym: 216L agar
definition: An organic rich, solid marine microbiological culture medium containing acetate, tryptone, yeast extract, citrate, ammonium nitrate, with a seawater base. Used for the cultivation of Marispirillum.

ZoBell marine medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_132769
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32030
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_34683
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_36383
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_60720
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63038
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 6636
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_76208
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: ZoBell 2216e broth
has exact synonym: ZoBell 2216e
has exact synonym: ZoBell medium
has exact synonym: MA2216
has exact synonym: Zobell's medium
has exact synonym: Marine broth 2216
definition: An organic-rich, mineral-salts, liquid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Used for the cultivation of heterotrophic marine microorganisms.
has exact synonym: ZoBell broth
IAO_0000119: From: http://himedialabs.com/TD/M384.pdf Zobell Marine Agar 2216 Zobell Marine Agar 2216 is recommended for cultivation, isolation and enumeration of heterotrophic marine bacteria. Composition Ingredients (Gms/Litre) Peptic digest of animal tissue 5.000 Yeast extract 1.000 Ferric citrate 0.1000 Sodium chloride 19.450 Magnesium chloride 8.800 Sodium sulfate 3.240 Calcium chloride 1.800 Potassium chloride 0.550 Sodium bicarbonate 0.160 Potassium bromide 0.080 Strontium chloride 0.034 Boric acid 0.022 Sodium silicate 0.004 Sodium fluorate 0.0024 Ammonium nitrate 0.0016 Disodium phosphate 0.008 Final pH (25˚C) 7.6+/-0.2
has exact synonym: MB
created by: Carrine Blank
has exact synonym: ZoBell's

microbiological culture medium
type: Class
subclass of: OBI_0000079
subclass of: Restriction
  on property: has ingredient
  some values from: ENVO_00002006
definition: A culture medium used to select for, grow, and maintain prokaryotic microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) forms.
has broad synonym: growth medium
has broad synonym: growth media
has broad synonym: culture media
created by: Carrine Blank
has broad synonym: media
has broad synonym: medium

defined microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Class
    complement of: undefined microbiological culture medium
disjoint with: undefined microbiological culture medium
has exact synonym: defined mineral medium
has exact synonym: defined medium
created by: Carrine Blank
definition: A chemically defined microbiological culture medium where all chemicals used are known. Does not contain any plant, animal, or microbiological cell extracts.
has exact synonym: mineral media
has exact synonym: defined media
has exact synonym: mineral medium

liquid microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Class
    complement of: solid microbiological culture medium
disjoint with: solid microbiological culture medium
has exact synonym: liquid media
definition: broth
definition: A microbiological culture medium that is liquid.
created by: Carrine Blank
has exact synonym: liquid medium

solid microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
has exact synonym: solid medium
has exact synonym: solid media
created by: Carrine Blank
definition: A microbiological culture medium that is solidified with a gelling agent, such as agar, agarose, gelatin, or pectin.
has exact synonym: agar medium

undefined microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: undefined organic chemical mixture
has exact synonym: basal media
has exact synonym: complex medium
has exact synonym: basal medium
has exact synonym: complex media
definition: A microbiological culture medium that has components that are chemically heterogeneous, unknown, or uncharacterized mixtures or cellular extracts.
created by: Carrine Blank

Balch medium 1
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_23414
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32954
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_62946
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_62965
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63036
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75836
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_76209
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_91248
  intersection of: Restriction
    on property: has ingredient
    some values from: Balch vitamin solution
  intersection of: Restriction
    on property: has ingredient
    some values from: Trypticase peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001561
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      intersection of: CHEBI_16526
      intersection of: Class
        intersection of: Restriction
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001386
  intersection of: Restriction
    on property: has salinity
    all values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    all values from: MICRO_0001383
IAO_0000232: pH is not noted in the original publication. However, pH of the medium is reported to be 7.0 in The Prokaryotes: Vol 3: Archaea. Bacteria: Firmicutes, Actinomycetes, p. 213, copyrighted 2006.
has exact synonym: mineral medium and H2 + CO2
definition: A mineral-salts liquid microbiological culture medium containing acetate, formate, yeast extract, trypticase, cysteine and sulfide with H2 and CO2 in the headspace gas mixture. Used for the growth of methanogenic archaea.
definition: A mineral-salts, liquid microbiological culture medium containing acetate, formate, yeast extract, trypticase, cysteine and sulfide with hydrogen and carbon dioxide in the headspace gas mixture. Used for the growth of methanogenic archaea.
created by: Carrine Blank
has exact synonym: mineral medium with H2-CO2
IAO_0000119: From: Balch WE et al, 1979. Methanogens: reevaluation of a unique biological group. Microbiol Rev 43(2):260. Ingredients are added to distilled water to give a final volume of 1L. Cysteine and Na2S are added after boiling the medium under an 80% N2-20% CO2 gas mixture, the final gas phase of tubed medium being an 80% H2-CO2 gas mixture at two atmospheres of pressure. 50 mL mineral 1 solution (6 g K2HPO4 per liter) 50 mL mineral 2 solution (per liter: KH2PO4, 6 g; (NH4)2SO4, 6 g, NaCl, 12 g; MgSO4x7H2O, 2.6 g; CaCl2x2H2O, 0.16 g) 10 mL trace minerals (pH to 7.0 with KOH; per liter: nitrilotriacetic acid, 1.5 g; MgSO4x7H2O, 3.0 g; MnSO2x2H2O, 0.5 g; NaCl, 1.0 g; FeSO4x7H2O, 0.1g; CoSO4 or CoCl2, 0.1 g; CaCl2x2H2O, 0.1 g; ZnSO4, 0.1 g; CuSO4x5H2O, 0.01 g; AlK(SO4)2, 0.01 g; H3BO3, 0.01 g; Na2MoO4x2H2O, 0.01g); dissolve nitrilotriacetic acid with KOH to pH 6.5 then proceed to add minerals) 10 mL trace vitamines (contains in milligrams per liter: biotin, 2; folic acid, 2; pyridoxine hydrochloride, 10; thiamine hydrochloride, 5; riboflavin, 5; nicotinic acid, 5; DL-calcium pantothenate, 5; vitamin B12, 0.1; p-aminobenzoic acid, 5; lipoic acid, 5) 0.002 g FeSO4x7H2O 5.0 g NaHCO3 2.5g sodium acetate 2.5 g sodium formate 2.0 g yeast extract 2.0 g trypticase (BBL) 0.5 g L-Cysteine hydrochloridexH2O 0.5 g Na2Sx9H2O
has exact synonym: minerals salts-H2/CO2 medium

artificial kinneret water medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31346
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32599
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 6636
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: artificial kinneret water
definition: A dilute, mineral-salts liquid microbiological culture medium formulated to mimic Lake Kinneret (Sea of Galilee) water. Used to cultivate freshwater autotrophic microorganisms.
IAO_0000232: Could not find in any references the pH of AKW, however the pH of Lake Kinneret varies from about 8.6 at the surface to 7.8 at depth. http://kinneret.ocean.org.il/ar_grp.aspx
has narrow synonym: artificial lake kinneret water
has exact synonym: AKW
has exact synonym: AKW media
created by: Carrine Blank
IAO_0000119: From Table 1 in: Sherr BF, Sherr EB, Berman T. 1983. Grazing, growth, and ammonium excretion rates of a heterotrophic microflagellate fed with four species of bacteria. Appl Environ Microbiol 45(4):1196-1201. Salt Amt (mg L-1 of distilled water) NaHCO3 197 NaCl 155 CaCl2 130 MgCl2 124 MgSO4 65 KCl 13 CaSO4 9.5 Total salts, 693.5 mg L-1. Total solids in Lake Kinneret water range from 640 to 714 mg L-1.

Gram stain quality
type: Class
equivalent class: Class
  intersection of: prokaryotic cell part quality
  intersection of: Restriction
    on property: RO_0000080
    some values from: Class
      union of: GO_0009275
      union of: GO_0009276
created by: Carrine Blank
definition: Prokaryotic cell part quality, describing the nature of the cell wall. Determined from the results of the Gram stain assay.

MGM medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86345
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 9754
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001293
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: MGM liquid medium
definition: A hypersaline, liquid microbiological culture medium that contains mineral salts, peptone, and yeast extract. Used for the cultivation of Haloarchaeobium iranensis.
created by: Carrine Blank
has exact synonym: MGM broth
IAO_0000119: From:Makhdoumi-Kakhki et al 2011. Haloarchaeobium iranensis gen.nov., sp. nov., an extremeley halophilic archaeon isolated from the saline lake Aran-Bidgol, Iran. Int J. Syst. Evol. MIcrobiol. doi:10.1099/ijs.0.033167-0 and Dyall-Smith. 2009. Halohandbook. http://www.haloarchaea.com/resources/halohandbook/ Add the following to a large beaker: Salt water (30% stock), 767 Pure water, 200 Peptone (Oxoid), 5 yeast extract, 1 Stir to dissolve, adjust pH up to 7.5 with 1M Tris pH 7.5, using 5 mL per liter. Adjust to 1L with pure water. For solid medium add 15g Difco Bacto-agar. 30% Salt water stock solution (the CaCl2 is not added until just before pouring plates and some TrisHCl pH 7.5 is added): per liter: H2O, 850 mL NaCl, 240 g MgCl2x6H2O, 30g KCl, 7g 1M TrisHCL pH 7.5, 20 mL

modified 9K medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26836
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31440
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32149
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53503
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_62946
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63036
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_64205
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75213
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75836
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_77775
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86254
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86360
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001381
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Zhou H et al. 2008. Isolation and characterization of Ferroplasma thermophilum sp. nov., a novel extremely acidophilic, moderately thermophilic archaeon and its role in bioleaching of chalcopyrite. J Appl Microbiol 105:591. Modified 9K medium contained (per litre): 3.0 g (NH4)2SO4, 0.5 g KH2PO4, 0.1 g KCl, 0.5 g MgSO4x7H2O, 0.01 g Ca(NO3)2. Trace elements (per litre) comprised: 11.0 mg FeCl3x6H2O, 0.5 mg CuSO4x5H2O, 50 mg Na2SO4, 2.0 mg H3BO3, 2.0 mg MnSO4, 0.8 mg Na2MoO4x2H2O, 0.6 mg CoCl2x6H2O, 0.9 mg ZnSO4x7H2O and 0.1 mg Na2SeO4. The pH of the medium was adjusted to 1.0 by adding 50% (v ⁄ v) H2SO4, was autoclaved, and then filter-sterilized (0.2 um filter paper) trace elements and FeSO4x7H2O were added in the medium.
created by: Carrine Blank
definition: An acidic, liquid, mineral-salts microbiological culture medium, high in ferrous iron. Used for the cultivation of Ferroplasma thermophilum.

NOM-1 medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31206
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50144
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75228
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: fish peptone
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001293
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: NOM-1 liquid medium
IAO_0000119: From: Heng-Lin Cui, Xin-Yi Li, Xia Gao, Xue-Wei Xu, Yu-Guang Zhou, Hong-Can Liu, Aharon Oren and Pei-Jin Zhou. 2010. Halopelagius inordinatus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. IJSEM 60:2089-2093. per liter: yeast extract, 0.2 g fish peptone, 0.2 g sodium pyruvate, 2.0 g sodium lactate, 2.0 g KCl, 5.4 g K2HPO4, 0.3 g NH4Cl, 0.5 g MgSO4x7H2O, 20.0 g NaCl, 200.0 g pH 7.0-7.2.
has exact synonym: neutral oligotrophic haloarchaeal medium
definition: A hypersaline, liquid microbiological culture medium containing mineral-salts, magnesium sulfate, pyruvate, lactate, peptone, and yeast extract. Used for the cultivation of Halopelagius inordinatus.
created by: Carrine Blank

modified R2A medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50144
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53258
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_64220
  intersection of: Restriction
    on property: has ingredient
    some values from: casamino acids
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: fish peptone
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001293
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: A hypersaline, liquid microbiological culture medium containing mineral-salts, magnesium sulfate, pyruvate, glucose, glutamate, citrate, and peptones. Used for the cultivation of Halogranum rubrum and Halosarcina limi.
has related synonym: CM2 medium
has related synonym: CM2 liquid medium
IAO_0000119: From: Cui H-L, et al. 2010. Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern. Int J Syst Evol Microbiol 60:1366. Modified R2A medium: Contains the following ingredients per liter: Casamino acids 0.5g yeast extract, 0.5g sodium pyruvate, 0.5 g fish peptone, 0.5g glucose, 0.5g sodium glutamate, 0.5g trisodium citrate, 3.0g KCl, 2.0g K2HPO4, 0.3g CaCl2, 0.5g MgSO4x7H2O, 20.0g NaCl, 200.0 g pH 7.0-7.2
created by: Carrine Blank
has exact synonym: MR2A
IAO_0000119: From: Cui H-L et al. 2010. Halosarcina limi sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halosarcina. Int J. Syst. Evol. Microbiol. 60:2462. CM2 Recipe: Per liter: Casamino acids (Difco), 0.5 g yeast extract (Difco), 0.5 g sodium pyruvate, 0.5 g fish peptone, 0.5 g glucose, 5.0 g sodium glutamate, 0.5 g trisodium citrate, 3.0 g KCl, 2.0 g K2HPO4, 0.3 g CaCl2, 0.5 g MgSO4x7H2O, 20 g NaCl, 230.0 g pH 7.0–7.2
has exact synonym: MR2A liquid medium

defined inorganic chemical mixture
type: Class
subclass of: MICRO_0000571
definition: Inorganic compounds or mixtures of inorganic compounds added to culture media to support growth or metabolism of a microorganism. Because the exact composition of the mixture is known, it is referred to as "defined".
created by: Carrine Blank

DSMZ Medium 954
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: is culture medium used by
    some values from: NCBITaxon_1227498
  intersection of: Restriction
    on property: is culture medium used by
    some values from: NCBITaxon_1455609
  intersection of: Restriction
    on property: is culture medium used by
    some values from: NCBITaxon_179637
  intersection of: Restriction
    on property: is culture medium used by
    some values from: NCBITaxon_413815
  intersection of: Restriction
    on property: is culture medium used by
    some values from: NCBITaxon_453847
  intersection of: Restriction
    on property: is culture medium used by
    some values from: NCBITaxon_795797
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 6636
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 9754
  intersection of: Restriction
    on property: has ingredient
    some values from: casamino acids
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001293
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: Halococcus dombrowskii medium
IAO_0000232: DSM strains: 19505 Haladaptatus cibarius 18796 Halalkalicoccus jeotgali B3 14522 Halococcus dombrowskii 19504 Halorubrum cibi 18794 Haloterrigena jeotgali A29 18795 Natronococcus jeotgali DSM 18795
has exact synonym: Medium for Halococcus dombrowskii
created by: Carrine Blank
IAO_0000119: From: http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium954.pdf 954. Medium for Halococcus dombrowskii. Casamino acids 5.00 g Yeast extract 5.00 g TRIS 12.10 g KCl 2.00 g MgCl2x6H2O 20.00 g CaCl2x2H2O 0.20 g NaCl 200.00 g Agar 20.00 g Distilled water 1000.00 mL Adjust pH to 7.4. Add the agar after dissolving all ingredients in the water and adjustment of pH. © 2007 DSMZ GmbH - All rights reserved
definition: A hypersaline, organic-rich, solid microbiological culture medium containing mineral-salts, tris, casamino acids, and yeast extract. Used to cultivate Halococcus dombrowskii (DSM 14522).

Hayflick medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31991
  intersection of: Restriction
    on property: has ingredient
    some values from: PPLO medium
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001235
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From:http://www.atcc.org/~/media/B61DC4844DBE4D51867A06D49DE22564.ashx ATCC Medium: 2820 HAYFLICK Medium Yeast Extract…………………………………..19.6 g PPLO…………………………………………...17.7 g Phenol Red……………………………………24 mg DNA sodium salt (Sigma, D1501)………...…0.24 g Horse serum (aseptically add)……………….157 ml DI Water………………………………………..843 ml Combine all ingredients except for the horse serum. Adjust pH to 7.8 +/- 0.2. Autoclave at 121C and let medium cool to 55C. Aseptically add horse serum and dispense as required.
created by: Carrine Blank
definition: An organic-rich, liquid microbiological culture medium containing beef heart infusion, peptone, and sodium chloride. Developed for the growth of Mycoplasma pneumoniae.

nutrient broth
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: beef extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Nutrient Broth (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Nutrient Broth has the formula originally designed for use in the Standard Methods for the Examination of Water and Wastewater. It is not a recommended bacteriological medium in later editions of this publication. It is one of several nonselective media recommended for use in the Most Probable Number (MPN) technique of estimating the density of viable organisms in food samples1 and is useful in routine cultivation of microorganisms. Principles of the Procedure This relatively simple formulation supports the growth of nonfastidious microorganisms due to its content of peptone and beef extract. Formula Difco™ Nutrient Broth Approximate Formula* Per Liter Beef Extract.................................................................. 3.0 g Peptone....................................................................... 5.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 6.8 ± 0.2
created by: Carrine Blank
has broad synonym: nutrient medium
has exact synonym: NB
definition: An organic-rich, liquid culture medium comprised of beef extract and peptone.
has exact synonym: nutrient broth
has exact synonym: nutrient broth media

ZoBell phytagel
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_132769
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32030
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_34683
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_36383
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_60720
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63038
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 6636
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_76208
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_85248
  intersection of: Restriction
    on property: has ingredient
    some values from: citrated blood
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: http://himedialabs.com/TD/M384.pdf Zobell Marine Agar 2216 Zobell Marine Agar 2216 is recommended for cultivation, isolation and enumeration of heterotrophic marine bacteria. Composition Ingredients (Gms/Litre) Peptic digest of animal tissue 5.000 Yeast extract 1.000 Ferric citrate 0.1000 Sodium chloride 19.450 Magnesium chloride 8.800 Sodium sulfate 3.240 Calcium chloride 1.800 Potassium chloride 0.550 Sodium bicarbonate 0.160 Potassium bromide 0.080 Strontium chloride 0.034 Boric acid 0.022 Sodium silicate 0.004 Sodium fluorate 0.0024 Ammonium nitrate 0.0016 Disodium phosphate 0.008 Final pH (25˚C) 7.6+/-0.2
IAO_0000119: Barbeyron T, L'Haridon S, Corre E, Kloareg B & Potin P. 2001. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. IJSEM 51:985-997.: When it was desirable to avoid attack of the substratum, strains were grown on ZoBell solidified with 0.7% (w/v) Phytagel (a gellan gum; Sigma).
created by: Carrine Blank
definition: An organic-rich, mineral-salts, liquid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Solidified using Phytagel (gellan gum) instead of agar. Used for the cultivation of heterotrophic marine microorganisms capable of degrading agar.
has exact synonym: ZoBell phytagel plates
has exact synonym: ZoBell phytagel agar

medium containing ruminal fluid
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: clarified rumen fluid
      union of: UBERON_0010228
created by: Carrine Blank
definition: A microbiological culture medium that contains bovine rumen fluid (or ruminal fluid), used for the culture of microorganisms that live in the rumen.

Sehgal and Gibbons medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30812
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53258
  intersection of: Restriction
    on property: has ingredient
    some values from: casamino acids
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001293
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: Sehgal and Gibbons, 1960, Effect of some metal ions on the growth of Halobacterium cutirubrum. Can J Microbiol 6:165.
definition: A hypersaline, organic-rich liquid medium containing casamino acids, yeast extract, and salts. Used for the growth of Halobacterium cutirubrum.
IAO_0000119: Original citation: Sehgal SN, Gibbons NE (1960) Effect of some metal ions on the growth of Halobacterium cutirubrum. Can J Microbiol 6:165–169. The routine medium contained 7.5 g casamino acids (Difco), 10 g yeast extract (Difco), 3 g trisodium citrate, 2 g potassium chloride, 20 g magnesium sulphate heptahydrate, 250 g sodium chloride, aid distilled water to 1 liter. The ingredients were dissolved in 800 ml water, the pH adjusted to 7.5-7.8 with N potassium hydroxide, and the medium autoclaved 5 minutes at 120˚C. It was then filterecl to remove the precipitate, the pH mas adjusted to 7.4 with N hydrochloric acid, and the medium made up to final volume.
has exact synonym: S-G medium
IAO_0000119: From: Schneegurt MA, Chapter 2, Media and conditions for the growth of halophilic and halotolerant bacteria and archaea. pg. 39, Table 2.1. In Vreeland RH (ed) Advances in Understanding the Biology of Halophilic Microorganisms. DOI 10.1007/978-94-007-5539-0_2 Medium composition in grams per liter: NaCl, 250 MgSO4x7H2O, 20 FeCl2, 0.023 Na-citrate, 3 Casamino acids, 7.5 yeast extract, 10
created by: Carrine Blank

Brucella agar with sheep blood
type: Class
equivalent class: Class
  intersection of: MICRO_0000595
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_28384
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50385
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001230
IAO_0000119: From: Brucella Agar with 5% Sheep Blood, Hemin and Vitamin K1 (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Brucella Agar with 5% Sheep Blood, Hemin and Vitamin K1 is used for the isolation and cultivation of fastidious, obligately anaerobic microorganisms.
has exact synonym: BRU
created by: Carrine Blank
definition: An organic-rich, solid microbiological culture medium, containing peptones, yeast extract, glucose, and sodium bisulfite as a reducing agent. Supplemented with 5% sheep blood, hemin, and vitamin K. Used for the growth of Brucella.

Zobell phytagel starch
type: Class
equivalent class: Class
  intersection of: ZoBell phytagel
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_28017
has exact synonym: Starch phytagel plates
created by: Carrine Blank
has exact synonym: Zobell phytagel starch agar
definition: An organic-rich, mineral-salts, liquid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Solidified using Phytagel instead of agar. Supplemented with starch. Used for the cultivation of heterotrophic marine microorganisms capable of degrading agar.
IAO_0000119: Barbeyron T, L'Haridon S, Corre E, Kloareg B & Potin P. 2001. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. IJSEM 51:985-997. The strain was assayed for amylase activity using starch at a concentration of 0.2 % (w/v) in ZoBell agar or in ZoBell Phytagel plates.

BRN medium
type: Class
equivalent class: Class
  intersection of: Balch medium 1
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_124991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3745
  intersection of: Restriction
    on property: has ingredient
    some values from: clarified rumen fluid
subclass of: Balch medium 1
subclass of: Restriction
  on property: has ingredient
  some values from: clarified rumen fluid
subclass of: Restriction
  on property: has ingredient
  some values from: CHEBI_124991
subclass of: Restriction
  on property: has ingredient
  some values from: CHEBI 3745
IAO_0000119: Balch et al. 1979. Methanogens: reevaluation of a unique biological group. Microbiol Rev 43(2):260.
definition: A liquid, mineral-salts microbiological culture medium containing acetate, formate, yeast extract, trypticase, cysteine and sulfide with H2 and CO2 in the headspace gas mixture. Supplemented with additional 0.1% NH4Cl, 10% rumen fluid, 2% agar, and with clindamycin and cephalotin (cefalotin). Used for the growth of Methanobrevibacter from feces.
IAO_0000119: Miller, 2001. In Bergey's Manual of Systematic Bacteriology, v. 1, 2nd ed. p.219.
created by: Carrine Blank
IAO_0000119: Miller TL et al, 1982. Isolation of Methanobrevibacter smithii from human feces. Appl Environ Microbiol 43(1):227.

MGM agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86345
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 9754
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001293
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From:Makhdoumi-Kakhki et al 2011. Haloarchaeobium iranensis gen.nov., sp. nov., an extremeley halophilic archaeon isolated from the saline lake Aran-Bidgol, Iran. Int J. Syst. Evol. MIcrobiol. doi:10.1099/ijs.0.033167-0 and Dyall-Smith. 2009. Halohandbook. http://www.haloarchaea.com/resources/halohandbook/ Add the following to a large beaker: Salt water (30% stock), 767 Pure water, 200 Peptone (Oxoid), 5 yeast extract, 1 Stir to dissolve, adjust pH up to 7.5 with 1M Tris pH 7.5, using 5 mL per liter. Adjust to 1L with pure water. For solid medium add 15g Difco Bacto-agar. 30% Salt water stock solution (the CaCl2 is not added until just before pouring plates and some TrisHCl pH 7.5 is added): per liter: H2O, 850 mL NaCl, 240 g MgCl2x6H2O, 30g KCl, 7g 1M TrisHCL pH 7.5, 20 mL
definition: A hypersaline, organic-rich, solid microbiological culture medium that contains mineral-salts, tris, peptone, and yeast extract. Used for the cultivation of Haloarchaeobium iranensis.
created by: Carrine Blank

microbiological culture medium containing blood
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001227
has exact synonym: blood agar
has exact synonym: BAP
has exact synonym: Blood agar plates
definition: A microbiological culture medium that contains blood, treated blood, lysed blood cells, blood serum, or treated blood serum.
created by: Carrine Blank

citrated blood
type: Class
subclass of: MICRO_0001233
subclass of: Restriction
  on property: has ingredient
  some values from: Class
    union of: CHEBI_35804
    union of: CHEBI_35808
    union of: CHEBI_50744
created by: Carrine Blank
IAO_0000119: From: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/AnimalBloodProd.htm Animal Blood, Citrated is blood that has been washed and treated with sodium citrate as the anticoagulant. It serves as a source of erythrocytes for serological procedures.
definition: Blood medium ingredient comprised of animal blood where citrate has been added to prevent coagulation. Used in the cultivation of microorganisms.

equine serum-containing microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001235
created by: Carrine Blank
has exact synonym: media containing 1% serum fraction
definition: A liquid microbiological culture medium that contains horse (equine) serum.
has exact synonym: horse serum containing agar
has exact synonym: media containing 20% horse serum

microbiological culture medium, containing procine serum
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001238
created by: Carrine Blank
definition: A microbiological culture medium (a blood serum agar), made with porcine (pig) blood serum.

PPLO medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: beef heart infusion
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: PPLO serum fraction
has exact synonym: PPLO media
has exact synonym: PPLO broth
definition: An organic-rich, liquid microbiological culture medium containing various peptones and sodium chloride. Developed for the growth of mycoplasmas.
IAO_0000119: From: PPLO Media (Mycoplasma Media) (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use PPLO (Mycoplasma) agars and broths, when supplemented with nutritive enrichments, are used for isolating and cultivating Mycoplasma. Mycoplasma Broth Base (Frey) is used for the cultivation of avian mycoplasmas. Principles of the Procedure Meat digests, peptones, beef extract and yeast extract provide the nitrogen, vitamins, amino acids and carbon in these media. Sodium chloride maintains the osmotic balance of these formulations. Agar, the solidifying agent, is used in PPLO (Mycoplasma) Agar at a concentration slightly reduced from usual to ensure formation of the largest possible colonies because the organisms grow into the agar with only slight surface growth.13 The base media are supplemented with Mycoplasma Supplement or Mycoplasma Enrichment w/o Penicillin because Mycoplasma spp. are fastidious in their growth requirements. 14 Mycoplasma Supplement contains fresh yeast extract and horse serum. Yeast extract provides the preformed nucleic acid precursors that are required by Mycoplasma spp.14 Horse serum supplies cholesterol, a growth stimulant.14 Mycoplasma Enrichment without Penicillin is a selective enrichment containing the inhibitor thallium acetate, to which a penicillin of choice (penicillin G or a broad-spectrum semisynthetic penicillin) can be added at the time of use to make it selective against gram-positive and gram-negative bacteria. Formulae Difco™ PPLO Agar Approximate Formula* Per Liter Beef Heart, Infusion from 50 g..................................... 6.0 g Peptone..................................................................... 10.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 14.0 g Difco™ PPLO Broth Consists of the the same ingredients without the agar. pH 7.8 ± 0.2 BBL™ Mycoplasma Agar Ba…
created by: Carrine Blank

SP-4 medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17334
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2682
  intersection of: Restriction
    on property: has ingredient
    some values from: PPLO medium
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: pancreatic digest of gelatin
  intersection of: Restriction
    on property: has ingredient
    some values from: Yeastolate
  intersection of: Restriction
    on property: has ingredient
    some values from: CMRL-1066 medium with glutamine
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001660
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: CHEBI_59063
      union of: CHEBI 8309
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: An organic-rich, liquid microbiological culture medium containing pancreatic digests of casein and gelatin, PPLO broth (without CV, i.e. without crystal violet), fetal bovine serum (fetal calf serum), CMRL 1066 medium (a mixture of amino acids, vitamins, co-factors, and organic micronutrients), yeast extract, and polymyxin B, Amphotericin B, and penicillin. Used for the growth of mycoplasmas.
created by: Carrine Blank
has exact synonym: SP-4 media
IAO_0000119: From: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/SP4Media.htm SP4 Broth, Plain**: Pancreatic Digest of Casein 10.0gm Pancreatic Digest of Gelatin 5.0gm PPLO Broth without CV 3.5gm Polymyxin B 50.0mg Amphotericin B 5.0mg Fetal Bovine Serum 170.0ml CMRL 1066 Medium (10X) 50.0ml Yeast Extract 35.0ml Yeastolate 10% 20.0ml Penicillin 1,000,000U Final pH at 25 degrees C.: SP4 Broth, Plain SP4 Broth with Arginine 7.0 +/- 0.2

horse blood agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001234
created by: Carrine Blank
definition: A solid microbiological culture medium (a blood agar), containing horse blood.
has exact synonym: horse blood agar

slant culture medium
type: Class
subclass of: solid microbiological culture medium
definition: A slant culture is where liquified (melted) solid medium has been added to a sterile test tube and allowed to solidify (cool) at an angle with respect to the horizontal, such that the solid medium surface is at an angle with respect to the sides of the test tube. The slant culture allows for a larger surface of the agar to be exposed to oxygen.

blue green medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_29377
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30769
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31440
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31604
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_34683
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_46760
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63005
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_64734
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75213
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86214
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86368
  intersection of: Restriction
    on property: has ingredient
    some values from: soil extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001773
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: blue-green medium
created by: Carrine Blank
has exact synonym: BG media
definition: A mineral-salts, marine, liquid microbiological culture medium containing soil extract. Used for the growth of photoautotrophic microorganisms.
IAO_0000119: http://www-cyanosite.bio.purdue.edu/media/table/bg.html From: Moss,B. 1972. The influence of environmental factors on the distribution of freshwater algae: an experimental study. J. Ecol. 60:917-932. Blue-Green (BG) Medium This medium is made up in 2 parts. Autoclave parts 1 and 2 separately at 15 psi, allow to cool them then mix aseptically. For agar plates, add 15 g non-nutrient agar per L. Part 1: Tricine 0.50 g Soil extract (SE1) 25.00 mL Extra nutrient salts 3.75 mL Filtered natural seawater to 1.0 L Adjust pH to 7.6-7.8 with 1M NaOH or HCl. Part 2: NaNO3 1.500 g K2HPO4x3H2O 0.040 g MgSO4x7H2O 0.075 g CaCl2x2H2O 0.036 g Citric acid 0.006 g Ammonium ferric citrate green 0.006 g EDTANa2 0.001 g Na2CO3 0.020 g Trace metal solution 1.00 mL Distilled water to 1.0 L Adjust pH to 7.4. Extra nutrient salts: NaNO3 3.00 g Na2HPO4 0.12 g K2HPO4 0.10 g Distilled water to 100.0 mL Trace metal solution: H3BO3 0.286 g MnCl2x4H2O 0.022 g Na2MoO4x2H2O 0.039 g CuSO4x5H2O 0.008 g Co(NO3)2x6H2O 0.005 g Distilled water to 100 mL
has exact synonym: BG medium

Lindstrom medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131361
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_48843
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_49976
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53503
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_60720
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63005
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_64758
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75213
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86254
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86368
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: L-medium No. 16
has exact synonym: Lindstrom media
definition: A mineral-salts, liquid microbiological culture medium comprised mainly of sodium bicarbonate. Used to cultivate autotrophic microorganisms from lakes.
has exact synonym: L 16
created by: Carrine Blank
IAO_0000119: From: Lindstrom, K. 1983. Selenium as a growth factor for plankton algae in laboratory experiments and in some Swedish lakes. Hydrobiologia 101:35-48. Macronutrients (all values mg per L) NaHCO3 84.00 NaNO3 12.75 CaCl2x2H2O 14.70 MgSO4x7H2O 12.32 K2HPO4 1.74 Na2SiO3x9H2O 1.14 Micronutrients FeCl3x6H2O 0.108 Na2MoO4x2H2O 0.048 ZnCl2 0.027 MnCl2x4H2O 0.010 CoCl2x6H2O 0.0096 Na2SeO3x5H2O 0.000184 EDTA 0.558 pH 8.1

Aa medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15940
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15956
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16494
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17015
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_27470
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_29377
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30411
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30753
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30961
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31440
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32138
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_44557
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_49105
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53503
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_62946
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63036
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75213
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75836
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_76209
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86356
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86465
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 8806
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_91247
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      intersection of: CHEBI_16526
      intersection of: Restriction
        on property: has ingredient
        some values from: CHEBI_17997
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001386
definition: A mineral-salts, liquid microbiological culture medium containing sodium acetate, potassium phosphate, sodium carbonate, ammonium sulfate, cysteine hydrochloride, sodium sulfide, magnesium sulfate, calcium chloride, sodium chloride, ferrous sulfate, nitrilotriacetic acid, manganese sulfate, cobalt chloride, zinc sulfate, resazurin, copper sulfate, potassium aluminum sulfate, boric acid, sodium molybdate, pyridoxine hydrochloride, thiamine hydrochloride, riboflavin, nicotinic acid, p-aminobenzoic acid (4-aminobenzoic acid), lipoic acid, biotin, folic acid, and vitamin B12 (cobalamin). Prepared under an atmosphere of dinitrogen and carbon dioxide. Used for the growth of Methanosaeta concillii.
created by: Carrine Blank
IAO_0000119: From: Patel GB. 1984. Characterization and nutritional properties of Methanothrix concilii sp. nov., a mesophilic, aceticlastic methanogen. Can J Microbiol 30:1383-1396. The composition of the Aa medium used for isolation and stock culture maintenance was as follows (in milligrams per litre): CH3COONa·3H2O, 6800; K2HPO4, 2190; KH2PO4, 1500; Na2CO3, 480; (NH4)2SO4, 450; cysteine-HCl, 125; Na2S·9H2O, 125; MgSO4·7H2O, 120; CaCl2·2H2O, 60; NaCl, 54; FeSO4 ·7H2O, 21; nitrilotriacetic acid, 15; MnSO4 · 2H2O, 5; CoCl2-6H2O, 1; ZnSO4·7H2O, I; resazurin, I; CuSO4·5H2O, 0.1; AIK(SO4)2- 12H2O, 0.1; H3BO3, 0.1; Na2Mo04·2H2O, 0.1; pyridoxine-HCl, 0.1; thiamine-HCl, riboflavin, nicotinic acid, p-aminobenzoic acid, lipoic acid, each 0.05; biotin and folic acid, each 0.02; vitamin B-12, 0.005. The Aa medium ingredients, except Na2CO3 and cysteine- Na2S, were 'mixed and adjusted to pH 7.8. The medium was then reduced with cysteine- Na2S, and Na2CO3 was added, using the Hungate (1950) technique. The reduced medium was dispensed in 10-mL aliquots into 60-mL serum vials (Miller and Wolin 1974) under 80% N2: 20% CO2 gas phase. The postautoclave (121°C, 15 min) pH was 7.2 ± 0.1. If the same medium contained 10000 mg/L of CH3COONa·3H20, it was referred to as AA medium.

prokaryotic quality
type: Class
subclass of: PATO_0001241
subclass of: Restriction
  on property: RO_0000080
  some values from: Class
    union of: CL_0000520
    union of: GO_0044464
    union of: MICRO_0002468
created by: Carrine Blank
definition: Quality that inheres in a prokaryotic cell, group of cells, prokaryotic colony, or part of a prokaryotic cell.

L-proline arylamidase assay using nitroanilide
type: Class
equivalent class: Class
  intersection of: MICRO_0003604
  intersection of: Restriction
    on property: is an assay for the enzymatic substrate
    some values from: temp_0000224
  intersection of: Restriction
    on property: is an assay for the enzymatic product
    some values from: temp_0000202
has related synonym: L-proline 4-nitroanilide
created by: Carrine Blank
definition: L-proline arylamidase that uses the substrate L-proline 4-nitroanilide (L-proline-p-nitroanilide). Proline arylamidase activity (which could be from proline aminopeptidase as well as other dipeptidase enzymes) cleaves the substrate, releasing 4-nitroaniline which is bright yellow in color. A positive test is yellow; a negative test is colorless.
has related synonym: Proline p-nitroanilide
has exact synonym: PRO
has related synonym: L-proline-p-nitroanilide

water filter
type: Class
subclass of: BFO_0000040
definition: A filter with a specified pore size that filters solid material above the specified pore size out of a liquid medium.
created by: Carrine Blank

Berkefeld filter candle
type: Class
equivalent class: Class
  intersection of: water filter
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000117
subclass of: water filter
subclass of: Restriction
  on property: has size
  some values from: PATO_0000117
definition: A gravity-driven water filter made by the British Berkefeld® company.
created by: Carrine Blank

prokaryotic cell quality
type: Class
equivalent class: Class
  intersection of: prokaryotic quality
  intersection of: Restriction
    on property: RO_0000080
    some values from: CL_0000520
definition: Physical object quality of a prokaryotic cell.
created by: Carrine Blank

trichome pole
type: Class
equivalent class: Class
  intersection of: trichome part
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002476
subclass of: trichome part
subclass of: Restriction
  on property: has position
  some values from: PATO_0002476
disjoint with: trichome
created by: Carrine Blank
definition: A trichome part, refering to the poles (terminal ends) of a prokaryotic trichome. May involve one cell or multiple cells along the trichome.

mesophilic
type: Class
equivalent class: Class
  intersection of: MICRO_0001311
  intersection of: Restriction
    on property: is prokaryotic physiological quality of
    all values from: MICRO_0001437
subclass of: MICRO_0001311
subclass of: Restriction
  on property: is prokaryotic physiological quality of
  all values from: MICRO_0001437
created by: Carrine Blank
definition: Temperature optimum quality, where growth rates at moderate temperatures (20-40˚C) are higher than growth rates at other temperatures.

ZoBell marine agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_132769
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32030
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32149
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_34683
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_36383
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_60720
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63038
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 6636
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has broad synonym: MA
IAO_0000119: From: http://himedialabs.com/TD/M384.pdf Zobell Marine Agar 2216 Zobell Marine Agar 2216 is recommended for cultivation, isolation and enumeration of heterotrophic marine bacteria. Composition Ingredients (Gms/Litre) Peptic digest of animal tissue 5.000 Yeast extract 1.000 Ferric citrate 0.1000 Sodium chloride 19.450 Magnesium chloride 8.800 Sodium sulfate 3.240 Calcium chloride 1.800 Potassium chloride 0.550 Sodium bicarbonate 0.160 Potassium bromide 0.080 Strontium chloride 0.034 Boric acid 0.022 Sodium silicate 0.004 Sodium fluorate 0.0024 Ammonium nitrate 0.0016 Disodium phosphate 0.008 Final pH (25˚C) 7.6+/-0.2
has exact synonym: MA2216 agar
has broad synonym: MA plates
has exact synonym: ZMA
has exact synonym: MA solid medium
definition: An organic-rich, mineral-salts, solid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Used for the cultivation of heterotrophic marine microorganisms.
created by: Carrine Blank
has exact synonym: Marine agar
has broad synonym: MA medium
has exact synonym: marine agar 2216
has exact synonym: Marine 2216 agar
has exact synonym: Zobell marine agar
has exact synonym: Zobell 2216E agar

tryptic soy broth
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: soy peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: Trypticase soy broth
IAO_0000119: From: Bacto™ Tryptic Soy Broth/Trypticase™ Soy Broth (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Tryptic (Trypticase) Soy Broth (Soybean-Casein Digest Medium) is a general purpose medium used in qualitative procedures for the cultivation of fastidious and nonfastidious microorganisms from a variety of clinical and nonclinical specimens. Principles of the Procedure Enzymatic digests of casein and soybean provide amino acids and other complex nitrogenous substances. Dextrose is an energy source. Sodium chloride maintains the osmotic equilibrium. Dibasic potassium phosphate acts as a buffer to control pH. The addition of 6.5% sodium chloride to Trypticase Soy Broth permits the differentiation of salt-tolerant enterococci, which are resistant to the high salt content, from the salt-intolerant S. bovis group and other streptococcal species. At this concentration, the sodium chloride is a selective agent that interferes with membrane permeability and osmotic and electrokinetic equilibria.4 Fildes Enrichment is a peptic digest of sheep blood that supplies the X (hemin) and V (nicotinamide adenine dinucleotide, NAD) factors necessary for the growth of H. influenzae. Dextrose is omitted from the formula for Tryptic Soy Broth without Dextrose to permit use of the medium in fermentation studies. The carbohydrate concentration used most frequently in fermentation reactions is 0.5% or 1%. Tryptic Soy Broth and Trypticase Soy Broth are provided as prepared media in a variety of bottle styles. In addition, Tryptic Soy Broth is provided as a Sterile Pack Bottle; i.e., the bottle has been terminally sterilized inside of autoclavable double-bags. All varieties of bottled TSB conform with requirements for Ready- To-Use Media as described in the USP. Formulae Bacto™ Tryptic Soy Broth (Soybean-Casein Digest Medium) Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 17.0 g Papaic Diges…
has exact synonym: Soya broth media
has exact synonym: Tryptone soya broth
definition: An organic-rich, liquid culture medium comprised of pancreatic digest of casein (casitone), papaic digest of soybean (soy peptone), dextrose (D-glucose), sodium chloride, and dipotassium phosphate (potassium dibasic phosphate).
has exact synonym: Tryptic soy broth
IAO_0000119: Wikipedia:Tryptic_soy_broth Tryptic soy broth (frequently abbreviated as TSB) is used in microbiology laboratories as a culture broth to grow aerobic bacteria. It is frequently used in commercial diagnostics in conjunction with the additive Thio which promotes growth of anaerobes.
has exact synonym: Soya broth
has related synonym: tryptic soy medium
has exact synonym: TSB
created by: Carrine Blank

tryptic soy agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001795
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: TSBA plates
has exact synonym: Tryptone soy agar
has exact synonym: TSA
has exact synonym: Tryptone Soya Agar
has exact synonym: TSA agar
has exact synonym: Tryptic soy broth agar
has exact synonym: Trypticase soy broth agar
has exact synonym: Trypticase soy agar
has exact synonym: TSBA
has exact synonym: Tryptic soy agar
has exact synonym: Trypticase-Soy agar
definition: An organic-rich, solid medium containing casitone (pancreatic digest of casein), Phytone peptone (papaic digest of soybean), and sodium chloride. Used for the cultivation of aerobic heterotrophic microorganisms.
IAO_0000119: From: Tryptic Soy Agar/Trypticase™ Soy Agar (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Tryptic (Trypticase) Soy Agar (TSA) is used for the isolation and cultivation of nonfastidious and fastidious microorganisms. It is not the medium of choice for anaerobes. Principles of the Procedure The combination of casein and soy peptones in TSA renders the medium highly nutritious by supplying organic nitrogen, particularly amino acids and longer-chained peptides. The sodium chloride maintains osmotic equilibrium. Agar is the solidifying agent. Haemophilus species may be differentiated by their requirements for X and V factors. Paper strips impregnated with these factors are placed on the surface of the medium after inoculation with the test organism. Following incubation, a zone of growth around the strip indicates a requirement for the factor(s). Formulae Difco™ Tryptic Soy Agar Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 15.0 g Papaic Digest of Soybean............................................. 5.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 15.0 g pH 7.3 ± 0.2 BBL™ Trypticase™ Soy Agar Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 15.0 g Papaic Digest of Soybean............................................. 5.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 15.0 g *Adjusted and/or supplemented as required to meet performance criteria.
created by: Carrine Blank

prokaryotic metabolic process
type: Class
subclass of: Class
  intersection of: GO_0044710
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: MICRO_0001444
      intersection of: Restriction
        on property: RO_0000086
        some values from: MICRO_0001488
created by: Carrine Blank
definition: A single-organism metabolic process that is present in a prokaryotic metabolically differentiated cell.

chemical mixture, serving as microbiological medium ingredients
type: Class
equivalent class: Class
  intersection of: CHEBI_60004
  intersection of: Restriction
    on property: is an ingredient of
    some values from: microbiological culture medium
created by: Carrine Blank
definition: A solid or liquid mixture of chemicals which are used as ingredients in microbiological culture media used to grow and propogate prokaryotic microorganisms.

sub-cylindrical
type: Class
equivalent class: Class
  intersection of: flattened cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002226
subclass of: flattened cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002226
definition: A flattened prokaryotic cell where the shape is partially spherical.
has exact synonym: sub-cylindrical

thermophilic
type: Class
equivalent class: Class
  intersection of: MICRO_0001311
  intersection of: Restriction
    on property: is prokaryotic physiological quality of
    all values from: MICRO_0001537
subclass of: MICRO_0001311
subclass of: Restriction
  on property: is prokaryotic physiological quality of
  all values from: MICRO_0001537
created by: Carrine Blank
definition: Temperature optimum quality, where growth rates at elevated temperatures (40-85˚C) are higher than growth rates at ambient temperatures.

filament septation
type: Class
equivalent class: Class
  intersection of: cell filament
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      union of: GO_0000936
      union of: Restriction
        on property: BFO_0000051
        all values from: Class
created by: Carrine Blank
definition: A filament of prokaryotic cells relating to the presence or absence of septa separating the individual cells that make up the filament.

cyanobacterial filament part
type: Class
equivalent class: Class
  intersection of: GO_0005575
  intersection of: Restriction
    on property: BFO_0000050
    some values from: cyanobacterial filament
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1117
created by: Carrine Blank
definition: Cell part of a cyanobacterial filament.
has exact synonym: filamentous

distinctively shaped filament
type: Class
equivalent class: Class
  intersection of: cell filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000052
created by: Carrine Blank
definition: A cell filament that has a distinctive shape.

spatially differentiated filaments
type: Class
equivalent class: Class
  intersection of: morphologically differentiated filament part
  intersection of: Restriction
    on property: has position
    some values from: PATO_0000140
subclass of: morphologically differentiated filament part
subclass of: Restriction
  on property: has position
  some values from: PATO_0000140
definition: A filament morphological quality where the filaments have a particular spatial orientation with respect to a substrate or surface.
created by: Carrine Blank

scytonematoid-branched filaments
type: Class
equivalent class: Class
  intersection of: false-branched filaments
  intersection of: Restriction
    on property: RO_0002202
    some values from: necritic cell
has exact synonym: loop-formation
has exact synonym: loop formation
has exact synonym: Scytonema-like false branching
has exact synonym: filaments in loop-like formations
has exact synonym: common lateral loops
has related synonym: Scytonema-type
has exact synonym: false scytonematoid branching
has related synonym: S-type
has exact synonym: scytonematoid false branching
definition: False-branched filaments, where branches initiate at a necridic cell. Branches often appear as pairs.
created by: Carrine Blank
has exact synonym: filaments make sometimes typical loop-like lateral formations

tolypothrixoid-branched filaments
type: Class
equivalent class: Class
  intersection of: false-branched filaments
  intersection of: Restriction
    on property: RO_0002202
    some values from: heterocyte
definition: False-branched filaments, where branches initiate at a heterocyte. Branches only sometimes appear as pairs.
has exact synonym: tolypotrichoid branched
has exact synonym: Tolypothrix-type false branching
has exact synonym: Tolypothrix-like false branching
created by: Carrine Blank
has related synonym: Tolypothrix-type
has exact synonym: Tolypothrix-like false branched
has related synonym: T-type

X-branched filaments
type: Class
equivalent class: Class
  intersection of: true-branched filaments
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1123
  intersection of: Restriction
    on property: RO_0000086
    some values from: cell cluster
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      intersection of: MICRO_0001297
      intersection of: Restriction
        on property: has spatial pattern
        some values from: Class
has related synonym: X-branching
created by: Carrine Blank
has broad synonym: Chlorogloeopsis-type branching
definition: True-branched filaments, where the cells divide irregularly in different planes and form clusters of cells. The cells remain physiologically attached.
has broad synonym: irregular clustering

T-branched filaments
type: Class
equivalent class: Class
  intersection of: true-branched filaments
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1190
      union of: NCBITaxon_162985
      union of: NCBITaxon_221292
  intersection of: Restriction
    on property: RO_0001025
    some values from: MICRO_0001284
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      intersection of: MICRO_0001296
      intersection of: Restriction
        on property: has spatial pattern
        some values from: Class
has broad synonym: T-type branching
created by: Carrine Blank
has broad synonym: perpendicular branching
has exact synonym: true branching lateral (usually unilateral)
has exact synonym: laterally true branched
has exact synonym: T-type of branching
has exact synonym: branching type "T"
has exact synonym: type of branching: T-type
has exact synonym: branching of T-type
has exact synonym: erect true branches develop usually unilaterally after the lengthwise cell division
has exact synonym: true branching lateral
has broad synonym: Westiella-type
has broad synonym: lateral T-branching
has exact synonym: irregularly lateral true branched
has exact synonym: lateral T-type
has exact synonym: branching lateral
has broad synonym: Hapalosiphon-type
has exact synonym: branching lateral (T-type)
has broad synonym: Stigonema-type
has broad synonym: Fischerella-type
IAO_0000232: zzzz 'inheres in' some (Stigonema or Fischerella or Hapalosiphon or Westiella) Westiella is in NCBI Tax browser, but not in OntoFox.
definition: True-branched filaments, where a cell in the trichome divides longitudinally (parallel to the axis of the filament) and the trichome branch starts to grow perpendicular to one side of the main trichome.
has related synonym: T-branching

V-branched filaments
type: Class
equivalent class: Class
  intersection of: true-branched filaments
  intersection of: Restriction
    on property: RO_0001025
    some values from: apical cell
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      intersection of: MICRO_0001296
      intersection of: Restriction
        on property: has spatial pattern
        some values from: Class
has exact synonym: pseudodichotomous branches arise by longitudinal division of the apical cells
has broad synonym: Hyphomorpha-type
has exact synonym: branching type "V"
has broad synonym: Loriella-type
has exact synonym: pseudodichotomously true branched
has exact synonym: pseudodichotomously divaricated branches
created by: Carrine Blank
IAO_0000232: zzzz 'inheres in' some (Hyphomorpha or Pulvinularia or Colteronema or Loriella or Mastigocoleopsis) - no NCBI entries.
has exact synonym: pseudodichotomously branched
has exact synonym: pseudodichotomously divaricated at the ends
has related synonym: V-branching
has broad synonym: Mastigocoleopsis-type
has exact synonym: pseudodichotomous branchings
has exact synonym: pseudodichotomously divaricated
has exact synonym: V-type
has exact synonym: V-type of branching
has exact synonym: pseudodichotomous V-type
definition: True-branched filaments, where an apical cell divides longitudinally, from which grows obliquely two equivalent branches.
has exact synonym: branching lateral (V-type)
has exact synonym: pseudodichotomously divaricated free filaments
has broad synonym: pseudodichotomous

reverse Y-branched filaments
type: Class
equivalent class: Class
  intersection of: true-branched filaments
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1203
      union of: NCBITaxon_29417
  intersection of: Restriction
    on property: RO_0001025
    some values from: MICRO_0001284
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      intersection of: MICRO_0001296
      intersection of: Restriction
        on property: has spatial pattern
        some values from: Class
created by: Carrine Blank
has exact synonym: reverse Y-like branching
has exact synonym: Y-type
definition: True-branched filaments, where branches arise in the intercalary (medial) cells after oblique cell division at an intercalary (medial cell).
has exact synonym: reverse Y-type
has exact synonym: Y-branching
IAO_0000232: zzzz 'inheres in' some (Scytonema or Brachytrichia or Mastigocladus) Brachytrichia is in NCBI Tax Browser, but not in OntoFox.
has related synonym: reverse Y-branching

biseriate filament
type: Class
equivalent class: Class
  intersection of: multiseriate filament
  intersection of: Restriction
    on property: RO_0000053
    some values from: Class
      intersection of: PATO_0000921
      intersection of: Restriction
        on property: has measurement
        some values from: Class
subclass of: multiseriate filament
subclass of: Restriction
  on property: RO_0000053
  some values from: Class
    intersection of: PATO_0000921
    intersection of: Restriction
      on property: has measurement
      some values from: Class
        intersection of: Restriction
definition: Filament with one trichome in the sheath, where the trichome is two cells in width. Arises as a result of cell division occuring in two planes,one perpendicular to the axis of the trichome and one parallel to the axis of the trichome.
has exact synonym: bi-seriate
created by: Carrine Blank
has exact synonym: with 2 cells aside

extracellular sheath
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament part
  intersection of: Restriction
    on property: has structure
    some values from: Class
      intersection of: PATO_0002124
      intersection of: Restriction
        on property: has structure
        some values from: Class
  intersection of: Restriction
    on property: has chemical composition
    some values from: Class
      intersection of: CHEBI_72813
      intersection of: Restriction
        on property: has chemical composition
        some values from: CHEBI_90127
subclass of: cyanobacterial filament part
subclass of: Restriction
  on property: has structure
  some values from: Class
    intersection of: PATO_0002124
    intersection of: Restriction
      on property: has structure
      some values from: Class
        intersection of: PATO_0002134
        intersection of: Restriction
subclass of: Restriction
  on property: has chemical composition
  some values from: Class
    intersection of: CHEBI_72813
    intersection of: Restriction
      on property: has chemical composition
      some values from: CHEBI_90127
disjoint with: trichome
definition: An extracellular sheath in cyanobacteria is typically a laminated (lamellated, laminar), fibrillar, extracellular structure made of polysaccharides (glycan). It plays a role in desiccation tolerance and often contains pigments (such as scytonemin) which protect from photodamage caused by uv light. It also has proteins (including water stress proteins, pectases). Often multilayered and colored.
created by: Carrine Blank
has broad synonym: sheath

trichome
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament part
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1161
      union of: NCBITaxon 1189
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001360
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002023
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001295
IAO_0000119: Wikipedia: trichome Algal trichomes Certain, usually filamentous, algae have the terminal cell produced into an elongate hair-like structure called a trichome. The same term is applied to such structures in some cyanobacteria, such as Spirulina and Oscillatoria. Cyanobacteria trichomes may be unsheathed, as in Oscillatoria, or sheathed, as in Calothrix.[1] These structures play an important role in preventing soil erosion, particularly in cold desert climates.[citation needed] The filamentous sheaths form a persistent sticky network that helps maintain soil structure.
created by: Carrine Blank
definition: A prokaryotic filament part, comprised of a chain of cells that has undergone binary fission in a single plane, where the cells remain attached after cell division. Found in the Nostocales and Stigonematales (Cyanobacteria).

isopolar trichome
type: Class
equivalent class: Class
  intersection of: trichome
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1162
      union of: NCBITaxon 1182
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: trichome pole
      intersection of: Restriction
        on property: BFO_0000051
        some values from: basal heterocyte
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002023
  intersection of: Restriction
    on property: has morphology
    all values from: Class
      intersection of: Class
        complement of: PATO_0001500
      intersection of: Restriction
        on property: has symmetry
        some values from: PATO_0000632
has exact synonym: apical cells not differentiated
definition: A prokaryotic trichome where the two poles of the trichome have the cell diameter (i.e., are symmetrical and not tapered). Caused by the development of a basal heterocyte.
has exact synonym: trichomes isopolar
has exact synonym: morphologically not diversified in "main" filaments and branches
has exact synonym: simple trichomes
has exact synonym: trichomes not distinctly diversified
has exact synonym: filaments simple
created by: Carrine Blank
has exact synonym: simple filaments
has exact synonym: apical cells morphologically not different from other cells

heteropolar trichome
type: Class
equivalent class: Class
  intersection of: trichome
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1182
      union of: NCBITaxon 1185
      union of: NCBITaxon_119859
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: trichome pole
      intersection of: Restriction
        on property: BFO_0000051
        some values from: basal heterocyte
  intersection of: Restriction
    on property: has morphology
    some values from: Class
      intersection of: PATO_0001500
      intersection of: Restriction
        on property: has symmetry
        some values from: PATO_0000616
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002023
has exact synonym: filaments polarized
definition: A prokaryotic trichome where the two poles of the trichome have different cell diameters (i.e. trichomes are tapered on end end and asymmetrical). Caused by the development of a basal heterocyte.
has exact synonym: trichomes heteropolar
has exact synonym: filaments differentiated into basal and apical parts
has exact synonym: trichomes, oriented by their bases with heterocytes to their substrate and by their apical hir-like parts to the surface
created by: Carrine Blank
has exact synonym: free apical end
has exact synonym: filaments distinctly divided into basal end with a heterocyte and the apical end
has exact synonym: differentiating into basal and apical parts

apical cell
type: Class
equivalent class: Class
  intersection of: MICRO_0001285
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002476
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002099
  intersection of: Restriction
    on property: RO_0001025
    some values from: BSPO_0000057
subclass of: MICRO_0001285
subclass of: Restriction
  on property: has position
  some values from: PATO_0002476
subclass of: Restriction
  on property: RO_0001025
  some values from: BSPO_0000057
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002099
created by: Carrine Blank
has exact synonym: free apical end
definition: A trichome cell that is located terminally in a trichome, and which has undergone differentiation. Found in trichomes with apical-basal polarity.

susceptibility to lysis by hypotonic solution
type: Class
equivalent class: Class
  intersection of: prokaryotic cell wall lysis susceptibility
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005618
      intersection of: Restriction
        on property: RO_0000053
        some values from: Class
definition: Prokaryotic cell wall lysis susceptibility that defines how susceptible the cell wall is to lysis when the cell is placed in the presence of an environment with an altered chemical composition (hypotonic solution).
created by: Carrine Blank

basal prostrate filaments
type: Class
equivalent class: Class
  intersection of: prostrate filaments
  intersection of: Restriction
    on property: has position
    some values from: Class
      intersection of: PATO_0000631
      intersection of: Restriction
        on property: RO_0001025
        some values from: BSPO_0000074
subclass of: prostrate filaments
subclass of: Restriction
  on property: has position
  some values from: Class
    intersection of: PATO_0000631
    intersection of: Restriction
      on property: RO_0001025
      some values from: BSPO_0000074
definition: Filament orientation quality where erect filaments and prostrate filaments are present, refers to the basal filaments that are prostrate to the substrate.
created by: Carrine Blank

necritic cell
type: Class
equivalent class: Class
  intersection of: MICRO_0001285
  intersection of: Restriction
    on property: RO_0000086
    some values from: Class
      intersection of: PATO_0002099
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0001422
subclass of: MICRO_0001285
subclass of: Restriction
  on property: RO_0000086
  some values from: Class
    intersection of: PATO_0002099
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0001422
has exact synonym: nectrotic cells
created by: Carrine Blank
has exact synonym: trichomes disintegrating in separated cells within filaments
has exact synonym: trichomes often disintegrate soon after heterocyte formation between heterocytes
definition: A trichome cell comprised of a cell that has undergone differentiation such that it is dead (nectritic).

chroococcoid cell cluster
type: Class
equivalent class: Class
  intersection of: cell cluster
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: CL_0000520
      intersection of: Restriction
        on property: has shape
        some values from: Class
has exact synonym: chroococcoidal
has exact synonym: chroococcoid clusters of cells
has exact synonym: old trichomes change often in chroococcoid stages
has exact synonym: chroococcoid stage
has exact synonym: known chroococcal stages
has exact synonym: chroococcoid cell clusters arise
definition: Cell clusters, where the cells are chroococcoid (spherical).
created by: Carrine Blank

differentiated meristematic zone
type: Class
equivalent class: Class
  intersection of: differentiated cyanobacterial filament part
  intersection of: Restriction
    on property: BFO_0000051
    some values from: meristematic zone
  intersection of: Restriction
    on property: has position
    some values from: PATO_0000140
subclass of: differentiated cyanobacterial filament part
subclass of: Restriction
  on property: BFO_0000051
  some values from: meristematic zone
subclass of: Restriction
  on property: has position
  some values from: PATO_0000140
has exact synonym: not all cells capable of dividing
has exact synonym: not all cells capable to divide
has exact synonym: distinct merstematic zones
definition: Filament differentiation quality with respect to the positioning of the meristematic zone along the length of the trichome.
has exact synonym: not all cells capable of division
created by: Carrine Blank

tapered trichome
type: Class
equivalent class: Class
  intersection of: MICRO_0000997
  intersection of: Restriction
    on property: BFO_0000051
    some values from: tapered trichome
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000052
subclass of: MICRO_0000997
subclass of: Restriction
  on property: has shape
  some values from: PATO_0000052
subclass of: Restriction
  on property: BFO_0000051
  some values from: tapered trichome
has broad synonym: trichomes variable width
created by: Carrine Blank
has exact synonym: trichomes tapered
definition: Heteropolar trichome where the width of the trichome varies such that the trichome is tapered.
has related synonym: trichome tapering

hair cell
type: Class
equivalent class: Class
  intersection of: apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001409
subclass of: apical cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001154
has broad synonym: apical hairs
definition: An apical cell or cells in a heteropolar filament that is differentiated to form an elongated hair-like extension.
has exact synonym: long tapering to the hair-like ends
has exact synonym: hair-like apical ends
has exact synonym: long hairs
has exact synonym: hair-like ends
has exact synonym: terminal hairs
has exact synonym: hyaline hairs
has exact synonym: in the apical part narrowed in elongated, cellular hair
has broad synonym: elongated hyaline cells
has exact synonym: hair formation
has exact synonym: hyaline cells
has exact synonym: cellular hair
has exact synonym: hairs
created by: Carrine Blank
has exact synonym: trichomes elongated in cellular hair-like ends
has exact synonym: apical hair-like ends
has exact synonym: hair-cells

vacuolized apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: gas vacuole
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: gas vacuole
has exact synonym: vacuolized cells at the ends
has exact synonym: apical cells vacuolated
has exact synonym: vacuolized apical cells
has exact synonym: terminal cells vacuolized
has exact synonym: end cells sometimes vacuolated
created by: Carrine Blank
definition: Apical cell that is vacuolized (has gas vacuoles).

morphologically distinctive apical cell
type: Class
equivalent class: Class
  intersection of: differentiated apical cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: apical cell
      intersection of: Restriction
        on property: has morphology
        some values from: PATO_0000051
subclass of: differentiated apical cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: apical cell
    intersection of: Restriction
      on property: has morphology
      some values from: PATO_0000051
definition: Cyanobacterial filament part, where the apical cell is morphologically distinctive.
created by: Carrine Blank

conical-rounded apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0002021
      intersection of: Restriction
        on property: has shape
        some values from: PATO_0001950
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0002021
    intersection of: Restriction
      on property: has shape
      some values from: PATO_0001950
has exact synonym: end cells conical-rounded
has exact synonym: rounded-conical apical cells
created by: Carrine Blank
has exact synonym: apical cells conical-rounded
definition: Apical cell that is conical-rounded (conical-blunt).

conical apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002021
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002021
has exact synonym: apical cells conical
has exact synonym: end cells conical
has exact synonym: terminal cells conical
definition: Apical cell that is conical.
has exact synonym: terminal cells are conical
created by: Carrine Blank

pointed apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001500
subclass of: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001500
has exact synonym: pointed at the ends
has exact synonym: apical cells pointed
definition: Apical cell that is pointed (tapered).
created by: Carrine Blank
has exact synonym: pointed terminal cells

rounded apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001950
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001950
has exact synonym: club-shaped ends of trichomes and branches
has exact synonym: end cells spherical
has exact synonym: terminal cells are rounded
has exact synonym: rounded apical cells
has exact synonym: rounded at the ends
has exact synonym: rounded terminal cell
has exact synonym: end cells rounded
has exact synonym: terminal cells rounded
has exact synonym: apical cells rounded
definition: Apical cell that is rounded (blunt).
created by: Carrine Blank
has exact synonym: rounded at the apex
has exact synonym: rounded end cells
has exact synonym: rounded apical cell
has exact synonym: end cells widely spherical
has exact synonym: end cells widely rounded
has exact synonym: end cells widened-rounded
has exact synonym: end cells rounded at apex

elongated apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001154
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001154
definition: Apical cell that is elongated.
has broad synonym: apical cells long
has broad synonym: apical cells cylindrical
has exact synonym: terminal cells elongated
has exact synonym: apical cells elongated
has exact synonym: end cells cylindrical
has broad synonym: apical part elongated
created by: Carrine Blank

narrowed apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000599
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: has size
  some values from: PATO_0000599
has exact synonym: apical cells narrowed
has exact synonym: terminal cells are narrowed
has exact synonym: end cells narrowed
created by: Carrine Blank
has exact synonym: apical part narrowed
definition: Apical cell that is narrowed (has decreased width).
has exact synonym: terminal cells narrow

apical cell develops into nanocytes
type: Class
equivalent class: Class
  intersection of: differentiated apical cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: nanocytes
  intersection of: Restriction
    on property: RO_0002354
    some values from: GO_0032502
has exact synonym: terminal cells of branches divide often repeatedly in nanocytes
definition: Apical cell quality related the developmental transformation of the apical cell into nanocytes.
created by: Carrine Blank
has broad synonym: transforms into nanocytes

hyaline apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001409
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001409
has exact synonym: apical cells hyaline
definition: Apical cell that is hyaline (spindle-shaped).
created by: Carrine Blank

elongated-rounded apical cell
type: Class
equivalent class: Class
  intersection of: morphologically distinctive apical cell
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0001154
      intersection of: Restriction
        on property: has shape
        some values from: PATO_0001950
subclass of: morphologically distinctive apical cell
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0001154
    intersection of: Restriction
      on property: has shape
      some values from: PATO_0001950
definition: Apical cell that is elongated-rounded (elongated-blunt).
created by: Carrine Blank
has exact synonym: terminal cells elongated-rounded

bluntly pointed apical cell
type: Class
equivalent class: Class
  intersection of: pointed apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001982
subclass of: Class
  intersection of: pointed apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001982
created by: Carrine Blank
definition: Pointed apical cell that is bluntly pointed (attenuate).
has exact synonym: end cells bluntly pointed
has exact synonym: terminal cells are bluntly pointed
has exact synonym: apical cells bluntly pointed

sharply pointed apical cell
type: Class
equivalent class: Class
  intersection of: pointed apical cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002228
subclass of: pointed apical cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002228
has exact synonym: apical cells acuminate
has broad synonym: apical cells sharply pointed
definition: Pointed apical cell that is sharply pointed (acuminate).
created by: Carrine Blank

vacuolized sub-apical cell
type: Class
equivalent class: Class
  intersection of: MICRO_0001282
  intersection of: Restriction
    on property: BFO_0000051
    some values from: gas vacuole
subclass of: MICRO_0001282
subclass of: Restriction
  on property: BFO_0000051
  some values from: gas vacuole
has exact synonym: vacuolized subapical cells
created by: Carrine Blank
definition: Sub-apical cell quality where the sub-apical cell is vacuolized (has gas vacuoles).

subterminal meristematic zones
type: Class
equivalent class: Class
  intersection of: differentiated meristematic zone
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002475
subclass of: differentiated meristematic zone
subclass of: Restriction
  on property: has position
  some values from: PATO_0002475
has exact synonym: subapical meristematic zones
created by: Carrine Blank
has broad synonym: apical cells are not able to divide
definition: Meristematic zone position quality where the position is subterminal.

terminal meristematic zones
type: Class
equivalent class: Class
  intersection of: differentiated meristematic zone
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002476
subclass of: differentiated meristematic zone
subclass of: Restriction
  on property: has position
  some values from: PATO_0002476
has exact synonym: in the apical part sometimes with meristematic zones
has exact synonym: meristematic zons near the ends of branches
definition: Meristematic zone position quality where the position is terminal.
created by: Carrine Blank
has exact synonym: meristematic (mainly apical) zones

tapered by apical widening
type: Class
equivalent class: Class
  intersection of: tapered trichome
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001955
subclass of: tapered trichome
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001955
has broad synonym: branches dilated terminal portions
has exact synonym: end cells enlarged
has exact synonym: trichomes sometimes with slightly widened apical parts
has exact synonym: end cells widened-rounded
has exact synonym: end cells widened
definition: Tapered trichome quality where the trichome is wider at the apical end, and narrower at the basal end (cuneate-shaped).
has exact synonym: apical cell is larger than the other ones
created by: Carrine Blank

tapered by apical narrowing
type: Class
equivalent class: Class
  intersection of: tapered trichome
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001982
subclass of: tapered trichome
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001982
has exact synonym: apical cells attenuated
definition: Tapered trichome quality where the trichome is narrower at the apical end, and wider at the basal end (attenuate-shaped).
has broad synonym: trichomes widened at the base
created by: Carrine Blank

trace elements solution TES
type: Class
equivalent class: Class
  intersection of: trace elements solution
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53503
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53542
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75213
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86318
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86368
created by: Carrine Blank
IAO_0000119: From: Irgens RL. 1977. Meniscus, a new genus of aerotolerant, gas-vacuolated bacteria. Int J Syst Bacteriol 27(1):38-43. The TES, modified from Pfennig’s formula (personal communication), contained (per liter): ZnSO4x7H2O, 0.10 g; MnCl2x4H2O, 0.03 g; H3BO3, 0.3 g; CoCl2x6H20, 0.2 g; CuCl2x2H2O,0.01 g ; NiCl2x6H2O, 0.02 g; Na2MoO4x 2H2O, 0.03g; pH3 to 4.
definition: A trace elements solution containing zinc sulfate, manganese chloride, boric acid, cobalt chloride, copper chloride, nickel chloride, and sodium molybdate.

Balch vitamin solution
type: Class
equivalent class: Class
  intersection of: vitamin solution
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15940
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15956
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16494
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16709
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17015
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_27470
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30411
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30753
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31345
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_49105
created by: Carrine Blank
IAO_0000119: From: Balch WE et al, 1979. Methanogens: reevaluation of a unique biological group. Microbiol Rev 43(2):260. Trace vitamines (contains in milligrams per liter: biotin, 2; folic acid, 2; pyridoxine hydrochloride, 10; thiamine hydrochloride, 5; riboflavin, 5; nicotinic acid, 5; DL-calcium pantothenate, 5; vitamin B12, 0.1; p-aminobenzoic acid, 5; lipoic acid, 5) Also reported in Wolin EA, Wolin MJ, Wolfe RS. 1963. Formation of methane by bacterial extracts. J Biol Chem 238(8):2882-2886.
definition: A solution of vitamins containing biotin, folic acid, pyridoxine, thiamine, riboflavin, nicotinic acid, calcium pantothenate, cobalamin (vitamin B12), 4-aminobenzoic acid (p-aminobenzoic acid), and lipoic acid. Used to support growth of methanogenic archaea.
has related synonym: Balch trace vitamines

prokaryotic metabolite
type: Class
equivalent class: Class
  intersection of: CHEBI_24431
  intersection of: Restriction
    on property: is metabolic product assayed by
    some values from: GO_0044710
subclass of: CHEBI_24431
subclass of: Restriction
  on property: is metabolic product assayed by
  some values from: GO_0044710
created by: Carrine Blank
definition: A chemical entity produced by a prokaryotic cell, as a result of metabolism.

organic chemical mixture
type: Class
equivalent class: Class
  intersection of: chemical mixture, serving as microbiological medium ingredients
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50860
created by: Carrine Blank
definition: Organic compounds or mixtures of organic compounds added to culture media to support growth or metabolism of a microorganism.

methane produced by methanogenesis
type: Class
subclass of: prokaryotic metabolite
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: CHEBI_16183
    intersection of: Restriction
      on property: is metabolic product assayed by
      some values from: GO_0015948
has exact synonym: methane production
has exact synonym: formation of methane
has exact synonym: methane formed
has exact synonym: CH4 formation
definition: Prokaryotic metabolite where methane is produced as a result of methanogenesis.
has exact synonym: CH4 formed
has exact synonym: forming CH4
has exact synonym: produce methane
has exact synonym: CH4 as the product
has exact synonym: CH4 production
has exact synonym: methane generated
has exact synonym: methane as the product
has exact synonym: methanogens
has exact synonym: formation of CH4
has exact synonym: production of CH4
has exact synonym: CH4 generated
has exact synonym: methane formation
IAO_0000119: Wikipedia:methanogenesis Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In most environments, it is the final step in the decomposition of biomass.
has exact synonym: methanogenic
has exact synonym: CO2 reduction to methane
has exact synonym: produces CH4
has exact synonym: CO2 reduction to CH4
has exact synonym: methane as the end product
has exact synonym: CH4 as the end product
has exact synonym: methanogenesis
has exact synonym: produce CH4
has exact synonym: methane produced
has exact synonym: CH4 produced
created by: Carrine Blank
has exact synonym: forming methane
has exact synonym: production of methane
has exact synonym: produces methane

obligate methanogen
type: Class
equivalent class: Class
  intersection of: MICRO_0001444
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 2157
  intersection of: Restriction
    on property: contains prokaryotic metabolic process
    all values from: GO_0015948
definition: Prokaryotic metabolically differentiated cell, specialized for the production of methane. Found only in the archaeal domain of life.
has broad synonym: obligately methanogenic
created by: Carrine Blank

undefined organic chemical mixture
type: Class
subclass of: organic chemical mixture
created by: Carrine Blank
definition: A mixture of dry or liquid organic compounds added to culture media to support growth or metabolism of a microorganism. Because the exact composition of the mixture is unknown or uncharacterized, it is referred to as "undefined".

tetrathionate reduction
type: Class
subclass of: GO_0006790
created by: Carrine Blank
definition: The process in which tetrathionate is reduced to sulfide.

microbiological medium ingredient, derived from aqueous extracts of animal tissues or fluids
type: Class
subclass of: MICRO_0001370
subclass of: Restriction
  on property: is an aqueous extract derived from
  some values from: NCBITaxon_40674
definition: Undefined mixture of complex organic compounds deriving from the aqueous extraction (an extraction using water, such as hot water or steam) of animal organs, animal tissues, or animal secretions. Used in the cultivation of microorganisms.
created by: Carrine Blank

microbiological medium ingredient, derived from extracts of microbial organisms
type: Class
subclass of: MICRO_0001370
subclass of: Restriction
  on property: is an aqueous extract derived from
  some values from: NCBITaxon_131567
definition: Undefined mixtures of complex organic compounds deriving from the aqueous extraction (an extraction using water, such as hot water or steam) of microbial (prokaryotic or microbial eukaryotic) cells. Used in the cultivation of microorganisms.
created by: Carrine Blank

microbiological medium ingredient, derived from oil
type: Class
subclass of: undefined organic chemical mixture
subclass of: Restriction
  on property: has chemical composition
  some values from: Class
    union of: CHEBI_15904
    union of: CHEBI_83563
subclass of: Restriction
  on property: is an oleaginous extract derived from
  some values from: BFO_0000040
definition: Undefined mixtures of complex organic compounds derived from hydrophobic substances including lipids, fatty acids, and triacylglycerols, derived from the chemical or physical extraction of oil from an organism, the part of an organism, or a naturally occurring substance (such as crude oil).
created by: Carrine Blank

microbiological medium ingredient, derived from extracts of proteinaceous material
type: Class
subclass of: undefined organic chemical mixture
subclass of: Restriction
  on property: is an extract derived from
  some values from: CHEBI_36080
definition: An undefined mixture of complex organic compounds (peptides, sometimes with additional undefined vitamins and cofactors) derived from enzymatic, acid, or base digests of protein from plant or animal sources. Used in the cultivation of microorganisms.
created by: Carrine Blank

microbiological medium ingredient, derived from chemical hydrolysis of protein
type: Class
subclass of: microbiological medium ingredient, derived from extracts of proteinaceous material
subclass of: Restriction
  on property: is an acid hydrolytic extract derived from
  some values from: CHEBI_36080
disjoint with: microbiological medium ingredient, derived from enzymatic hydrolysis of protein
definition: Undefined mixtures of complex organic compounds derived (typically amino acids) from the acid hydrolysis of animal or plant protein added to culture media.
created by: Carrine Blank

microbiological medium ingredient, derived from enzymatic hydrolysis of protein
type: Class
subclass of: microbiological medium ingredient, derived from extracts of proteinaceous material
subclass of: Restriction
  on property: RO_0002354
  some values from: CHMO_0001494
subclass of: Restriction
  on property: is an enzymatic hydrolytic extract derived from
  some values from: CHEBI_36080
IAO_0000119: BD Bionutrients Technical Manual (3rd edition revised).
created by: Carrine Blank
definition: Protein hydrolysates, also called peptones, are the result of the enzymatic hydrolysis of protein.

Trypticase peptone
type: Class
subclass of: MICRO_0000606
has exact synonym: Biotrypticase
definition: Trademarked commercial name for pancreatic digest of casein (milk protein from cow's milk, Bos taurus), used for the culturing of microorganisms.
IAO_0000119: Reference for Bio-trypticase: "Rapport de Mission au Centre National de l'Elevage et de Recherches Veterinaires de Nouakchott du 12/07 au 02/08/1999"; Institute Senegalais de Recherches Agricoles. Retired name for "peptone pancreatique du caseine"; produced by Bio-Merieux (www.biomerieux.com) or Oxoid (www.remel.com/Microbiology).
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): BBL™ Trypticase™ Peptone is a pancreatic digest of casein and is the primary nitrogen source in Trypticase Soy Broth and Agar. Ash content is 5.7% NaCl content is 0.1%
created by: Carrine Blank
has exact synonym: TrypticaseTM Peptone
has exact synonym: bio-trypticase
has broad synonym: Trypticase

meat peptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of mammalian protein
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: Class
      intersection of: NCBITaxon_40674
      intersection of: Restriction
        on property: is an enzymatic hydrolytic extract derived from
        some values from: UBERON_0002385
definition: An enzymatic hydrolysis of meat (muscle tissue) proteins from mixed animal (mammalian) sources, used for the culturing of microorganisms.
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): Meat peptones are proteins from animal sources that have been hydrolyzed, or broken down into amino acids and peptides, to provide nitrogen for microorganisms. Meat peptones can be tailored to specific nutritive needs of microorganisms by controlling the quality and origin of the protein, the quality and source of the enzyme used to digest the protein, and the methods used for hydrolysis, concentration and drying the peptone. Peptone manufacture methods are discussed in the section titled Hydrolysis to Hydrolysate. Sources of animal protein include meat from muscle tissue or offal (waste parts, entrails) and gelatin. Muscular tissue and offal are utilized fresh, frozen or dried. Gelatin is extracted by boiling collagen, the fibrous protein found in connective tissue, bone and cartilage. A variety of proteolytic enzymes, or proteases, may be used to accomplish enzymatic hydrolysis of animal protein. Pepsin and trypsin are widely used for animal peptone manufacture. Pepsin is isolated from porcine or other animal stomach. Trypsin, along with chymotrypsin, carboxypeptidase A, carboxypeptidase B, and elastase, are enzymes isolated from animal pancreas.
created by: Carrine Blank

neopeptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of mammalian protein
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: Class
      intersection of: NCBITaxon_40674
      intersection of: Restriction
        on property: is an enzymatic hydrolytic extract derived from
        some values from: UBERON_0002385
created by: Carrine Blank
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Neopeptone is an enzymatic digest of protein. Neopeptone contains a wide variety of peptide sizes in combination with vitamins, nucleotides and minerals. Ash content is 6.9% NaCl content is 1.4%
definition: An enzymatic digest of meat, used for the culturing of microorganisms.

peptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of mammalian protein
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: NCBITaxon_40674
has exact synonym: bacterial peptone
definition: An enzymatic digest of animal (mammalian) protein (of unspecified orgin), used for the culturing of microorganisms.
has exact synonym: peptones
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised).: Bacto™ Peptone is an enzymatic digest of animal protein. Bacto Peptone was first introduced in 1914 and became the standard Peptone for the preparation of bacteriological culture media. The nutritive value of Bacto Peptone is largely dependent on the amino acid content that supplies essential nitrogen. Bacto Peptone contains only a negligible quantity of proteoses and more complex constituents. Ash content is 6.9% NaCl content is 1.7%
created by: Carrine Blank
has exact synonym: Bacto-peptone
has exact synonym: Bacto Peptone

polypeptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from extracts of proteinaceous material
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
created by: Carrine Blank
definition: A mixture of peptones (pancreatic digest of casein and peptic digest of animal/mammalian tissue - meat), used for the culturing of microorganisms.
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised).: BBL™ Polypeptone™ Peptone is a mixture of peptones made up of equal parts of pancreatic digest of casein and peptic digest of animal tissue. Polypeptone Peptone includes the high content of amino acids and small polypeptides characteristic of pancreatic digest of casein and the larger polypeptides characteristic of peptic digest of animal tissue. Ash content is 9.7% NaCl content is 2.7%

proteose peptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of mammalian protein
  intersection of: Class
    intersection of: Restriction
      on property: is an enzymatic hydrolytic extract derived from
      some values from: NCBITaxon_40674
    intersection of: Restriction
      on property: is an enzymatic hydrolytic extract derived from
      some values from: UBERON_0002385
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised). The Bacto™ Proteose Peptones are enzymatic digests of protein. Studies of peptic digests of animal tissue prepared under varying digestion parameters led to the development of Proteose Peptone, Proteose Peptone No. 2 and Proteose Peptone No. 3. Data accumulated during these studies demonstrated that no one peptone is the most suitable nitrogen source for every microbiological application. Bacto Proteose Peptone No. 4 is a spray-dried version of Bacto Proteose Peptone. BiTek™ Proteose Peptone and BiTek Proteose Peptone No. 3 are enzymatic digests of protein, developed to offer alternatives to the Bacto Proteose Peptones for scale-up to production applications. Ash content is 7.8% NaCl content is 4.9%
has broad synonym: Peptic digest of animal tissue
definition: A peptic digest of protein derived from animal (mammalian) tissue, used for the culturing of microorganisms.
has exact synonym: meat peptic digest
created by: Carrine Blank
has narrow synonym: Bacto(TM) Proteose Peptone
has exact synonym: bacto proteose peptone

soy peptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of protein
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: Class
      intersection of: NCBITaxon 4513
      intersection of: Restriction
        on property: is an enzymatic hydrolytic extract derived from
        some values from: MICRO_0001341
has exact synonym: soytone
has exact synonym: soya peptone
has exact synonym: bacto soytone
definition: A mixed enzymatic digest of flour made of the seed of the soybean (Hordeum vulgare), used for the culturing of microorganisms.
has narrow synonym: Bacto™ Soytone
has exact synonym: papaic digest of soybean
has broad synonym: soytone
created by: Carrine Blank
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): Enzymeatic digests of soy flour. Soy contains several heat labile protease inhibitors. The most common way of eliminating these factors is to heat or toast the defatted soy beans in a processing plant under controlled conditions. Soy flour, the principle substrate in a soy peptone, is rich in high-quality protein, carbohydrates, calcium and B vitamins. The enzymes used in the digestion of soy flour are typically from animal-free sources or from microorganisms that have been grown in animal-free media. Ash content is 12% NaCl content is 0.2%

tryptone
type: Class
subclass of: MICRO_0001366
has narrow synonym: Proteose Tryptone
has narrow synonym: Bacto-Tryptone
IAO_0000119: From: Wikipedia:Tryptone Tryptone is the assortment of peptides formed by the digestion of casein by the protease trypsin.
definition: An enzymatic hydrolysate of casein (a milk protein from cow's milk, Bos taurus) made using the hydrolytic enzyme trypsin, used for the culturing of microorganisms.
has exact synonym: bacto-tryptone
created by: Carrine Blank
IAO_0000119: From BD Bionutrients(TM) Techical Manual (3rd edition, revised): Bacto™ Tryptone is a pancreatic digest of casein. It was developed by Difco Laboratories while investigating a peptone particularly suitable for the elaboration of indole by bacteria. It is also notable for the absence of detectable levels of carbohydrates. Ash content is 6.6% NaCl content is 0.0%
has narrow synonym: Bacto Tryptone

tryptose
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of mammalian protein
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: NCBITaxon_40674
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised).: Bacto™ Tryptose is a mixed enzymatic hydrolysate with distinctive nutritional properties. The digestive process of Tryptose results in assorted peptides of higher molecular weight suitable for long-chain amino acid requirements. Ash content is 8.8% NaCl content is 3.2%
created by: Carrine Blank
definition: A mixed enzymatic hydrolysate of protein (animal meat of unspecified origin), used for the cultivation of microorganisms.

casamino acids
type: Class
subclass of: microbiological medium ingredient, derived from chemical hydrolysis of protein
subclass of: Restriction
  on property: is an acid hydrolytic extract derived from
  some values from: ENVO_0010035
subclass of: Restriction
  on property: is an acid hydrolytic extract derived from
  some values from: NCBITaxon 9913
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Casamino Acids is an acid hydrolysate of casein, prepared according to the method described by Mueller and Miller. The method described, reduces the sodium chloride and iron content of the hydrolyzed casein. This hydrolyzed casein, supplemented with inorganic salts, growth factors, cystine, maltose and an optimum amount of iron was used by Mueller and Miller to prepare diptheria toxin. Bacto Casamino Acids duplicate this specially treated hydrolyzed casein. Ash content is 18.3% NaCl content is 12.1%
has exact synonym: Casein Hydrolysate
has exact synonym: acid digest of casein
created by: Carrine Blank
definition: An acid hydrolysate of casein (milk protein from cow's milk, Bos taurus), used for the culturing of microorganisms.

crude oil
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from oil
  intersection of: Restriction
    on property: is an oleaginous extract derived from
    some values from: ENVO_00002984
  intersection of: Restriction
    on property: has chemical composition
    some values from: CHEBI_24632
definition: A complex mixture of unrefined petrolium hydrocarbons, pumped from subsurface geologic formations, used in the cultivation of microorganisms.
created by: Carrine Blank

egg yolk oil
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from oil
  intersection of: Restriction
    on property: is an oleaginous extract derived from
    some values from: Class
      intersection of: NCBITaxon 9031
      intersection of: Restriction
        on property: is an oleaginous extract derived from
        some values from: UBERON_0007378
created by: Carrine Blank
IAO_0000119: From Wikipedia: Yolk: The yolk of one large egg (50 g total, 17 g yolk) contains approximately: 2.7 g protein, 210 mg cholesterol, 0.61 g carbohydrates, and 4.51 g total fat. All of the fat-soluble vitamins (A, D, E, and K) are found in the egg yolk. Egg yolk is one of the few foods naturally containing vitamin D. The composition (by weight) of the most prevalent fatty acids in egg yolk is typically as follows: Unsaturated fatty acids: Oleic acid, 47% Linoleic acid, 16% Palmitoleic acid, 5% Linolenic acid, 2% Saturated fatty acids: Palmitic acid, 23% Stearic acid, 4% Myristic acid, 1%
definition: Oil extracted from yolk of chicken eggs, used in the cultivation of microorganisms.

disproportionation of thiosulfate
type: Class
subclass of: GO_0006790
definition: The process by which thiosulfate undergoes disproportionation to sulfate and hydrogen sulfide.
created by: Carrine Blank

olive oil
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from oil
  intersection of: Restriction
    on property: is an oleaginous extract derived from
    some values from: Class
      intersection of: NCBITaxon 4146
      intersection of: Restriction
        on property: is an oleaginous extract derived from
        some values from: MICRO_0001339
created by: Carrine Blank
definition: Oil extracted from olives (the fruit of Olea europaea), used in the cultivation of microorganisms.
IAO_0000119: From Wikipedia:Olive_oil: Olive oil is a fat obtained from the olive (the fruit of Olea europaea; family Oleaceae), a traditional tree crop of the Mediterranean Basin. The oil is produced by pressing whole olives. Olive oil is composed mainly of the mixed triglyceride esters of oleic acid and palmitic acid and of other fatty acids, along with traces of squalene (up to 0.7%) and sterols (about 0.2% phytosterol and tocosterols).

glutamate deaminase assay
type: Class
equivalent class: Class
  intersection of: MICRO_0000849
  intersection of: Restriction
    on property: is an assay for the enzymatic substrate
    some values from: Class
      intersection of: Class
        union of: CHEBI_16015
        union of: CHEBI_29985
        union of: CHEBI_29988
      intersection of: Restriction
        on property: is an assay for the enzymatic substrate
        some values from: ENVO_00002006
  intersection of: Restriction
    on property: is an assay for the enzymatic product
    some values from: Class
      intersection of: Class
        union of: CHEBI_16810
        union of: CHEBI_30915
        union of: CHEBI_30916
      intersection of: Restriction
        on property: is an assay for the enzymatic product
        some values from: CHEBI_16134
subclass of: MICRO_0000849
subclass of: Restriction
  on property: is an assay for the enzymatic substrate
  some values from: Class
    intersection of: Class
      union of: CHEBI_16015
      union of: CHEBI_29985
      union of: CHEBI_29988
    intersection of: Restriction
      on property: is an assay for the enzymatic substrate
      some values from: ENVO_00002006
subclass of: Restriction
  on property: is an assay for the enzymatic product
  some values from: Class
    intersection of: Class
      union of: CHEBI_16810
      union of: CHEBI_30915
      union of: CHEBI_30916
    intersection of: Restriction
      on property: is an assay for the enzymatic product
      some values from: CHEBI_16134
has related synonym: glutamate dehydrogenase
definition: The purpose of this assay is to determine if a microbial isolate is capable of metabolizing glutamate. This enzyme is important for the synthesis of urea and in nitrogen assimilation. Glutamate is deaminated via a hydrolysis reaction to produce 2-oxoglutarate, ammonia, and either NADH or NADPH. Activity can be assayed using colorimetric assays for NADH production. 2-oxoglutarate is also known as alpha-ketoglutarate. Activity could also be determined using a pH sensitive indicator dye. Glutamate dehydrogenase catalyzes the following reaction: L-Glutamate + H2O <-> 2-oxoglutarate + NH3 + NADH/NADHP + H+ L-Glutamate + H2O <-> alpha-ketoglutarate + NH3 + NADH/NADHP + H+
created by: Carrine Blank

archaea cell extract
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from extracts of microbial organisms
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: NCBITaxon 2157
definition: An extract made from archaeal cells, used for culturing microorganisms.
created by: Carrine Blank

bacterial cell extract
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from extracts of microbial organisms
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: NCBITaxon 2
definition: An extract made from bacterial cells, used for culturing microorganisms.
created by: Carrine Blank

beef heart infusion
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from aqueous extracts of animal tissues or fluids
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: Class
      intersection of: NCBITaxon 9913
      intersection of: Restriction
        on property: is an aqueous extract derived from
        some values from: UBERON_0000948
IAO_0000119: From http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM1032&cat=&sec=1: Heart Infusion Broth has been developed to give the same performance characteristics as Brain Heart Infusion (BHI) Broth. However, as bovine brain is a specified risk material, the exclusion of it from the Heart Infusion Broth means that the regulatory requirements when using it are lower. The medium has been developed to give equivalent performance to Brain Heart Infusion but the exclusion of calf brain infusion means that Heart Infusion Broth carries a lower regulatory burden. Simple additions may be made to the medium to make it suitable for the cultivation of yeasts and moulds and for use in blood culture. A highly nutritious infusion medium recommended for the cultivation of streptococci, pneumococci, meningococci and other fastidious organisms.
has broad synonym: heart infusion
created by: Carrine Blank
definition: A water extract of bovine (Bos taurus) heart, used in the cultivation of microorganisms.
has exact synonym: bovine heart infusion

brain heart infusion
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from aqueous extracts of animal tissues or fluids
  intersection of: Class
    intersection of: Restriction
      on property: is an aqueous extract derived from
      some values from: Class
        intersection of: UBERON_0000948
        intersection of: UBERON_0000955
    intersection of: Restriction
      on property: is an aqueous extract derived from
      some values from: Class
        union of: NCBITaxon 9823
        union of: NCBITaxon 9913
IAO_0000119: From Wikipedia:Brain_heart_infusion_broth: Brain-heart infusion broth (BHI broth or BHIB) is a highly nutritious general-purpose growth medium for culturing fastidious and nonfastidious microorganisms, such as streptococci, pneumococci and meningococci. It is made by boiling cow or porcine hearts and brains. Boiling releases soluble factors into the broth. The broth can then be turned into powder for easy distribution. BHI broth contains sodium chloride which is used to differentiate enterococci from nonenterococcal group D streptococci. BHI broth is often used in food safety, water safety, and antibiotic sensitivity tests.
created by: Carrine Blank
definition: Hot water extract of bovine (Bos taurus) or porcine (Sus scrofa) hearts and brains, used in the cultivation of microorganisms.

Chlorella cell extract
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from extracts of microbial organisms
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: NCBITaxon_114055
created by: Carrine Blank
definition: An extract made from cellular paste from the culture of Chlorella spp., used for the culturing of microorganisms. Chlorella is a microscopic green alga in the Trebouxiophyceae.

fecal extract
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from aqueous extracts of animal tissues or fluids
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: Class
      intersection of: NCBITaxon_40674
      intersection of: Restriction
        on property: is an aqueous extract derived from
        some values from: ENVO_00002003
IAO_0000119: From "Materials and Methods in the Study of Protozoa", pg. 21, by Harold Kirby, University of California Press, 1950: "One part of caecal contents is mixed with 9 parts of Ringer solution, and the mixture strained through a sieve and then through a funnel with a thick pad of absorbent cotten."
created by: Carrine Blank
definition: A water extract of fecal material derived from some animal (mammal), used in the cultivation of microorganisms.

malt extract
type: Class
subclass of: microbiological medium ingredient, derived from extracts of plants
subclass of: Restriction
  on property: RO_0002354
  some values from: Class
    intersection of: CHMO_0001652
    intersection of: Class
      intersection of: Class
        intersection of: Restriction
      intersection of: Restriction
        on property: RO_0002354
        some values from: CHMO_0002770
subclass of: Restriction
  on property: is an aqueous extract derived from
  some values from: Class
    intersection of: NCBITaxon 4513
    intersection of: Restriction
      on property: is an aqueous extract derived from
      some values from: PO_0009010
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Malt Extract is the water-soluble portion of malted barley. The extraction process breaks down the polysaccharides into simple sugars. After the malting process is complete, the extract is prepared from the malted barley by cracking the grain in a mill and then extracting the grain with a warm liquor. The resulting “wort” is filtered and evaporated or dried under vacuum. Ash content is 0.3% NaCl content is 0.2%
definition: Water-soluble extract of malted (i.e. germinated) seeds of barley (Hordeum vulgare), used for the culturing of microorganisms. Prepared by malting the seed, cracking it (grinding) using a mill, heating it in water, then filtering the extract and drying it.
created by: Carrine Blank

horse manure extract
type: Class
equivalent class: Class
  intersection of: fecal extract
  intersection of: Restriction
    on property: is an aqueous extract derived from
    all values from: Class
      intersection of: NCBITaxon 9796
      intersection of: Restriction
        on property: is an aqueous extract derived from
        some values from: ENVO_00002003
created by: Carrine Blank
has broad synonym: manure extract
definition: A water extract of horse (Equus caballus) manure, used for the culturing of microorganisms.
IAO_0000119: From "Report of the New York State College of Agriculture at Cornell University, Ithaca, and of the Cornell University Agricultural Experiment Station", v. 25, Part 1, 1913, pg. 431: Manure extract agar. - Prepared as follows: To 100 grams of well-rotted horse manure was added 500 cc. of distilled water. This was allowed to stand for twenty-four hours at room temperature and then filtered. The filtrate was used as a stock solution.

meat extract
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from aqueous extracts of animal tissues or fluids
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: Class
      intersection of: NCBITaxon_40674
      intersection of: Restriction
        on property: is an aqueous extract derived from
        some values from: UBERON_0002385
definition: A water extract of animal (mammalian) meat, used for the culturing of microorganisms.
IAO_0000119: From Wikipedia:Meat_extract: Meat extract is highly concentrated meat stock, usually made from beef.
created by: Carrine Blank

pine needle extract
type: Class
subclass of: microbiological medium ingredient, derived from extracts of plants
subclass of: Restriction
  on property: RO_0002354
  some values from: Class
    intersection of: CHMO_0002770
    intersection of: Class
      intersection of: Restriction
        on property: RO_0002354
        some values from: CHMO_0001553
      intersection of: Restriction
        on property: RO_0002354
        some values from: CHMO_0001640
subclass of: Restriction
  on property: is an aqueous extract derived from
  some values from: Class
    intersection of: NCBITaxon_139271
    intersection of: Restriction
      on property: is an aqueous extract derived from
      some values from: PO_0025034
IAO_0000119: From Jeaon, J-R & Kim, J-Y. 2006. Effects of pine needle extract on differentiation of 3T3-L1 preadipocytes and obesity in high-fat diet fed rats. Biol. Pharm. Bull. 29(10):2111-2115: Pine needles were collected from Kyungbook Province, Republic of Korea, and were extracted using 20 kg of water for 2 h at 80 °C. The extract was filtered, and was then freeze-dried at 40 °C. Pine needle water extract (PNE) was stored at 4 °C until use.
definition: A hot water extract of pine needles (the adult leaves of Pinus spp.), used for the culturing of microorganisms. Formed as result of heating pine needles in warm water, filtering the extract and then drying it.
created by: Carrine Blank

soya extract
type: Class
subclass of: microbiological medium ingredient, derived from extracts of plants
subclass of: Restriction
  on property: RO_0002354
  some values from: Class
    intersection of: CHMO_0001624
    intersection of: Class
      intersection of: Class
        intersection of: Class
        intersection of: Restriction
      intersection of: Restriction
        on property: RO_0002354
        some values from: CHMO_0002770
subclass of: Restriction
  on property: has ingredient
  some values from: CHEBI_32145
subclass of: Restriction
  on property: is an aqueous extract derived from
  some values from: Class
    intersection of: NCBITaxon 3847
    intersection of: Restriction
      on property: is an aqueous extract derived from
      some values from: PO_0009010
IAO_0000119: From Roubos-van den Hil, Dalmas, Nout & Abee. 2009. Soya bean tempe extracts show antibacterial activity against Bacillus cerus cells and spores. J. Appl. MIcrobiol. 109(1):137-145: Fermented soya beans (tempe) and cooked soya beans, were freeze-dried and grounded passing through a 0·5-mm sieve (Ultra Centrifugal Mill ZM 200, Retsch GmbH, Haan, Germany) and were stored at −20°C until further processing. Freeze-dried products were suspended in distilled water (60 g l−1) and stirred with a magnetic stirrer for 3 h at room temperature. The pH was continually checked and adjusted to pH 8·0 with 1 mol l−1 NaOH. To obtain clear supernatants, the soluble extract was obtained by three consecutive centrifugation steps (10 min, 10 000 g, 20°C). Supernatants were freeze-dried and soluble dry matter was stored at −20°C and used as soya bean soluble dry matter in experiments.
definition: A water extract of ground beans (the seed) of soya (Glycine max), used for the culturing of microorganisms. Formed by fermenting the beans, heating (cooking) them, filtering the material and freeze dyring it. Next, the material is hydrated, treated with sodium hydroxide, centrifuged and freeze-dried.
has exact synonym: Soybean extract
has exact synonym: Soy extract
has exact synonym: Soya bean extract
created by: Carrine Blank

yeast extract
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from extracts of microbial organisms
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: NCBITaxon 4932
has exact synonym: Yeast extrakt
IAO_0000119: From www.SigmaAldrich.com: A water soluble extract of autolyzed yeast cells. Yeast extract is a mixture of amino acids, peptides, water soluble vitamins and carbohydrates and can be used as additive for culture media.
definition: A water-soluble extract of autolyzed yeast (Saccharomyces cerevisiae), used for the culturing of microorganisms.
created by: Carrine Blank
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Yeast Extract is one of the most complete and versatile fermentation bionutrients available. It is an important ingredient for the microbiological assay of vitamins. Yeast extract is also of value in the assay of antibiotics. B factor, a growth substance necessary for the production of rifampin in a Nocardia sp., can be isolated from yeast extract Ash content is 11.2% NaCl content is 0.1%
has exact synonym: Yeastrel

beef extract
type: Class
equivalent class: Class
  intersection of: meat extract
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: Class
      intersection of: NCBITaxon 9913
      intersection of: Restriction
        on property: is an aqueous extract derived from
        some values from: UBERON_0002385
definition: A water extract of beef (Bos taurus) protein, used for the culturing of microorganisms.
has exact synonym: beef infusion
created by: Carrine Blank
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised).: Beef Extract is derived from infusion of beef and provides an undefined source of nutrients. Beef Extract is not exposed to the harsh treatment used for protein hydrolysis, so it can provide some of the nutrients lost during peptone manufacture. Beef Extract is a mixture of peptides and amino acids, nucleotide fractions, organic acids, minerals and some vitamins. “Its function can therefore be described as complementing the nutritive properties of peptone by contributing minerals, phosphates, energy sources and those essential factors missing from peptone.” Beef Extract Powder is a meat extract dried to powder form. Bacto™ Beef Extract, Desiccated, is the dried form of Beef Extract paste. Ash content is 9.3% NaCl content is 0.3%

Gram stain assay
type: Class
equivalent class: Class
  intersection of: MICRO_0001188
  intersection of: Restriction
    on property: is an assay using the chemical reagent
    some values from: Class
      intersection of: CHEBI_41688
      intersection of: Restriction
        on property: is an assay using the chemical reagent
        some values from: Class
  intersection of: Restriction
    on property: is an assay for the quality
    some values from: Gram stain quality
  intersection of: Restriction
    on property: is an assay for the cellular component
    some values from: GO_0009274
disjoint with: MICRO_0001189
definition: Cell staining assay where a cell staining assay, performed by staining a smear of prokaryotic cells with two stains (Crystal Violet or Safranin). Delineates prokaryotes into two major groups (Gram positive and Gram negative, although results can be ambiguous in some taxa) that results from the different staining of cell wall types.
IAO_0000119: Wikipedia:Gram_staining Gram staining, also called Gram's method, is a method of differentiating bacterial species into two large groups (gram-positive and gram-negative). The name comes from the Danish bacteriologist Hans Christian Gram, who developed the technique. Gram staining differentiates bacteria by the chemical and physical properties of their cell walls by detecting peptidoglycan, which is present in a thick layer in gram-positive bacteria.[1] In a Gram stain test, gram-positive bacteria retain the crystal violet dye, while a counterstain (commonly safranin or fuchsine) added after the crystal violet gives all Gram-negative bacteria a red or pink coloring.
created by: Carrine Blank
IAO_0000232: zzzz has_participant some [ChEBI] safranin - Safranin is not in ChEBI yet.

morphologically distinct prokaryotic cell
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: has morphology
    some values from: PATO_0000051
definition: A prokaryotic cell, or group of cells, having a distinct morphology (shape or size).
created by: Carrine Blank

prokaryotic colony quality
type: Class
equivalent class: Class
  intersection of: prokaryotic quality
  intersection of: Restriction
    on property: RO_0000080
    some values from: MICRO_0002468
created by: Carrine Blank
definition: Physical object quality of a prokaryotic colony.

triple sugar iron agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17716
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17992
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32150
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: CHEBI_75836
      union of: CHEBI_76243
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: TSI
definition: An organic-rich, liquid microbiological culture medium that contains peptones, three sugars (glucose, lactose, and sucrose), ferric iron, thiosulfate, and phenol red (a pH indicator). If the sugars are fermented, the pH indicator will turn red indicating a lowered pH. If hydrogen sulfide is produced, the ferric iron will be reduced to ferrous sulfide, producing a black color.
IAO_0000119: From: http://www.microbelibrary.org/component/resource/laboratory-test/2842-triple-sugar-iron-agar-protocols RECIPE Pancreatic digest of casein USP (see Note) 10.0 g Peptic digest of animal tissue USP (see Note) 10.0 g Glucose 1.0 g Lactose 10.0 g Sucrose 10.0 g Ferrous sulfate or ferrous ammonium sulfate 0.2 g NaCl 5.0 g Sodium thiosulfate 0.3 g Phenol red 0.024 g Agar 13.0 g Distilled water 1,000 mL Note: The following combination of ingredients can substitute for the first two components listed: beef extract, 3.0 g; yeast extract, 3.0 g; and peptone, 20.0 g. Combine ingredients, and adjust the pH to 7.3. Boil to dissolve the agar, and dispense into tubes. Sterilize by autoclaving at 121°C for 15 min. Cool in a slanted position to give a 2.5-cm butt and a 3.8-cm slant.
created by: Carrine Blank

triple sugar iron agar
type: Class
equivalent class: Class
  intersection of: MICRO_0001182
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17992
has exact synonym: TSIA
created by: Carrine Blank
has exact synonym: Triple sugar iron agar
definition: An organic-rich, solid microbiological culture medium that contains peptones, three sugars (glucose, lactose, and sucrose), ferric iron, thiosulfate, and phenol red (a pH indicator). If the sugars are fermented, the pH indicator will turn red indicating a lowered pH. If hydrogen sulfide is produced, the ferric iron will be reduced to ferrous sulfide, producing a black color.
IAO_0000119: From:http://www.microbelibrary.org/component/resource/laboratory-test/2842-triple-sugar-iron-agar-protocols RECIPE Pancreatic digest of casein USP (see Note) 10.0 g Peptic digest of animal tissue USP (see Note) 10.0 g Glucose 1.0 g Lactose 10.0 g Sucrose 10.0 g Ferrous sulfate or ferrous ammonium sulfate 0.2 g NaCl 5.0 g Sodium thiosulfate 0.3 g Phenol red 0.024 g Agar 13.0 g Distilled water 1,000 mL Note: The following combination of ingredients can substitute for the first two components listed: beef extract, 3.0 g; yeast extract, 3.0 g; and peptone, 20.0 g. Combine ingredients, and adjust the pH to 7.3. Boil to dissolve the agar, and dispense into tubes. Sterilize by autoclaving at 121°C for 15 min. Cool in a slanted position to give a 2.5-cm butt and a 3.8-cm slant.

macroscopic optical quality assay
type: Class
equivalent class: Class
  intersection of: optical quality assay
  intersection of: Restriction
    on property: is an assay using the material entity
    some values from: OBI_0100060
subclass of: optical quality assay
subclass of: Restriction
  on property: is an assay using the material entity
  some values from: OBI_0100060
definition: An optical quality assay of a single prokaryotic cell, determined by visualization of a liquid culture of a prokaryotic microorganism (i.e., a clonal liquid suspension in a liquid culture medium).
created by: Carrine Blank

pigmented cell
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: has structure
    some values from: Class
      intersection of: PATO_0002248
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0000014
subclass of: CL_0000520
subclass of: Restriction
  on property: has structure
  some values from: Class
    intersection of: PATO_0002248
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0000014
created by: Carrine Blank
definition: A prokaryotic cell that is pigmented (in that it has a color imparted by a chemical pigment compound).

N-benzoyl-L-leucine peptidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
definition: An aminopeptidase activity which cleaves the chromogenic substrate N-benzoyl-L-leucine-beta-naphthylamide.

opalescent turbidity
type: Class
equivalent class: Class
  intersection of: macroscopic optical quality assay
  intersection of: Restriction
    on property: is an assay for the quality
    some values from: PATO_0002277
subclass of: macroscopic optical quality assay
subclass of: Restriction
  on property: is an assay for the quality
  some values from: PATO_0002277
has broad synonym: irridescent
created by: Carrine Blank
has broad synonym: irridescence
has broad synonym: opalescence
definition: The optical quality of a liquid culture of clonal prokaryotic organisms, which exhibits opalescent turbidity (refracting different wavelengths of light under white light illumination, or iridescence) after gentle shaking.

tyrosine agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17196
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17754
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17895
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75836
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000593
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
IAO_0000119: From: http://www.atcc.org/~/media/DF06C418BB3A44189AD1A3CEB59B8D6E.ashx ATCC Medium: 1776 Tyrosine Agar (ISP Medium 7) Glycerol 15.0 g L-Tyrosine 0.5 g L-Asparagine 1.0 g K2HPO4 0.5 g MgSO4x7H2O 0.5 g NaCl 0.5 g FeSO4x7H2O 10.0 mg Trace elemetns solution Ho-Le (see below) 1.0 mL Agar 20.0 g Distilled water 1.0 L Adjust medium for final pH 7.3 +/- 0.1. Autoclave at 121C for 15 minutes. Trace Elements Solution Ho-Le: H3BO3 2.85 g MnCl2x4H2O 1.8g FeSO4 1.36 g Sodium tartrate 1.77 g CuCl2x2H2O 26.9 mg ZnCl2 20.8 mg CoCl2x6H2O 40.4 mg Na2MoO4x2H2O 25.2 mg Distilled water 1.0 L
has exact synonym: L-tyrosine agar
definition: An organic-rich, mineral-salts, solid microbiological culture medium containing glycerol, tyrosine, asparagine, and minerals salts. Used for the growth of Streptoalloteichus.

endospore
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell, specialized for dormancy
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1239
  intersection of: Restriction
    on property: has position
    some values from: PATO_0000140
  intersection of: Restriction
    on property: RO_0002354
    some values from: GO_0034301
disjoint with: akinete
created by: Carrine Blank
has exact synonym: sporulating
has exact synonym: spore-forming
IAO_0000119: From Wikipedia:endospore: An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum. The name "endospore" is suggestive of a spore or seed-like form (endo means within), but it is not a true spore (i.e., not an offspring). It is a stripped-down, dormant form to which the bacterium can reduce itself. Endospore formation is usually triggered by a lack of nutrients, and usually occurs in Gram-positive bacteria. In endospore formation, the bacterium divides within its cell wall. One side then engulfs the other. Endospores enable bacteria to lie dormant for extended periods, even centuries. Revival of spores millions of years old has been claimed. When the environment becomes more favorable, the endospore can reactivate itself to the vegetative state. Most types of bacteria cannot change to the endospore form. Examples of bacteria that can form endospores include Bacillus and Clostridium.
definition: A differentiated prokaryotic cell, found in the Firmicutes, which is specialized for extreme tolerance to desiccation, radiation, and exposure to ultraviolet light. Characterized by thick cell walls.
has exact synonym: spore-former

gas vacuole
type: Class
equivalent class: Class
  intersection of: GO_0031410
  intersection of: GO_0043232
  intersection of: Restriction
    on property: BFO_0000055
    some values from: GO_0031413
subclass of: GO_0031410
subclass of: GO_0043232
subclass of: Restriction
  on property: BFO_0000055
  some values from: GO_0031413
IAO_0000119: Wikipedia:bacterial_cell_structure Gas vacuoles are membrane-bound, spindle-shaped vesicles, found in some planktonic bacteria and Cyanobacteria, that provides buoyancy to these cells by decreasing their overall cell density. Positive buoyancy is needed to keep the cells in the upper reaches of the water column, so that they can continue to perform photosynthesis. They are made up of a shell of protein that has a highly hydrophobic inner surface, making it impermeable to water (and stopping water vapour from condensing inside) but permeable to most gases. Because the gas vesicle is a hollow cylinder, it is liable to collapse when the surrounding pressure becomes too great.
has exact synonym: aerotopes
has exact synonym: gas vesicles
has exact synonym: vacuolized
has exact synonym: gas vacuole
has exact synonym: gas-vacuolated
definition: An intracellular non-membran-bound organelle (cytoplasmic vesicle) made of protein which functions to provide buoyancy to the cell in the water column.
created by: Carrine Blank

intracellular granule
type: Class
equivalent class: Class
  intersection of: GO_0044444
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0001759
subclass of: GO_0044444
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0001759
definition: Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy.
has exact synonym: granule
has exact synonym: granulated
has exact synonym: globule
has exact synonym: granular
has exact synonym: central granule
has exact synonym: intracellular globule
IAO_0000119: Wikipedia:granule_(cell biology) In cell biology, a granule is a small particle. It can be any structure barely visible by light microscopy.
created by: Carrine Blank

magnetosome
type: Class
subclass of: GO_0043231
subclass of: Restriction
  on property: BFO_0000055
  some values from: GO_0071259
IAO_0000119: Wikipedia:magnetosome Magnetosome chains are membranous prokaryotic structures present in magnetotactic bacteria. They contain 15 to 20 magnetite crystals that together act like a compass needle to orient magnetotactic bacteria in geomagnetic fields, thereby simplifying their search for their preferred microaerophilic environments. Each magnetite crystal within a magnetosome is surrounded by a lipid bilayer, and specific soluble and transmembrane proteins are sorted to the membrane. Recent research has shown that magnetosomes are invaginations of the inner membrane and not freestanding vesicles. Magnetite-bearing magnetosomes have also been found in eukaryotic magnetotactic algae, with each cell containing several thousand crystals.
created by: Carrine Blank
definition: Intracellular membrane-bound organelle that form chains, comprised of magnetic iron minerals that function to orient the cell axis along the Earth's magnetic field lines. Found in magnetotactic prokaryotes.

isopolar subsymmetric
type: Class
equivalent class: Class
  intersection of: differentiated isopolar trichome
  intersection of: Restriction
    on property: BFO_0000051
    some values from: intercalary heterocyte
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000616
subclass of: differentiated isopolar trichome
subclass of: Restriction
  on property: has symmetry
  some values from: PATO_0000616
subclass of: Restriction
  on property: BFO_0000051
  some values from: intercalary heterocyte
definition: An isopolar trichome morphology quality where heterocysts are rarely present along the length of the trichome such that the trichome morphology is asymmetric.
created by: Carrine Blank

xylose minimal medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_18222
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32599
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63043
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75832
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: CHEBI_17883
      union of: CHEBI_32145
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: XeMM
IAO_0000119: From:Humphry DR, George, A, Black GW, Cumming& s SP. 2001. Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. IJSEM 51:1235-1243. Minimal medium (MM) containing the following (w/v): 0.02% FeSO4, 0.02% MgSO4, 0.075% KNO3, 0.05% K2HPO4 and 0.004% CaCl2. The pH was adjusted to 7.2 with 1 M NaOH or 1M HCl.
definition: A mineral-salts, liquid microbiological culture medium comprised of ferrous sulfate, magnesium sulfate, potassium nitrate, potassium phosphate, and calcium chloride, supplemented with 0.5% w/v xylose. Used for the cultivation of Flavobacterium frigidarium.
created by: Carrine Blank

dispersed thylakoids
type: Class
equivalent class: Class
  intersection of: thylakoid-containing cell
  intersection of: Restriction
    on property: RO_0000086
    some values from: Class
      intersection of: PATO_0001630
      intersection of: Restriction
        on property: RO_0000086
        some values from: Class
has broad synonym: irregular thylakoids
definition: Thylakoid-containing cell where thylakoids are dispered irregularly (asymmetrically) throughout the interior of the cell.
has broad synonym: dispersed thylakoids
created by: Carrine Blank

parietal thylakoids
type: Class
equivalent class: Class
  intersection of: thylakoid-containing cell
  intersection of: Restriction
    on property: RO_0000086
    some values from: Class
      intersection of: PATO_0000627
      intersection of: Restriction
        on property: RO_0000086
        some values from: Class
has exact synonym: peripherally stacked thylakoid
has exact synonym: radially arranged thylakoids
has exact synonym: concentrically arranged thylakoids
has exact synonym: concentric thylakoid membranes
created by: Carrine Blank
definition: Thylakoid-containing cell where thylakoids are located around the inside periphery of the interior of the cell.
has broad synonym: parietal thylakoids

radial thylakoids
type: Class
equivalent class: Class
  intersection of: thylakoid-containing cell
  intersection of: Restriction
    on property: RO_0000086
    some values from: Class
      intersection of: PATO_0000627
      intersection of: Restriction
        on property: RO_0000086
        some values from: Class
has broad synonym: radial thylakoids
created by: Carrine Blank
definition: Thylakoid-containing cell where thylakoids are distributed throughout the inside of the cell and have a radial (like spokes on a wheel) arrangement.

greigite magnetosome
type: Class
equivalent class: Class
  intersection of: magnetosome
  intersection of: Restriction
    on property: has chemical composition
    some values from: CHEBI_86238
subclass of: magnetosome
subclass of: Restriction
  on property: has chemical composition
  some values from: CHEBI_86238
created by: Carrine Blank
definition: Intracellular membrane-bound organelle that form chains, comprised of magnetic iron minerals made of greigite that function to orient the cell axis along the Earth's magnetic field lines. Found in magnetotactic prokaryotes.
IAO_0000119: Wikipedia:magnetosome Magnetotactic bacteria usually mineralize either iron oxide magnetosomes, which contain crystals of magnetite (Fe3O4), or iron sulfide magnetosomes, which contain crystals of greigite (Fe3S4).

magnetite magnetosome
type: Class
equivalent class: Class
  intersection of: magnetosome
  intersection of: Restriction
    on property: has chemical composition
    some values from: CHEBI_46726
subclass of: magnetosome
subclass of: Restriction
  on property: has chemical composition
  some values from: CHEBI_46726
definition: Intracellular membrane-bound organelle that form chains, comprised of magnetic iron minerals made of magnetite that function to orient the cell axis along the Earth's magnetic field lines. Found in magnetotactic prokaryotes.
IAO_0000119: Wikipedia:magnetosome Magnetotactic bacteria usually mineralize either iron oxide magnetosomes, which contain crystals of magnetite (Fe3O4), or iron sulfide magnetosomes, which contain crystals of greigite (Fe3S4).
created by: Carrine Blank

granulated cell
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: BFO_0000051
    some values from: intracellular granule
created by: Carrine Blank
definition: A prokaryotic cell which has intracellular granules.

gas vacuole quality
type: Class
equivalent class: Class
  intersection of: prokaryotic cell part quality
  intersection of: Restriction
    on property: RO_0000080
    some values from: gas vacuolated cell
definition: A prokaryotic cell part quality that has gas vacuoles (gas vesicles).
created by: Carrine Blank

intracellular carbon storage granule
type: Class
equivalent class: Class
  intersection of: intracellular granule
  intersection of: Restriction
    on property: RO_0002215
    some values from: intracellular storage of carbon
subclass of: intracellular granule
subclass of: Restriction
  on property: RO_0002215
  some values from: intracellular storage of carbon
created by: Carrine Blank
definition: An intracellular granule that is specialized for the storage of carbon.

intracellular nitrogen storage granule
type: Class
equivalent class: Class
  intersection of: intracellular granule
  intersection of: Restriction
    on property: RO_0002215
    some values from: intracellular storage of nitrogen
subclass of: intracellular granule
subclass of: Restriction
  on property: RO_0002215
  some values from: intracellular storage of nitrogen
definition: An intracellular granule that is specialized for the storage of nitrogen.
created by: Carrine Blank

intracellular phosphorus storage granule
type: Class
subclass of: intracellular granule
subclass of: Restriction
  on property: RO_0002215
  some values from: MICRO_0001342
definition: An intracellular granule that is specialized for the storage of nitrogen.
created by: Carrine Blank

intracellular sulfur granule
type: Class
equivalent class: Class
  intersection of: intracellular granule
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_33403
subclass of: intracellular granule
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_33403
has exact synonym: intracellular sulfur globule
definition: Intracellular granule composed of elemental sulfur.
has exact synonym: sulfur globule
has exact synonym: sulphur granule
IAO_0000119: Wikipedia:Chromatiaceae The Chromatiaceae are the main family of purple sulfur bacteria. Many members conduct an anoxygenic photosynthesis. They are distinguished from the Ectothiorhodospiraceae by producing sulfur globules and storing them within their cells.
has exact synonym: sulphur globule
created by: Carrine Blank
has exact synonym: intracellular sulphur globule

cell having small gas vacuole
type: Class
equivalent class: Class
  intersection of: gas vacuolated cell
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0000587
subclass of: gas vacuolated cell
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0000587
has exact synonym: small gas vacuole
definition: A gas vacuolated cell, were gas vacuoles are small (decreased) in size.
has exact synonym: small vesicles
created by: Carrine Blank
has exact synonym: small vacuole

cell having large gas vacuole
type: Class
equivalent class: Class
  intersection of: gas vacuolated cell
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0000586
subclass of: gas vacuolated cell
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0000586
has exact synonym: large vacuole
definition: A gas vacuolated cell, were gas vacuoles are large (increased) in size.
created by: Carrine Blank
has exact synonym: large vesicles
has exact synonym: large gas vacuole

gas vacuolated cell
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: BFO_0000051
    some values from: gas vacuole
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0000117
has broad synonym: vacuolated
has broad synonym: vesicles
has broad synonym: vaculoes
created by: Carrine Blank
has broad synonym: vesiculated
definition: A prokaryotic cell that has gas vacuoles (gas vesicles).

polyphosphate granule
type: Class
equivalent class: Class
  intersection of: intracellular phosphorus storage granule
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_16838
subclass of: intracellular phosphorus storage granule
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_16838
has exact synonym: volutin granule
has exact synonym: metachromatic granule
definition: Intracellular phosphorus storage granule composed of polyphosphate.
IAO_0000119: Wikipedia:volutin_granules Volutin granules are an intracytoplasmic (inside the cytoplasm of a cell) storage form of complexed inorganic polyphosphate, the production of which is used as one of the identifying criteria when attempting to isolate Corynebacterium diphtheriae on Löffler's medium. Polyphosphate granules are called metachromatic granules due to their displaying the metachromatic effect; they appear red or blue when stained with the blue dyes methylene blue or toluidine blue.
created by: Carrine Blank

cyanophycin granule
type: Class
equivalent class: Class
  intersection of: intracellular carbon storage granule
  intersection of: intracellular nitrogen storage granule
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_65318
subclass of: intracellular carbon storage granule
subclass of: intracellular nitrogen storage granule
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_65318
IAO_0000119: Wikipedia:cyanophycin Cyanophycin, or multi-L-arginyl-poly (L-aspartic acid), is a non-protein, non-ribosomally produced amino acid polymer composed of an aspartic acid backbone and arginine side groups.
created by: Carrine Blank
definition: Intracellular carbon and nitrogen storage granule composed of cyanophycin macromolecules.

yeast water medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: Filippini M, Svercel M, Laczko E, Kaech A, Ziegler U & Bagheri HC. 2011. Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008. IJSEM 61:184-189. 0.5% yeast water
created by: Carrine Blank
definition: An organic-rich, liquid microbiological culture medium consisting of a solution of yeast extract (0.5%) in water.
IAO_0000119: From: Filippini M, Kaech A, Ziegler U & Bagheri HC. 2011. Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats. IJSEM 61:1418-1424. 0.5% yeast water

poly-beta-hydroxyalkanoate granule
type: Class
equivalent class: Class
  intersection of: intracellular carbon storage granule
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_78037
subclass of: intracellular carbon storage granule
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_78037
created by: Carrine Blank
IAO_0000119: Wikipedia:polyhydroxyalkanoates Polyhydroxyalkanoates or PHAs are linear polyesters produced in nature by bacterial fermentation of sugar or lipids. They are produced by the bacteria to store carbon and energy. More than 150 different monomers can be combined within this family to give materials with extremely different properties. These plastics are biodegradeable and are used in the production of bioplastics.
has exact synonym: PHA
has exact synonym: polyhydroxyalkanoate
definition: Intracellular carbon storage granule composed of poly-beta-hydroxyalkanoate.

poly-beta-hydroxybutyric acid granule
type: Class
equivalent class: Class
  intersection of: poly-beta-hydroxyalkanoate granule
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI 8295
subclass of: poly-beta-hydroxyalkanoate granule
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI 8295
has exact synonym: polyhydroxybutyric acid
definition: Intracellular carbon storage granule composed of poly-beta-hydroxybutyrate.
created by: Carrine Blank
has exact synonym: PHB
has exact synonym: polyhydroxybutyrate
has exact synonym: poly-beta-hydroxybutyrate
IAO_0000119: Wikipedia:polyhydroxybutyrate Polyhydroxybutyrate (PHB) is a polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probably the most common type of polyhydroxyalkanoate, but other polymers of this class are produced by a variety of organisms: these include poly-4-hydroxybutyrate (P4HB), polyhydroxyvalerate (PHV), polyhydroxyhexanoate (PHH), polyhydroxyoctanoate (PHO) and their copolymers.

starch granule
type: Class
equivalent class: Class
  intersection of: intracellular carbon storage granule
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_28017
subclass of: intracellular carbon storage granule
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_28017
has exact synonym: starch
definition: Intracellular carbon storage granule composed of starch.
created by: Carrine Blank

coursely granulated
type: Class
equivalent class: Class
  intersection of: granulated cell
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000586
has exact synonym: course granules
has exact synonym: large granule
created by: Carrine Blank
definition: Granulated cell, where the granual size is coarse (has an increased size).

finely granulated
type: Class
equivalent class: Class
  intersection of: granulated cell
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000587
has exact synonym: fine granules
created by: Carrine Blank
definition: Granulated cell, where the granule size is fine (has a decreased size).

numerously granulated
type: Class
equivalent class: Class
  intersection of: granulated cell
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0000470
  intersection of: Restriction
    on property: RO_0002180
    on class: intracellular granule
    min qualified cardinality: 2
has exact synonym: numerous granules
definition: Granulated cell, where there are many granules (an increased number) per cell.
created by: Carrine Blank

singularly granulated
type: Class
equivalent class: Class
  intersection of: granulated cell
  intersection of: Restriction
    on property: RO_0002180
    on class: intracellular granule
    qualified cardinality: 1
has exact synonym: single granule
has exact synonym: solitary granules
definition: Granulated cell, where there are one granule per cell.
created by: Carrine Blank
has exact synonym: singular granule

central endospore
type: Class
equivalent class: Class
  intersection of: endospore
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002268
subclass of: endospore
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002268
created by: Carrine Blank
definition: An endospore that forms in the middle of the cell.

lateral endospore
type: Class
equivalent class: Class
  intersection of: endospore
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0000626
subclass of: endospore
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0000626
created by: Carrine Blank
definition: An eEndospore that forms laterally to the long axis of a cell.

subterminal endospore
type: Class
equivalent class: Class
  intersection of: endospore
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002475
subclass of: endospore
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002475
created by: Carrine Blank
definition: An endospore that forms near the ends (or the poles) of the cell, but not at the extreme ends of the cell.

terminal endospore
type: Class
equivalent class: Class
  intersection of: endospore
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002476
subclass of: endospore
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002476
created by: Carrine Blank
definition: An endospore that forms at the pole (end) of the cell.

filaments
type: Class
subclass of: GO_0009289
definition: Amorphously described generic term for filament- or pili-like structures.
has exact synonym: tuft of filaments
has exact synonym: pili-like structures
created by: Carrine Blank

akinete
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell, specialized for dormancy
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1161
      union of: NCBITaxon 1189
  intersection of: Restriction
    on property: RO_0002354
    some values from: GO_0034302
created by: Carrine Blank
definition: A differentiated prokaryotic cell, found in the Nostocales (Cyanobacteria), which play a role in dormancy (such as overwintering in lake sediments). Characterized by thick cell walls.
IAO_0000119: From Wikipedia:akinete: An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell. It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. Under magnification, akinetes appear thick walled with granular-looking cytoplasms.

akinete, adjacent to heterocyte
type: Class
equivalent class: Class
  intersection of: MICRO_0001543
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002259
subclass of: MICRO_0001543
subclass of: Restriction
  on property: has position
  some values from: PATO_0002259
disjoint with: akinete, distal to heterocyte
has exact synonym: akinetes adjacent to heterocysts
IAO_0000119: Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563.
definition: An akinete which is proximally located to a heterocyst.
has exact synonym: paraheterocytic
created by: Carrine Blank

akinete, distal to heterocyte
type: Class
equivalent class: Class
  intersection of: MICRO_0001543
  intersection of: Restriction
    on property: has position
    some values from: Class
      intersection of: PATO_0001234
      intersection of: Restriction
        on property: has position
        all values from: Class
subclass of: MICRO_0001543
subclass of: Restriction
  on property: has position
  some values from: Class
    intersection of: PATO_0001234
    intersection of: Restriction
      on property: has position
      all values from: Class
        complement of: PATO_0002259
created by: Carrine Blank
has exact synonym: apoheterocytic
definition: An akinete that isdistally located from the heterocytes. May occur multiply in chains that, in the absence of combined nitrogen, are initiated at a site that is equidistant from two intercalary or terminal heterocysts.
has exact synonym: akinetes distant from heterocysts
IAO_0000119: Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563.

yeast extract tryptone medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
has broad synonym: YT
has exact synonym: YT broth
definition: An organic-rich, liquid microbiological culture medium containing pancreatic digest of casein, yeast extract, and sodium chloride. Used for the cultivation of Escherichia coli.
IAO_0000119: From: 2x Yeast Extract Tryptone (2X YT) Medium (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use 2x YT Medium is used for cultivating recombinant strains of Escherichia coli. Principles of the Procedure Peptone and yeast extract provide the necessary nutrients and cofactors required for excellent growth of E. coli. Sodium chloride is included to provide a suitable osmotic environment. 2x YT Medium formula per Liter: Pancreatic digest of casein 16.0 g Yeast extract 10.0 g Sodium chloride 5.0 g pH 7.0 ± 0.2

yeast extract tryptone agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
definition: An organic-rich, solid microbiological culture medium containing pancreatic digest of casein, yeast extract, and sodium chloride. Used for the cultivation of Escherichia coli.
IAO_0000119: From: 2x Yeast Extract Tryptone (2X YT) Medium (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use 2x YT Medium is used for cultivating recombinant strains of Escherichia coli. Principles of the Procedure Peptone and yeast extract provide the necessary nutrients and cofactors required for excellent growth of E. coli. Sodium chloride is included to provide a suitable osmotic environment. 2x YT Medium formula per Liter: Pancreatic digest of casein 16.0 g Yeast extract 10.0 g Sodium chloride 5.0 g Agar pH 7.0 ± 0.2
has exact synonym: YT agar

Todd-Hewitt medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_29377
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_34683
  intersection of: Restriction
    on property: has ingredient
    some values from: beef heart infusion
  intersection of: Restriction
    on property: has ingredient
    some values from: Biosate peptone
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
has related synonym: Todd-Hewitt broth
has exact synonym: Todd Hewitt Broth
has exact synonym: From: http://www.neogen.com/Acumedia/pdf/ProdInfo/7161_PI.pdf Intended Use Todd Hewitt Browth is used for the cultivation of steptococci and other fastidious microorganisms. Formula / Liter: Heart infusion (dehydrate) 3.1 g Yeast enriched peptone 20 g Dextrose 2 g Sodium chloride 2 g Disodium phosphate 0.4 g Sodium carbonate 2.5 g Final pH: 7.8 +/- 0.2 at 25˚C. Directions: 1. Dissolve 30 g of the medium in one liter of purified water. 2. Heat with frequent agitation to compeltely dissolve the medium. 3. Autoclave at 121 ˚C for 15 minutes.
definition: An organic-rich, liquid microbiological culture medium containing heart infusion (beef heart infusion), yeast enriched peptone (Biosate peptone), dextrose (D-glucose), sodium chloride, disodium hydrogenphosphate, and sodium carbonate. Used for the cultivation of Streptococci.

sheath
type: Class
subclass of: GO_0030112
has exact synonym: sheath
created by: Carrine Blank
has exact synonym: mucilaginous
has exact synonym: slime
has exact synonym: mucilage
IAO_0000119: Castenholz, 2001, in Bergey's Manual of Systematic Bacteriology, vol 1, 2nd ed., pg. 474. An "envelope" outside of the outer membrane.... variously called the sheath, glycocalyx, or capsule, or depending on the consistency, may be referred to as gel, mucilage, or slime. Many sheaths show a microfibrillar substructure. The sheaths of cyanobacteria are predominantly composed of polysaccharide, but in some strains >20% of the weight may consist of polypeptides. ... pigments may accumulate and mask the color of the cells.
has exact synonym: capsule
has exact synonym: extracellular polymeric material
definition: Part of the glycocalyx, or envelope of a prokaryotic cell, that lies outside the outer membrane.
has exact synonym: gel
has exact synonym: gelatinous matrix
has exact synonym: mucous
has exact synonym: extracellular polymeric substance
has exact synonym: ensheathed
has exact synonym: EPS
has exact synonym: exopolysaccharide

laminated sheath
type: Class
equivalent class: Class
  intersection of: MICRO_0000800
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002124
subclass of: MICRO_0000800
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002124
has exact synonym: layered sheath
has exact synonym: striated steath
has exact synonym: lamillated sheath
definition: A sheath having a layered, laminated (i.e., laminar) structure.
has exact synonym: striated sheathed structure
created by: Carrine Blank

pigmented sheath
type: Class
equivalent class: Class
  intersection of: MICRO_0000800
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002248
subclass of: MICRO_0000800
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002248
definition: A sheath that is pigmented (contains pigmented compounds).
definition: colored sheath
created by: Carrine Blank

proteinaceous sheath
type: Class
equivalent class: Class
  intersection of: sheath
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_36080
subclass of: sheath
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_36080
definition: A sheath comprised largely of protein.
created by: Carrine Blank

tryptone glucose extract agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: tryptone
  intersection of: Restriction
    on property: has ingredient
    some values from: beef extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
IAO_0000119: From: Tryptone Glucose Extract Agar (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Tryptone Glucose Extract Agar is used for cultivating and enumerating microorganisms in water and dairy products. Principles of the Procedure Nutrients, including amino acids, carbon compounds, carbohydrates, minerals and trace substances, are supplied by the tryptone, beef extract and dextrose. Agar is the solidifying agent in Tryptone Glucose Extract Agar. Formulae Difco™ Tryptone Glucose Extract Agar Approximate Formula* Per Liter Beef Extract.................................................................. 3.0 g Tryptone...................................................................... 5.0 g Dextrose (Glucose)....................................................... 1.0 g Agar.......................................................................... 15.0 g pH 7.0 ± 0.2 Difco™ m TGE Broth Approximate Formula* Per Liter Beef Extract.................................................................. 6.0 g Tryptone.................................................................... 10.0 g Dextrose (Glucose)....................................................... 2.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 7.0 ± 0.2
definition: An organic-rich, solid microbiological culture medium containing beef extract, tryptone, and glucose. Used for cultivation of microorganisms from water and dairy products.
has exact synonym: TGE agar

pseudopeptidoglycan-based cell wall
type: Class
equivalent class: Class
  intersection of: GO_0005618
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: CHEBI_59640
      intersection of: Restriction
        on property: BFO_0000051
        some values from: CHEBI_85106
  intersection of: Restriction
    on property: BFO_0000050
    all values from: NCBITaxon 2157
has exact synonym: pseudomurein
IAO_0000119: Wikipedia:pseudopeptidoglycan Pseudopeptidoglycan (also known as pseudomurein) is a major cell wall component of some archaea that differs from bacterial peptidoglycan in chemical structure, but resembles eubacterial peptidoglycan in morphology, function, and physical structure. The basic components are N-acetylglucosamine and N-acetyltalosaminuronic acid (peptidoglycan has N-acetylmuramic acid instead), which are linked by β-1,3-glycosidic bonds. Lysozyme, a host defense mechanism, is ineffective against organisms with pseudopeptidoglycan cell walls. Lysozyme can break β-1,4-glycosidic bonds to degrade peptidoglycan; however, pseudopeptidoglycan has β-1,3-glycosidic bonds, rendering lysozyme useless.
created by: Carrine Blank
definition: Cell wall composed a polymer of N-acetylglucosamine and N-acetyltalosaminuronic acid (2-amino-2-deoxy-L-taluronic acid), linked by beta-1,3-glycosidic bonds. Found in the archaeal domain of life.

Biosate peptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from extracts of proteinaceous material
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
has broad synonym: yeast enriched peptone
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): BBL™ Biosate™ Peptone is a mixed hydrolysate comprised of 65% pancreatic digest of casein and 35% yeast extract. Ash content is 7.7% NaCl content is 0.3%
has narrow synonym: BBL(TM) Biosate(TM) Peptone
definition: A mixed hydrolysate of pancreatic digest of casein (65%) and yeast extract (35%). Biosate is a Trademark of BD.
created by: Carrine Blank

teichoic acid-based cell wall
type: Class
equivalent class: Class
  intersection of: GO_0005618
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_30049
  intersection of: Restriction
    on property: BFO_0000050
    all values from: MICRO_0001372
created by: Carrine Blank
IAO_0000119: Wikipedia:teichoic acid Teichoic acids (cf. Greek τεῖχος, teīkhos, "wall", more specifically a fortification wall, as opposed to τοῖχος, toīkhos, a regular wall) are bacterial polysaccharides of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds. Teichoic acids are found within the cell wall of Gram-positive bacteria such as species in the genera Staphylococcus, Streptococcus, Bacillus, Clostridium, Corynebacterium and Listeria, and appear to extend to the surface of the peptidoglycan layer. Teichoic acids are not found in Gram-negative bacteria. They can be covalently linked to N-acetylmuramic acid of the peptidoglycan layer, to the lipids of the cytoplasmic membrane, or to a terminal D-alanine in the tetrapeptide crosslinkage between N-acetylmuramic acid units. Teichoic acids that remain anchored to lipids are referred to as lipoteichoic acids, while teichoic acids that are covalently bound to peptidoglycan are referred to as wall teichoic acids.
definition: Cell wall composed of polysaccharides of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds, found in the peptidoglycan cell walls of Gram-positive bacteria.

TBBP medium
type: Class
equivalent class: Class
  intersection of: tryptic soy broth
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_28669
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_59063
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 8309
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001230
definition: An organic-rich, liquid medium containing animal and plant peptones and sodium chloride. Supplemented with sheep blood, yeast extract, bacitracin, and polymyxin B. Used for the cultivation of Capnocytophaga spp.
created by: Carrine Blank
definition: From: Mashimo PA, Yamamoto Y, Nakamura M & Slots J. 1983. Selective recovery of oral Capnocytophaga spp. with sheep blood agar containing bacitracin and polymyxin B. J Clin Microbiol 17:187-91. TBBP medium consists of 4% Trypticase soy agar (BBL Microbiology Systems, Coceysville, Md.), 5% sheep blood, 0.1 % yeast extract, 50 micrograms of bacitracin per mL, and 100 micrograms of polymyxin B per mL.

TBBP agar
type: Class
equivalent class: Class
  intersection of: tryptic soy agar
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_28669
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_59063
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 8309
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001230
created by: Carrine Blank
IAO_0000119: From: Mashimo PA, Yamamoto Y, Nakamura M & Slots J. 1983. Selective recovery of oral Capnocytophaga spp. with sheep blood agar containing bacitracin and polymyxin B. J Clin Microbiol 17:187-91. TBBP medium consists of 4% Trypticase soy agar (BBL Microbiology Systems, Coceysville, Md.), 5% sheep blood, 0.1 % yeast extract, 50 micrograms of bacitracin per mL, and 100 micrograms of polymyxin B per mL.
definition: An organic-rich, solid medium containing animal and plant peptones and sodium chloride. Supplemented with sheep blood, yeast extract, bacitracin, and polymyxin B. Used for the cultivation of Capnocytophaga spp.

diazocyte
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell, specialized for nitrogen fixation
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1205
disjoint with: heterocyte
created by: Carrine Blank
definition: A prokaryotic differentiated cell capable of nitrogen fixation, found in Trichodesmium species (Cyanobacteria). Diazocytes are mostly found in the center cells of Trichodesmium filaments.
IAO_0000119: From Sandh, Xu & Bergman, 2012, Diazocyte development in the marine diazotrophic cyanobacterium Trichodesmium. Microbiology 158:345-352.: The establishment of non-diazotrophic cultures of the filamentous marine cyanobacterium Trichodesmium erythraeum IMS101 enabled the first detailed investigation of the process leading to the development of its unique nitrogen-fixing cell type, the diazocyte.

extracellular mineral precipitates
type: Class
subclass of: CHEBI_46662
subclass of: Restriction
  on property: RO_0001025
  some values from: GO_0031240
subclass of: Restriction
  on property: RO_0002220
  some values from: MICRO_0000848
created by: Carrine Blank
definition: Crystalline, microcystalline, nanocrystalline, or amorphous inorganic chemical precipitates that form outside the cell as a result of the local presence of the cell or the activities of the cell.

extracellular iron precipitates
type: Class
subclass of: extracellular mineral precipitates
subclass of: Restriction
  on property: has chemical composition
  some values from: Class
    union of: CHEBI_50817
    union of: CHEBI_86235
    union of: CHEBI_86471
created by: Carrine Blank
has broad synonym: extracellular iron
definition: Crystalline, microcystalline, nanocrystalline, or amorphous inorganic chemical precipitates of iron minerals that form outside the cell as a result of the local presence of the cell or the activities of the cell.

extracellular sulfur globule
type: Class
subclass of: extracellular mineral precipitates
subclass of: Restriction
  on property: BFO_0000054
  some values from: NCBITaxon_72276
subclass of: Restriction
  on property: has chemical composition
  some values from: CHEBI_33403
definition: Crystalline, microcystalline, nanocrystalline, or amorphous inorganic chemical precipitates of elemental sulfur that forms outside the cell as a result of the local presence of the cell or the activities of the cell. Produced by Ectothiorhodospiraceae.
has exact synonym: extracellular sulphur granule
has exact synonym: extracellular sulfur globule
IAO_0000119: Wikipedia:Ectothiorhodospiraceae The Ectothiorhodospiraceae are a family of purple sulfur bacteria, distinguished by producing sulfur globules outside of their cells.
created by: Carrine Blank

fimbriae
type: Class
subclass of: GO_0009289
created by: Carrine Blank
definition: A pilus, that is thin and short.
has exact synonym: fimbriated
IAO_0000119: Wikipedia:Fimbria_(bacteriology) In bacteriology, a fimbria [(plural fimbriae); also referred to as a pilus (plural pili) by some scientists] is an appendage composed of curlin proteins that can be found on many Gram-negative and some Gram-positive bacteria that is thinner and shorter than a flagellum. This appendage ranges from 3-10 nanometers in diameter and can be up to several micrometers long. Fimbriae are used by bacteria to adhere to one another and to adhere to animal cells and some inanimate objects. A bacterium can have as many as 1,000 fimbriae. Fimbriae are only visible with the use of an electron microscope. They may be straight or flexible.
has exact synonym: fimbria

SWC medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32145
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32954
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86345
  intersection of: Restriction
    on property: has ingredient
    some values from: tryptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: beef extract
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      intersection of: MICRO_0001715
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0001163
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: A dilute organic-containing, liquid microbiological culture medium containing tryptone, yeast extract, beef extract, and acetate, in a base of half-strength artifical seawater.
IAO_0000119: From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. SWC contained (per liter of 1/2 strength artificial seawater [ASW]): tryptone, 0.5 g; yeast extract, 0.5 g; beef extract, 0.2 g; sodium acetate, 0.2 g. The pH was adjusted to 7.6 with a dilute solution of NaOH. ASW, 1/2 strength, contained (per liter): NaCl, 12.0 g; MgSO4x7H2O, 3.5 g; MgCl2x6H2O, 2.6 g; CaCl2x2H2O, 0.55 g; KCl, 0.35 g.
created by: Carrine Blank

tetrazolium reduction assay
type: Class
equivalent class: Class
  intersection of: MICRO_0000852
  intersection of: Restriction
    on property: is an assay for the metabolic substrate
    some values from: Class
      union of: CHEBI_75193
      union of: CHEBI_75198
      union of: CHEBI_78019
  intersection of: Restriction
    on property: is an assay for the biological process of
    some values from: GO_0045333
subclass of: MICRO_0000852
subclass of: Restriction
  on property: is an assay for the metabolic substrate
  some values from: Class
    union of: CHEBI_75193
    union of: CHEBI_75198
    union of: CHEBI_78019
subclass of: Restriction
  on property: is an assay for the biological process of
  some values from: GO_0045333
definition: An assay for the ability of a microorganism to reduce a compound that contains a tetrazoleum moiety. Tetrazolium compounds are redox indicators of microbial oxidation and reduction, and hence microbial respiration.
created by: Carrine Blank

multiply flagellated
type: Class
equivalent class: Class
  intersection of: flagellated cell
  intersection of: Restriction
    on property: RO_0002180
    on class: GO_0009288
    min qualified cardinality: 1
subclass of: flagellated cell
definition: Flagellated cell where the cell has more than one flagellum.
has exact synonym: numerous flagella
created by: Carrine Blank
has exact synonym: polytrichous

flagellated cell
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      union of: GO_0009288
      union of: GO_0055040
has broad synonym: flagellated
created by: Carrine Blank
definition: Prokaryotic cell which has either a bacterial-type flagellum (or flagella) or a periplasmic flagellum.

singly flagellated
type: Class
equivalent class: Class
  intersection of: flagellated cell
  intersection of: Restriction
    on property: RO_0002180
    on class: GO_0009288
    qualified cardinality: 1
created by: Carrine Blank
definition: Flagellated cell where the cell has only one flagellum.

monotrichous cell
type: Class
equivalent class: Class
  intersection of: singly flagellated
  intersection of: Restriction
    on property: has position
    some values from: Class
      intersection of: PATO_0000627
      intersection of: PATO_0002476
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000616
IAO_0000119: http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Monotrichous: Single polar flagellum e.g. Vibrio cholerae (Mneomonics: Mono means one)
has exact synonym: single flagellum
has exact synonym: single flagella
has exact synonym: monopolar flagella
has exact synonym: polar flagellum
has exact synonym: monopolar flagellum
definition: Flagellated cell where the cell has a single flagellum located at the end (pole) of the cell.
has broad synonym: monotrichous
has exact synonym: monotrichous flagella
created by: Carrine Blank

amphitrichous cell
type: Class
equivalent class: Class
  intersection of: multiply flagellated
  intersection of: Restriction
    on property: has position
    some values from: Class
      intersection of: PATO_0000627
      intersection of: PATO_0002476
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0001324
  intersection of: Restriction
    on property: RO_0002180
    on class: GO_0009288
    qualified cardinality: 2
created by: Carrine Blank
has broad synonym: amphitrichous
definition: Flagellated cell where the cell has two flagella, each located at the ends (poles) of the cell.
IAO_0000119: http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Amphitrichous: Single flagellum at both ends e.g. Alcaligenes faecalis (Mneomonics: Remember: the characteristics of Amphibians: live both in land and water)

lophotrichous cell
type: Class
equivalent class: Class
  intersection of: multiply flagellated
  intersection of: Restriction
    on property: has position
    some values from: PATO_0002476
  intersection of: Restriction
    on property: has structure
    some values from: PATO_0001861
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000616
  intersection of: Restriction
    on property: RO_0002180
    on class: GO_0009288
    min qualified cardinality: 2
created by: Carrine Blank
has exact synonym: tuft of polar flagella
definition: Flagellated cell where the cell has multiple flagella, located in a tuft at the end (pole) of the cell.
has related synonym: bundles of flagella
IAO_0000119: http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Lophotrichous: Tuft of flagella at one or both ends e.g. Spirilla
has exact synonym: polar flagella
has exact synonym: polar bundle of flagella
has exact synonym: polar tuft of flagella
has broad synonym: lophotrichous
has exact synonym: monopolar polytrichous flagella

cell having periplasmic flagella
type: Class
equivalent class: Class
  intersection of: flagellated cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0055040
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0000616
subclass of: flagellated cell
subclass of: Restriction
  on property: has symmetry
  some values from: PATO_0000616
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0055040
has broad synonym: axial fibrils
has exact synonym: axial filaments
has exact synonym: periplasmic fibrils
definition: Flagellated cell where the cell has multiple flagella, each located in tufts in the periplasmic space.
IAO_0000119: http://microbewiki.kenyon.edu/index.php/Spirochaeta The morphology and cellular structure of Spirochaeta spp. (and most other Spirochetes) is unique among prokaryotes. The cells are helical in shape and consist of an outer membrane, axial filaments (ultrastructurally similar to bacterial flagella), and a protoplasmic cylinder. The outer membrane or the outer sheath surrounds all of the structures including the axial filaments and the protoplasmic cylinder. The protoplasmic cylinder is the cell body of the organism. It is coiled and is composed of the cytoplasm, the nuclear region and the peptidoglycan-cytoplasmic membrane complex. The axial filaments are usually called the periplasmic flagella but are also known as periplasmic fibrils, axial fibrils and endoflagella.
created by: Carrine Blank
has exact synonym: periplasmic flagella
has exact synonym: endoflagella

peritrichous cell
type: Class
equivalent class: Class
  intersection of: multiply flagellated
  intersection of: Restriction
    on property: has position
    some values from: PATO_0001772
  intersection of: Restriction
    on property: has symmetry
    some values from: PATO_0001325
  intersection of: Restriction
    on property: has spatial pattern
    some values from: PATO_0001566
  intersection of: Restriction
    on property: RO_0002180
    on class: GO_0009288
    min qualified cardinality: 2
has exact synonym: lateral flagella
has related synonym: peritrichously
IAO_0000119: http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Peritrichous: Flagella surrounding the cell, e.g. Typhoid bacilli (Mneomonic: Remember Periphery)
definition: Flagellated cell where the cell has multiple flagella, all located at the periphery of the cell.
has related synonym: peritrichous
created by: Carrine Blank

tumbling motility
type: Class
subclass of: GO_0071978
database cross reference: Wikipedia:Listeria
definition: Prokaryotic motility that is characterized microscopically by end-over-end tumbling and employs a flagellum. This type of motility is typical of Listeria.
created by: Carrine Blank
has exact synonym: tumbling

heterocyte
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell, specialized for nitrogen fixation
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1161
      union of: NCBITaxon 1189
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0052386
  intersection of: Restriction
    on property: RO_0002354
    some values from: GO_0043158
has exact synonym: heterocystous
has exact synonym: heterocytous
created by: Carrine Blank
has exact synonym: heterocysts
IAO_0000119: From Wikipedia:heterocyst: Heterocysts are specialized nitrogen-fixing cells formed during nitrogen starvation by some filamentous cyanobacteria, such as Nostoc punctiforme, Cylindrospermum stagnale, and Anabaena sphaerica. They fix nitrogen from dinitrogen (N2) in the air using the enzyme nitrogenase, in order to provide the cells in the filament with nitrogen for biosynthesis. Nitrogenase is inactivated by oxygen, so the heterocyst must create a microanaerobic environment.
definition: A prokaryotic differentiated cell capable of nitrogen fixation, found in the filamentous Nostocales (Cyanobacteria). Heterocytes (which differentiate into heterocysts) have thick cell walls which exclude oxygen in the air and allow nitrogen fixation to occur. Are terminally differentiated cells, incapable of carrying out photosynthesis.

intercalary heterocyte
type: Class
equivalent class: Class
  intersection of: heterocyte
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002268
subclass of: heterocyte
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002268
disjoint with: terminal heterocyte
has exact synonym: bipored heterocyte
created by: Carrine Blank
definition: A heterocyte which develops at the middle or near the end (but not the end) of a filament (trichome).
has exact synonym: intercalary heterocyst
IAO_0000119: From Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563.: In the absence of combined nitrogen (ammonium or nitrate), 5-10% of the vegetative cells differentiate into heterocysts. These specialized cells are the sites of aerobic nitrogen fixation and may occupy terminal or intercalary positions in the trichomes.
has exact synonym: lateral heterocyte

terminal heterocyte
type: Class
equivalent class: Class
  intersection of: heterocyte
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002476
subclass of: heterocyte
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002476
has exact synonym: terminal heterocyst
created by: Carrine Blank
IAO_0000119: From Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563.: In the absence of combined nitrogen (ammonium or nitrate), 5-10% of the vegetative cells differentiate into heterocysts. These specialized cells are the sites of aerobic nitrogen fixation and may occupy terminal or intercalary positions in the trichomes.
definition: A heterocyte which develops at the end of a filament (trichome).
has exact synonym: unipored heterocyte

hormogonium
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell, specialized for asexual reproduction
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1150
      union of: NCBITaxon 1161
      union of: NCBITaxon 1189
  intersection of: Restriction
    on property: RO_0000086
    some values from: cell chain
  intersection of: Restriction
    on property: RO_0002215
    some values from: gliding motility
definition: Prokaryotic differentiated cell specialized for asexual reproduction comprised of short chains of motile filaments, found in the Nostocales, Stigonematales/Stigonemataceae, and Oscillatoriales (Cyanobacteria). Hormogonia are shorter than the typical length of vegetative filaments.
created by: Carrine Blank
has exact synonym: hormogonia
IAO_0000119: From Wikipedia:hormogonium: Hormogonia are motile filaments of cells formed by some cyanobacteria in the order Nostocales and Stigonematales. They are formed during asexual reproduction in unicellular, filamentous cyanobacteria some contain heterocysts and akinetes.

SWC-m medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31206
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63036
  intersection of: Restriction
    on property: has ingredient
    some values from: trace elements solution TES
  intersection of: Restriction
    on property: has ingredient
    some values from: tryptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: beef extract
  intersection of: Restriction
    on property: has ingredient
    some values from: Staley vitamin solution
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001715
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: CHEBI_17029
      union of: CHEBI_28017
      union of: CHEBI_35020
      union of: MICRO_0001242
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: SWCm salts
created by: Carrine Blank
definition: A dilute organic-containing, liquid microbiological culture medium containing tryptone, yeast extract, beef extract, and acetate, in a base of full-strength artifical seawater.
IAO_0000119: From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. SWC-m contained (per liter of full strength ASW): KH2PO4, 0.01 g; ferric citrate, 0.001 g; NH4Cl, 0.4 g; yeast extract, 0.4 g; beef extract, 0.4 g; tryptone, 0.4 g; vitamins, 10 mL; trace elements solution (TES), 2.0 mL; carbon source, 0.2 g; pH 7.0. The following macromolecular carbon sources were tested for hydrolysis on plates: starch, 1.0%; tributyrin, 1.0%; chitin, 1.0%; casein, 0.5%. xxxxxxx From: Irgens RL. 1977. Meniscus, a new genus of aerotolerant, gas-vacuolated bacteria. Int J Syst Bacteriol 27(1):38-43. The TES, modified from Pfennig’s formula (personal communication), contained (per liter): ZnSO4x7H2O, 0.10 g; MnCl2x4H2O, 0.03 g; H3BO3, 0.3 g; CoCl2x6H20, 0.2 g; CuCl2x2H2O,0.01 g ; NiCl2x6H2O, 0.02 g; Na2MoO4x 2H2O, 0.03g; pH3 to 4. xxxxxxx From: Staley JT. 1981. The genera Prosthecomicrobium and Ancalomicrobium. In: Starr MP, Stolp H, Truper HG, Balows A,Schlegel HG, (eds). The prokaryotes. Berlin: Springer-Verlag. Pg 68. Vitamin Solution B12 0.1 mg Biotin 2 mg Calcium pantothenate 5 mg Folic acid 2 mg nicotinamide 5 mg pyridoxine HCl 10 mg riboflavin 5 mg thiamine HCL 5 mg Add distilled water up to 1 L and sotre in 4˚C in a dark container.

conjugative pili
type: Class
subclass of: GO_0009289
definition: Pilus involved in the transfer of DNA from one bacterium (the donor) to another (the recipient).
IAO_0000119: Wikipedia:pilus Conjugative pili allow the transfer of DNA between bacteria, in the process of bacterial conjugation. They are sometimes called "sex pili", in analogy to sexual reproduction, because they allow for the exchange of genes via the formation of "mating pairs". Perhaps the most well-studied is the F pilus of Escherichia coli, encoded by the F plasmid or fertility factor.
created by: Carrine Blank

SWC-m agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31206
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63036
  intersection of: Restriction
    on property: has ingredient
    some values from: trace elements solution TES
  intersection of: Restriction
    on property: has ingredient
    some values from: tryptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: beef extract
  intersection of: Restriction
    on property: has ingredient
    some values from: Staley vitamin solution
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001715
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: CHEBI_17029
      union of: CHEBI_28017
      union of: CHEBI_35020
      union of: MICRO_0001242
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
definition: A dilute organic-containing, liquid microbiological culture medium containing tryptone, yeast extract, beef extract, and acetate, in a base of full-strength artifical seawater.
IAO_0000119: From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. Agar slants containted 1.5 % agar, agar plates contained 2.0 % agar, and soft agar tubes contained 0.2 % agar.
has exact synonym: SWCM agar
IAO_0000119: From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. SWC-m contained (per liter of full strength ASW): KH2PO4, 0.01 g; ferric citrate, 0.001 g; NH4Cl, 0.4 g; yeast extract, 0.4 g; beef extract, 0.4 g; tryptone, 0.4 g; vitamins, 10 mL; trace elements solution (TES), 2.0 mL; carbon source, 0.2 g; pH 7.0. The following macromolecular carbon sources were tested for hydrolysis on plates: starch, 1.0%; tributyrin, 1.0%; chitin, 1.0%; casein, 0.5%. xxxxxxx From: Irgens RL. 1977. Meniscus, a new genus of aerotolerant, gas-vacuolated bacteria. Int J Syst Bacteriol 27(1):38-43. The TES, modified from Pfennig’s formula (personal communication), contained (per liter): ZnSO4x7H2O, 0.10 g; MnCl2x4H2O, 0.03 g; H3BO3, 0.3 g; CoCl2x6H20, 0.2 g; CuCl2x2H2O,0.01 g ; NiCl2x6H2O, 0.02 g; Na2MoO4x 2H2O, 0.03g; pH3 to 4. xxxxxxx From: Staley JT. 1981. The genera Prosthecomicrobium and Ancalomicrobium. In: Starr MP, Stolp H, Truper HG, Balows A,Schlegel HG, (eds). The prokaryotes. Berlin: Springer-Verlag. Pg 68. Vitamin Solution B12 0.1 mg Biotin 2 mg Calcium pantothenate 5 mg Folic acid 2 mg nicotinamide 5 mg pyridoxine HCl 10 mg riboflavin 5 mg thiamine HCL 5 mg Add distilled water up to 1 L and sotre in 4˚C in a dark container.

distinctly shaped colony
type: Class
equivalent class: Class
  intersection of: morphologically distinct colony
  intersection of: Class
    intersection of: morphologically distinct colony
    intersection of: Restriction
      on property: has shape
      some values from: PATO_0000052
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has broad synonym: elevated
definition: A colony that has a distinct morphology manifested in its 2D or 3D shape.

physically distinct colony
type: Class
equivalent class: Class
  intersection of: MICRO_0002468
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001018
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
definition: A prokaryotic colony that has distinct physical characteristics (qualities).
created by: Carrine Blank

colony having distinct spatial pattern
type: Class
equivalent class: Class
  intersection of: physically distinct colony
  intersection of: Restriction
    on property: has spatial pattern
    some values from: PATO_0000060
definition: A colony having distinct physical quality that manifests in the spatial pattern of the elements of the colony.
created by: Carrine Blank

colony having distinct optical quality
type: Class
equivalent class: Class
  intersection of: colony having distinct electromagnetic (EM) radiation quality
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001300
definition: A prokaryotic colony that manifests in how light (visible electromagnetic radiation) passes through the colony.
created by: Carrine Blank

texturally distinct colony
type: Class
equivalent class: Class
  intersection of: morphologically distinct colony
  intersection of: Restriction
    on property: has texture
    some values from: PATO_0000150
subclass of: morphologically distinct colony
subclass of: Restriction
  on property: has texture
  some values from: PATO_0000150
created by: Carrine Blank
definition: A colony with a texture that manifests in the appearance of the surface characteristics.

satellite colonies
type: Class
equivalent class: Class
  intersection of: morphologically distinct colony
  intersection of: Class
    intersection of: Restriction
      on property: BFO_0000051
      some values from: Class
        intersection of: IDO_0000615
        intersection of: Restriction
    intersection of: Restriction
      on property: RO_0002219
      some values from: Class
        intersection of: IDO_0000615
        intersection of: Restriction
subclass of: morphologically distinct colony
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: IDO_0000615
      intersection of: Restriction
        on property: has size
        some values from: PATO_0000586
  intersection of: Restriction
    on property: RO_0002219
    some values from: Class
      intersection of: IDO_0000615
      intersection of: Restriction
        on property: has size
        some values from: PATO_0000587
created by: Carrine Blank
has exact synonym: satellite colonies
has broad synonym: satellite behavior
definition: A prokaryotic colony where small colonies surround larger colonies on an agar (or other solid) surface.
IAO_0000119: http://www.yourdictionary.com/satellite#americanheritage Satellite colonies occur when tiny colonies are found to surround a larger central colony.
has broad synonym: satellites

dense center colony
type: Class
equivalent class: Class
  intersection of: colony having distinct spatial pattern
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: BSPO_0000075
      intersection of: Restriction
        on property: has spatial pattern
        some values from: PATO_0001809
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: BSPO_0000078
      intersection of: Restriction
        on property: has spatial pattern
        some values from: PATO_0001609
subclass of: colony having distinct spatial pattern
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: BSPO_0000078
    intersection of: Restriction
      on property: has spatial pattern
      some values from: PATO_0001609
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: BSPO_0000075
    intersection of: Restriction
      on property: has spatial pattern
      some values from: PATO_0001809
created by: Carrine Blank
definition: A colony with distinct spatial pattern where the center part of the colony is tight (densely compacted) and the outer part of the colony is sparse (not densely compacted).
has broad synonym: dense center
has exact synonym: diffuse center colony

dry colony
type: Class
equivalent class: Class
  intersection of: physically distinct colony
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001824
subclass of: physically distinct colony
subclass of: Restriction
  on property: has physical quality
  some values from: PATO_0001824
disjoint with: glistening colony
disjoint with: mucoid colony
has exact synonym: dry colony
created by: Carrine Blank
definition: A colony having distinct physical quality that is dry (has a brittle, friable texture that breaks apart).
has broad synonym: friable
has broad synonym: dry

dull colony
type: Class
equivalent class: Class
  intersection of: colony having distinct optical quality
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0000328
subclass of: colony having distinct optical quality
subclass of: Restriction
  on property: has physical quality
  some values from: PATO_0000328
disjoint with: glistening colony
created by: Carrine Blank
has broad synonym: not shiny
definition: A colony with distinct optical quality that is dull (not shiny, with a low saturation) in its appearance.
has broad synonym: dull
has exact synonym: dull colony

granular center colony
type: Class
equivalent class: Class
  intersection of: MICRO_0001518
  intersection of: Restriction
    on property: has structure
    some values from: PATO_0001759
subclass of: MICRO_0001518
subclass of: Restriction
  on property: has structure
  some values from: PATO_0001759
has exact synonym: granular center colony
definition: A colony with a structure that has a grainy, or granular, appearance in its center.
has broad synonym: fine granulation
has broad synonym: granular
has broad synonym: granular centers
created by: Carrine Blank

glistening colony
type: Class
equivalent class: Class
  intersection of: colony having distinct electromagnetic (EM) radiation quality
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001373
has broad synonym: moist
has broad synonym: shiny surface
has broad synonym: wet
has broad synonym: shining aspect
has broad synonym: glistening
has broad synonym: shiny
definition: A colony with distinct EM radiation quality that has a wet appearance.
has exact synonym: glistening colony
created by: Carrine Blank
has broad synonym: shining
has broad synonym: glossy

mucoid colony
type: Class
equivalent class: Class
  intersection of: MICRO_0001518
  intersection of: Restriction
    on property: has structure
    some values from: PATO_0001371
subclass of: MICRO_0001518
subclass of: Restriction
  on property: has structure
  some values from: PATO_0001371
IAO_0000119: http://www.medilexicon.com/medicaldictionary.php
created by: Carrine Blank
has broad synonym: mucoid
has broad synonym: mucous
definition: A colony with a structure that is mucoid (has a sticky appearance due to the presence of exopolysaccharide capsular material).
has exact synonym: mucoid colony

rough colony
type: Class
equivalent class: Class
  intersection of: texturally distinct colony
  intersection of: Restriction
    on property: has texture
    some values from: PATO_0000700
subclass of: texturally distinct colony
subclass of: Restriction
  on property: has texture
  some values from: PATO_0000700
disjoint with: smooth colony
has exact synonym: rough colony
definition: A colony with a texture that is rough (i.e. not smooth).
created by: Carrine Blank
has exact synonym: rough surface

smooth colony
type: Class
equivalent class: Class
  intersection of: texturally distinct colony
  intersection of: Restriction
    on property: has texture
    some values from: PATO_0000701
subclass of: texturally distinct colony
subclass of: Restriction
  on property: has texture
  some values from: PATO_0000701
has broad synonym: smooth
has broad synonym: smooth-surfaced
has exact synonym: smooth colony
definition: A colony with a texture that is smooth.
created by: Carrine Blank

dendritic colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002045
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002045
has exact synonym: dendritic colony
created by: Carrine Blank
definition: A colony with a shape that has raised, branching features starting in the center of the colony, with an appearance that resembles veins or branches of a tree.
has broad synonym: veined
has broad synonym: dendiritic

wrinkled colony
type: Class
equivalent class: Class
  intersection of: texturally distinct colony
  intersection of: Restriction
    on property: has texture
    some values from: PATO_0001810
subclass of: texturally distinct colony
subclass of: Restriction
  on property: has texture
  some values from: PATO_0001810
has broad synonym: rugose
definition: A colony with a texture that is wrinkled (has a shriveled appearance).
has broad synonym: shriveled
created by: Carrine Blank
has exact synonym: wrinkled colony

cloudy colony
type: Class
equivalent class: Class
  intersection of: colony having distinct optical quality
  intersection of: Restriction
    on property: has physical quality
    some values from: Class
      intersection of: PATO_0000963
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0001354
subclass of: colony having distinct optical quality
subclass of: Restriction
  on property: has physical quality
  some values from: Class
    intersection of: PATO_0000963
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0001354
definition: A colony with distinct optical quality that is cloudy (semi-translucent or semi-opaque, whitish in color).
has broad synonym: semi-translucent
has exact synonym: cloudy colony
has broad synonym: cloudy
created by: Carrine Blank
has broad synonym: semi-opaque

iridescent colony
type: Class
equivalent class: Class
  intersection of: MICRO_0001525
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002277
subclass of: MICRO_0001525
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002277
definition: A colony having a distinct process quality where the colony is iridescent (appears to change color as the angle of illumination changes).
has broad synonym: iridescent
IAO_0000119: http://en.wikipedia.org/wiki/Iridescence
has broad synonym: opalescent
has exact synonym: irridescent colony
created by: Carrine Blank

pigmented colony
type: Class
equivalent class: Class
  intersection of: MICRO_0001518
  intersection of: Restriction
    on property: has structure
    some values from: PATO_0002248
subclass of: MICRO_0001518
subclass of: Restriction
  on property: has structure
  some values from: PATO_0002248
definition: A colony with a structure that contains coloration due to the presence of pigment compounds that absorb particular wavelengths of light.
has broad synonym: coloured
has broad synonym: colored
created by: Carrine Blank
has exact synonym: pigmented colony

opaque colony
type: Class
equivalent class: Class
  intersection of: colony having distinct optical quality
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0000963
subclass of: colony having distinct optical quality
subclass of: Restriction
  on property: has physical quality
  some values from: PATO_0000963
created by: Carrine Blank
has exact synonym: opaque colony
definition: A colony with distinct optical quality that is opaque (where light does not pass through).
has broad synonym: opaque

bovine albumin
type: Class
equivalent class: Class
  intersection of: defined organic chemical mixture
  intersection of: Class
    intersection of: Restriction
      on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
      some values from: NCBITaxon 9913
    intersection of: Restriction
      on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
      some values from: UBERON_0000178
  intersection of: Restriction
    on property: has chemical composition
    some values from: CHEBI_36080
created by: Carrine Blank
IAO_0000119: From: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/AnimalBloodProd.htm Bovine Albumin contains bovine albumin fraction V, 0.2% in 0.85% saline solution.
definition: A blood medium ingredient comprised of bovine (Bos taurus) albumin (a mixture of protein derived from blood). Used in the cultivation of microorganisms.

translucent colony
type: Class
equivalent class: Class
  intersection of: colony having distinct optical quality
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001354
subclass of: colony having distinct optical quality
subclass of: Restriction
  on property: has physical quality
  some values from: PATO_0001354
has exact synonym: translucent colony
created by: Carrine Blank
has broad synonym: translucent
has broad synonym: semi-transparent
has broad synonym: almost clear
definition: A colony with distinct optical quality that is translucent, where much light is able to pass through it without absorption of particular wavelengths of light.

transparent colony
type: Class
equivalent class: Class
  intersection of: colony having distinct optical quality
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0000964
subclass of: colony having distinct optical quality
subclass of: Restriction
  on property: has physical quality
  some values from: PATO_0000964
has broad synonym: transparent
created by: Carrine Blank
has broad synonym: clear
has exact synonym: transparent colony
definition: A colony with distinct optical quality that is completely or nearly completely clear or transparent, where nearly all light is able to pass through it.

anaerobic respiration, using sulfate as electron acceptor
type: Class
equivalent class: Class
  intersection of: GO_0009061
  intersection of: Restriction
    on property: uses electron acceptor
    some values from: CHEBI_16189
subclass of: GO_0009061
subclass of: Restriction
  on property: uses electron acceptor
  some values from: CHEBI_16189
definition: The process of anaerobic respiration, where sulfate is reduced to sulfite, tetrathionate, thiosulfate, elemental sulfur, or hydrogen sulfide.
created by: Carrine Blank

pyrazinamidase activity
type: Class
subclass of: GO_0016811
definition: A hydrolase activity, which hydrolyzes pyrazinamide (a drug used to treat tuberculosis) into pyrazinoic acid (the active agent against tuberculosis). Pyrazinamidase catalyzes the following reaction: Pyrazinamide + H2O <=> pyrazinoic acid (pyrazine-2-carboxylic acid) + NH3.
database cross reference: E.C. 3.5.1.b15
created by: Carrine Blank

anaerobic respiration, using elemental sulfur as electron acceptor
type: Class
equivalent class: Class
  intersection of: GO_0009061
  intersection of: Restriction
    on property: uses electron acceptor
    some values from: CHEBI_33403
subclass of: GO_0009061
subclass of: Restriction
  on property: uses electron acceptor
  some values from: CHEBI_33403
definition: The process of anaerobic respiration, where elemental sulfur reduced to hydrogen sulfide.
created by: Carrine Blank

aerobic respiration, using hydrogen sulfide as electron donor
type: Class
equivalent class: Class
  intersection of: GO_0019414
  intersection of: Restriction
    on property: uses electron donor
    some values from: CHEBI_26822
subclass of: GO_0019414
subclass of: Restriction
  on property: uses electron donor
  some values from: CHEBI_26822
definition: The process of aerobic respiration, where hydrogen sulfide is oxidized (using oxygen) to elemental sulfur, thiosulfate, tetrathionate, sulfite, or sulfate.
created by: Carrine Blank

aerobic respiration, using elemental sulfur as electron donor
type: Class
equivalent class: Class
  intersection of: GO_0019414
  intersection of: Restriction
    on property: uses electron donor
    some values from: CHEBI_33403
subclass of: GO_0019414
subclass of: Restriction
  on property: uses electron donor
  some values from: CHEBI_33403
definition: The process of aerobic respiration, where elemental sulfur is oxidized (using oxygen) to thiosulfate, tetrathionate, sulfite, or sulfate.
created by: Carrine Blank

anaerobic respiration, using thiosulfate as electron acceptor
type: Class
equivalent class: Class
  intersection of: GO_0009061
  intersection of: Restriction
    on property: uses electron acceptor
    some values from: Class
      union of: CHEBI_26977
      union of: Restriction
        on property: uses electron acceptor
        some values from: CHEBI_16094
subclass of: GO_0009061
subclass of: Restriction
  on property: uses electron acceptor
  some values from: Class
    union of: CHEBI_26977
    union of: Restriction
      on property: uses electron acceptor
      some values from: CHEBI_16094
definition: The process of anaerobic respiration, where thiosulfate is reduced to elemental sulfur or hydrogen sulfide.
created by: Carrine Blank

anaerobic respiration, using sulfite as electron acceptor
type: Class
equivalent class: Class
  intersection of: GO_0009061
  intersection of: Restriction
    on property: uses electron acceptor
    some values from: CHEBI_17359
subclass of: GO_0009061
subclass of: Restriction
  on property: uses electron acceptor
  some values from: CHEBI_17359
created by: Carrine Blank
definition: The process of anaerobic respiration, where sulfite is reduced to tetrationate, thiosulfate, elemental sulfur, or hydrogen sulfide.

chymotrypsin assay using BTEE
type: Class
equivalent class: Class
  intersection of: MICRO_0000672
  intersection of: Restriction
    on property: is an assay for the enzymatic substrate
    some values from: CHEBI_91051
  intersection of: Restriction
    on property: is an assay for the enzymatic product
    some values from: CHEBI_90091
definition: Chymotrypsin assay that uses the substrate N-Benzoyl-L-tyrosine ethyl ester (BTEE). Chymotrypsin activity will cleave the substrate, releasing N-Benzoyl-L-tyrosine. The presence of this produce is measured by recording the increase in absorbance at 256 nm.
created by: Carrine Blank

chymotrypsin assay using N-benzoyl-Phe-pNA
type: Class
equivalent class: Class
  intersection of: MICRO_0000672
  intersection of: Restriction
    on property: is an assay for the enzymatic substrate
    some values from: CHEBI_91056
  intersection of: Restriction
    on property: is an assay for the enzymatic product
    some values from: CHEBI_88330
created by: Carrine Blank
has related synonym: N-benzoyl-D-L-phenylalanine 2-naphthylamide
definition: Chymotrypsin assay that uses the substrate N-benzoyl-D-L-phenylalanine-2-naphthylamide at pH 7.1. Trypsin activity will cleave the substrate, releasing 2-naphthylamide. When reacted with Fast Blue BB it forms a colored insoluble precipitate that is purple in color.

trypsin assay using NA
type: Class
equivalent class: Class
  intersection of: MICRO_0000673
  intersection of: Restriction
    on property: is an assay for the enzymatic substrate
    some values from: CHEBI_91062
  intersection of: Restriction
    on property: is an assay for the enzymatic product
    some values from: CHEBI_88330
definition: Uses the substrate N-benzoyl-D-L-arginine 2-naphthylamide at pH 8.5. Trypsin activity will cleave the substrate, releasing 2-naphthylamide. When reacted with Fast Blue BB it forms a colored insoluble precipitate that is orange in color.
has related synonym: N-benzoyl-arginine-2-naphthylamide
created by: Carrine Blank
has related synonym: N-benzoyl-DL-arginine-2-naphthylamide

alanyl alanine arylamidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
definition: An aminopeptidaseeptidase activity which cleaves the chromogenic substrate L-alanyl-L-alanine-2-naphthylamide.

alanyl phenylalanyl proline arylamidase activity
type: Class
subclass of: GO_0004177
definition: An aminopeptidase activity which cleaves the chromogenic substrate L-alanyl-L-phenylalanyl-L-proline-2-naphthylamide.
created by: Carrine Blank

glutamyl glutamic acid arylamidase activity
type: Class
subclass of: GO_0004177
definition: An aminopeptidase activity which cleaves the chromogenic substrate L-glutamyl-L-glutamic acid-2-naphthylamide.
created by: Carrine Blank

glutamyl glycine arylamidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
definition: An aminopeptidase activity which cleaves the chromogenic substrate L-glutamyl-glycine-2-naphthylamide.

glutamyl glycyl arginine arylamidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
has exact synonym: GGAA
definition: An aminopeptidase activity which cleaves the chromogenic substrate L-glutamyl-glycyl-L-arginine-2-naphthylamide.

glutaryl phenylalanine arylamidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
definition: An aminopeptidase activity which cleaves the chromogenic substrate glutaryl-L-phenylalanine-2-naphthylamide.

glycyl phenylalanine arylamidase activity
type: Class
subclass of: GO_0004177
definition: An aminopeptidase activity which cleaves the chromogenic substrate glycyl-L-phenylalanine-2-naphthylamide.
created by: Carrine Blank

glycyl proline arylamidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
definition: An aminopeptidase activity which cleaves the chromogenic substrate glycyl-L-proline-2-naphthylamide.

glycyl tryptophan arylamidase activity
type: Class
subclass of: GO_0004177
definition: An aminopeptidase activity which cleaves the chromogenic substrate glycyl-L-tryptophan-2-naphthylamide.
created by: Carrine Blank

glycyl glycine arylamidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
definition: An aminopeptidase activity which cleaves the chromogenic substrate glycyl-glycine-2-naphthylamide.

leucyl glycine arylamidase activity
type: Class
subclass of: GO_0004177
definition: An aminopeptidase activity which cleaves the chromogenic substrate L-leucyl-L-glycine-2-naphthylamide.
created by: Carrine Blank

seryl tyrosine arylamidase activity
type: Class
subclass of: GO_0004177
definition: An aminopeptidase activity which cleaves the chromogenic substrate L-seryl-L-tyrosine-2-naphthylamide.
created by: Carrine Blank

N-carbobenzoyl-glycyl-glycyl-L-arginine peptidase activity
type: Class
subclass of: GO_0004177
definition: An aminopeptidase activity which cleaves the chromogenic substrate N-carbobenzoyl-glycyl-glycyl-arginine-beta-naphthylamide.
created by: Carrine Blank

irregular cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0005020
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0005020
has broad synonym: highly irregular
has broad synonym: irregular
created by: Carrine Blank
definition: Prokaryotic cell where the shape is irregular.
has broad synonym: irregular shape

microscopic optical quality assay
type: Class
equivalent class: Class
  intersection of: optical quality assay
  intersection of: Restriction
    on property: is an assay using the material entity
    some values from: Class
      intersection of: CL_0000520
      intersection of: Restriction
        on property: is an assay using the material entity
        some values from: OBI_0400169
subclass of: optical quality assay
subclass of: Restriction
  on property: is an assay using the material entity
  some values from: Class
    intersection of: CL_0000520
    intersection of: Restriction
      on property: is an assay using the material entity
      some values from: OBI_0400169
created by: Carrine Blank
definition: An optical quality assay of a single prokaryotic cell, determined by visualization under a microscope.

N-benzoyl-L-valyl-glycyl-L-arginine-4-methoxy peptidase activity
type: Class
subclass of: GO_0004177
created by: Carrine Blank
definition: An aminopeptidase activity which cleaves the chromogenic substrate N-benzoyl-L-valyl-glycyl-4-methoxy-beta-naphthylamide.

asymmetrical colony margin
type: Class
equivalent class: Class
  intersection of: MICRO_0002468
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: BSPO_0000682
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000616
has broad synonym: irregular margin
has broad synonym: irregular form
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
definition: A prokaryote colony where the shape of the colony margin is asymmetrical (i.e. irregular).
created by: Carrine Blank
has broad synonym: irregular edge

diffuse colony
type: Class
equivalent class: Class
  intersection of: colony having distinct spatial pattern
  intersection of: Restriction
    on property: has spatial pattern
    some values from: PATO_0001609
subclass of: colony having distinct spatial pattern
subclass of: Restriction
  on property: has spatial pattern
  some values from: PATO_0001609
definition: A colony with distinct spatial pattern where the colony is diffuse (sparse, where the colony is very thin).
has exact synonym: diffuse colony
created by: Carrine Blank
has broad synonym: diffuse

asymmetrical filamentous colony
type: Class
equivalent class: Class
  intersection of: filamentous colony
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0001360
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000616
subclass of: filamentous colony
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0001360
    intersection of: Restriction
      on property: has colony margin symmetry
      some values from: PATO_0000616
has exact synonym: asymmetrical filamentous colony
has broad synonym: irregular filamentous
definition: A filamentous colony with a shape that is fuzzy, or filamentous and where the colony margin is asymmetrical (i.e. irregular).
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol

undulate colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0000967
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000616
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0000967
    intersection of: Restriction
      on property: has colony margin symmetry
      some values from: PATO_0000616
has broad synonym: undulate margin
created by: Carrine Blank
definition: A colony with a shape that is undulate (wave-like) and where the colony margin is asymmetrical (i.e. irregular).
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
has exact synonym: undulate colony
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has broad synonym: undulate

symmetrical colony margin
type: Class
equivalent class: Class
  intersection of: MICRO_0002468
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: BSPO_0000682
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000632
definition: A prokaryotic colony where the shape of the colony margin is symmetrical (i.e. regular).
has broad synonym: regular margin
has broad synonym: regular edge
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
created by: Carrine Blank
has exact synonym: symmetrical colony margin

curled colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0000405
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000632
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0000405
    intersection of: Restriction
      on property: has colony margin symmetry
      some values from: PATO_0000632
IAO_0000119: http://www.ehow.com/list_6938999_types-bacteria-colonies.html
has broad synonym: curled
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
definition: A colony with a shape that has a curled edge, and where the colony margin is symmetrical (i.e. regular).
has broad synonym: wavy margin
created by: Carrine Blank
has exact synonym: curled colony

entire colony
type: Class
equivalent class: Class
  intersection of: circular colony
  intersection of: Restriction
    on property: has colony margin symmetry
    some values from: PATO_0000632
subclass of: circular colony
subclass of: Restriction
  on property: has colony margin symmetry
  some values from: PATO_0000632
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has exact synonym: entire colony
has broad synonym: entire
definition: A colony with a shape which is circular (round), and where the colony margin is symmetrical (i.e. is regular).

erose colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0001368
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000632
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0001368
    intersection of: Restriction
      on property: has colony margin symmetry
      some values from: PATO_0000632
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has broad synonym: erose
definition: A colony with a shape which is erose (i.e. has a notched, toothed, or indented appearance) and where the colony margin is symmetrical (i.e. regular).
has exact synonym: erose colony

symmetrical filamentous colony
type: Class
equivalent class: Class
  intersection of: filamentous colony
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0001360
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000632
subclass of: filamentous colony
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0001360
    intersection of: Restriction
      on property: has colony margin symmetry
      some values from: PATO_0000632
definition: A filamentous colony with a shape that is fuzzy, or filamentous and where the colony margin is symmetrical (i.e. regular).
has broad synonym: regular filamentous
created by: Carrine Blank
has exact synonym: symmetrical filamentous colony
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol

lobed colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0001979
      intersection of: Restriction
        on property: has colony margin symmetry
        some values from: PATO_0000616
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0001979
    intersection of: Restriction
      on property: has colony margin symmetry
      some values from: PATO_0000616
has broad synonym: lobate margin
definition: A colony with a shape that is lobed and where the colony margin is asymmetrical (i.e. irregular).
has exact synonym: lobel colony
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol

circular colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000411
subclass of: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000411
has broad synonym: round
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
definition: A colony with a shape that is circular (round).
has broad synonym: circular
has broad synonym: colony is round
has exact synonym: circular colony
created by: Carrine Blank

effuse colony
type: Class
equivalent class: Class
  intersection of: colony having distinct spatial pattern
  intersection of: Restriction
    on property: has spatial pattern
    some values from: PATO_0000635
subclass of: colony having distinct spatial pattern
subclass of: Restriction
  on property: has spatial pattern
  some values from: PATO_0000635
has broad synonym: effuse
created by: Carrine Blank
has exact synonym: effuse colony
definition: A colony with distinct spatial pattern where the colony is effuse (i.e. thin, unlocalized without defined margins, with a tendancy to spread).

filamentous colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001360
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001360
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
definition: A colony with a shape that is fuzzy, or filamentous.
has exact synonym: filamentous colony
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol

fried-egg colony
type: Class
equivalent class: Class
  intersection of: mulberry colony
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: BSPO_0000075
      intersection of: Restriction
        on property: has physical quality
        some values from: PATO_0000963
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: BSPO_0000078
      intersection of: Restriction
        on property: has physical quality
        some values from: PATO_0001354
subclass of: mulberry colony
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: BSPO_0000075
    intersection of: Restriction
      on property: has physical quality
      some values from: PATO_0000963
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: BSPO_0000078
    intersection of: Restriction
      on property: has physical quality
      some values from: PATO_0001354
has exact synonym: fried-egg colony
source: Fallon RJ. 1967. Mycoplasmas and their role as rodent pathogens. Lab Anim 1:43. DOI: 10.1258/002367767781006794.
IAO_0000119: http://medical-dictionary.thefreedictionary.com/Fried+Egg+Appearance
definition: A colony having distinct physical quality that has differential density. The center part of the colony is opaque and granular, while the surrounding perifery is flat and transulcent, giving the colony the appearance of a fried egg. This shape is typical of Mycoplasma species, and is due to colonies having a thicker center than edge. This appearance is typical of older (mature) colonies of Mycoplasma.
has broad synonym: fried egg
has broad synonym: fried eggs
created by: Carrine Blank

colony having distinct electromagnetic (EM) radiation quality
type: Class
equivalent class: Class
  intersection of: physically distinct colony
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001291
created by: Carrine Blank
definition: A colony having distinct physical quality that manifests in the electromagnetic (EM) radiation appearance of the colony.

mulberry colony
type: Class
equivalent class: Class
  intersection of: physically distinct colony
  intersection of: Restriction
    on property: has structure
    some values from: PATO_0002422
  intersection of: Restriction
    on property: has physical quality
    some values from: Class
      intersection of: PATO_0002416
      intersection of: Restriction
        on property: has physical quality
        some values from: PATO_0000963
subclass of: physically distinct colony
subclass of: Restriction
  on property: has structure
  some values from: PATO_0002422
subclass of: Restriction
  on property: has physical quality
  some values from: Class
    intersection of: PATO_0002416
    intersection of: Restriction
      on property: has physical quality
      some values from: PATO_0000963
has broad synonym: mulberry appearance
has exact synonym: mulberry colony
created by: Carrine Blank
source: Fallon RJ. 1967. Mycoplasmas and their role as rodent pathogens. Lab Anim 1:43. DOI: 10.1258/002367767781006794.
definition: A colony having distinct physical quality that is shaped like a mulberry (acinar), sunken, and opaque with little or no pale periphery. Is typical of young colonies of Mycoplasma species that will develop into colonies that have a fried egg appearance when more mature.
has broad synonym: mulberry

punctiform colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001366
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001366
definition: A colony with a shape that is very tiny, like a point (where colonies may have a diameter of less than 1 mm).
has exact synonym: punctiforme colony
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has broad synonym: punctiform
created by: Carrine Blank

rhizoidal colony
type: Class
equivalent class: Class
  intersection of: physically distinct colony
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001364
subclass of: physically distinct colony
subclass of: Restriction
  on property: has physical quality
  some values from: PATO_0001364
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has broad synonym: irregular rhizoid form
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
has exact synonym: rhizoid colony
has broad synonym: rhizoid form
definition: A colony having distinct physical quality that is rhizoidal (has margins or edges that resemble the roots of a tree, radiating out from the center of the colony).
created by: Carrine Blank
has broad synonym: rhizoidal
has broad synonym: rhizoid
has broad synonym: raised rhizoid growth

spindle colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001409
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001409
definition: A colony with a shape that is spindle-shaped (i.e. is thickest in the middle, tapering to both ends).
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has exact synonym: spindle colony
has broad synonym: fusiform
has broad synonym: spindle-shaped

crateriform colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002227
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002227
definition: A colony with a shape that has a depression (or crater) in the center of the colony, and thus has a 2D profile that is cup-shaped.
has broad synonym: cup-shaped
has exact synonym: crateriform colony
has broad synonym: crateriform
has broad synonym: dimpled
has broad synonym: collapsed center
has broad synonym: crater-shaped
created by: Carrine Blank

flat colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000407
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0000407
definition: A colony with a shape that is flat (has a flat profile).
has exact synonym: flat colony
has broad synonym: flat elevation
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol

raised colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001369
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001369
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has exact synonym: raised colony
created by: Carrine Blank
definition: A colony with a shape that is raised, or elevated from the surface of the agar.

pulvinate colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001357
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001357
has exact synonym: pulvinate colony
has broad synonym: pulvinate elevation
created by: Carrine Blank
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
definition: A colony with a shape that is pulvinate (is strongly elevated with a domed profile being shaped like a cushion).
has broad synonym: pulvinate
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology

convex colony
type: Class
equivalent class: Class
  intersection of: distinctly shaped colony
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001355
subclass of: distinctly shaped colony
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001355
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
has broad synonym: convex
created by: Carrine Blank
definition: A colony with a shape that has a convex, or domed, profile.
has exact synonym: convex colony
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
has broad synonym: convex elevation
has broad synonym: domed

umbonate colony
type: Class
equivalent class: Class
  intersection of: physically distinct colony
  intersection of: Restriction
    on property: has physical quality
    some values from: PATO_0001358
subclass of: physically distinct colony
subclass of: Restriction
  on property: has physical quality
  some values from: PATO_0001358
created by: Carrine Blank
has broad synonym: raised at the centres
has broad synonym: raised at the center
has exact synonym: umbonate colony
has broad synonym: umbonate elevation
definition: A colony having distinct physical quality that is umbonate (having a mushroom-like profile with a higher center and a lower margin).
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol
IAO_0000119: http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology
has broad synonym: raised in the center

prokaryotic cell autofluorescence
type: Class
equivalent class: Class
  intersection of: microscopic optical quality assay
  intersection of: Restriction
    on property: is an assay for the quality
    some values from: PATO_0001868
subclass of: microscopic optical quality assay
subclass of: Restriction
  on property: is an assay for the quality
  some values from: PATO_0001868
definition: The optical assay of a single prokaryotic cell, having the quality of autofluorescence when illuminated with a particular wavelength of light.
created by: Carrine Blank

blue-green autofluorescence
type: Class
subclass of: prokaryotic cell autofluorescence
subclass of: Restriction
  on property: is an assay for the quality
  some values from: PATO_0001868
subclass of: Restriction
  on property: is an assay for the biosynthetic production of
  some values from: CHEBI_43034
has broad synonym: blue-green fluorescence
definition: Autofluorescence of a prokaryotic cell that is blue-green in nature, occurring when the cells are illuminated with radiation at 420 nm. Occurs due to the presence of a particular fluorescent compound in the cell (e.g., Factor 420, also known as Coenzyme F420).
created by: Carrine Blank

lipase C10 activity
type: Class
subclass of: GO_0016298
created by: Carrine Blank
definition: A lipase that hydrolyzes C10 compounds. Assayed using the chromogenic substrate 5-bromo-3-indoxyl-caprate (5-bromo-3-indolyl decanoate; blue-caprate).

lipase C14 activity
type: Class
subclass of: GO_0016298
disjoint with: lipase C8 activity
definition: A lipase that hydrolyzes C14 compounds. Assayed using the chromogenic substrate 2-naphthyl myristate.
created by: Carrine Blank

lipase C8 activity
type: Class
subclass of: GO_0016298
definition: A lipase that hydrolyzes C8 compounds. Assayed using the chromogenic substrate 2-naphthyl caprylate.
created by: Carrine Blank

coccobacillus
type: Class
equivalent class: Class
  intersection of: bacilloid cell
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0001643
      intersection of: PATO_0001873
subclass of: bacilloid cell
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0001643
    intersection of: PATO_0001873
created by: Carrine Blank
has exact synonym: coccobacillary
has exact synonym: coccobacilli
has broad synonym: sub-coccoidal
IAO_0000119: Wikipedia:Coccobacillus A coccobacillus (plural coccobacilli) is a type of bacterium with a shape that is intermediate between cocci (spherical bacteria) and bacilli (rod-shaped bacteria). Coccobacilli are therefore in essence very short rods which may be mistaken for cocci. Haemophilus influenzae, Gardnerella vaginalis, and Chlamydia trachomatis are coccobacilli. Aggregatibacter actinomycetemcomitans is a gram-negative coccobacillus that is prevalent in subgingival plaques. Acinetobacter strains may grow on solid media as coccobacilli. Bordetella pertussis is a gram-negative coccobacillus responsible for causing whooping cough.
definition: A prokaryotic cell, being a bacillus where the long axis of the cell is only slightly longer than the short axis of the cell.
has exact synonym: ellipsoidal
has exact synonym: short rods
has related synonym: subspherical
has exact synonym: oval
has exact synonym: ovoid
has related synonym: subcoccoidal
has exact synonym: coccobacillus

spirillum
type: Class
equivalent class: Class
  intersection of: bacilloid cell
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: cylindrical cell
      intersection of: PATO_0000404
subclass of: bacilloid cell
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: cylindrical cell
    intersection of: PATO_0000404
IAO_0000119: Wikipedia:Spirillum Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral. It is the third distinct bacterial cell shape type besides coccus and bacillus cells.
created by: Carrine Blank
definition: A prokaryotic cell, where the long axis of the cell twists in a spiral.
has exact synonym: spiral
has exact synonym: coiled
has exact synonym: helical
has exact synonym: spirillum
has exact synonym: helix
has exact synonym: wavy

prokaryotic cell having distinct cell arrangement
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: has organismal quality
    some values from: PATO_0001992
has exact synonym: aggregates
definition: Prokaryotic cells and the physical relationships between the cells (whether they are physically attached, or connected, to one another).
created by: Carrine Blank
has exact synonym: aggregations

paired cells
type: Class
equivalent class: Class
  intersection of: multicellular prokaryote
  intersection of: Restriction
    on property: RO_0002180
    on class: CL_0000520
    qualified cardinality: 2
created by: Carrine Blank
has exact synonym: doublets
has exact synonym: diploid
definition: A multicellular relationship of prokaryotic cells where two cells are attached to one another in pairs.
has exact synonym: pairs

morphologically differentiated filament part
type: Class
equivalent class: Class
  intersection of: cell filament
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      union of: cell filament
      union of: cyanobacterial filament part
definition: A filament of prokaryotic cells, where the parts of the filament are morphologically differentiated.
created by: Carrine Blank

sarcina
type: Class
equivalent class: Class
  intersection of: cell cluster
  intersection of: Class
    union of: Restriction
      on property: RO_0002180
      on class: CL_0000520
      qualified cardinality: 8
    union of: Restriction
      on property: RO_0002180
      on class: CL_0000520
      qualified cardinality: 12
    union of: Restriction
      on property: RO_0002180
      on class: CL_0000520
      qualified cardinality: 16
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001297
has exact synonym: sarcinae
created by: Carrine Blank
definition: A multicellular relationship of prokaryotic cells where cells are attached to one another in multiples of four (8,12, or 16). This morphology forms as a result of cell division occurring in three planes.
has exact synonym: sarcinoid

cell cluster
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: multicellular prokaryote
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0001629
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      union of: MICRO_0001297
      union of: MICRO_0001298
has exact synonym: cell clusters
definition: A multicellular relationship of prokaryotic cells where cells are attached to one another end-to-end and side-to-side to form clumps or sheets after dividing. This morphology forms as a result of cell division taking place in multiple planes.
has exact synonym: clusters
has exact synonym: packet-like
created by: Carrine Blank
has exact synonym: packets
has exact synonym: clumps

cell chain
type: Class
equivalent class: Class
  intersection of: multicellular prokaryote
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001295
subclass of: multicellular prokaryote
subclass of: Restriction
  on property: RO_0002354
  some values from: MICRO_0001295
created by: Carrine Blank
has broad synonym: chains
definition: A multicellular relationship of prokaryotic cells where cells are attached to one another end-to-end to form chains. Forms when cell division occurs in one plane and cells become detached after cell division takes place.
has exact synonym: short chains

tetrad
type: Class
equivalent class: Class
  intersection of: multicellular prokaryote
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001296
  intersection of: Restriction
    on property: RO_0002180
    on class: CL_0000520
    qualified cardinality: 4
has broad synonym: tetrads
created by: Carrine Blank
definition: A multicellular prokaryotic morphological quality where cells are attached to one another in multiples of four. Forms when cell division occurs in two planes at right angles to one another.

unicellular prokaryote
type: Class
equivalent class: Class
  intersection of: prokaryotic cell having distinct cell arrangement
  intersection of: Restriction
    on property: has organismal quality
    some values from: PATO_0001994
subclass of: prokaryotic cell having distinct cell arrangement
subclass of: Restriction
  on property: has organismal quality
  some values from: PATO_0001994
disjoint with: multicellular prokaryote
definition: A prokaryotic cellularity where cells are isolated and singular, where the daughter cells detach from one another after cell division and septation occurs.
has broad synonym: unicellular
created by: Carrine Blank
has broad synonym: singly
has broad synonym: singular

streptobacillus
type: Class
equivalent class: Class
  intersection of: cell chain
  intersection of: Restriction
    on property: BFO_0000051
    some values from: bacillus
IAO_0000119: Wikipedia:Streptobacillus Streptobacillus is a genus of aerobic, gram-negative facultative anaerobe bacteria, which grow in culture as rods in chains.
definition: A multicellular relationship of prokaryotic cells where the shape of the cell is elongated (forming a bacillus, or short rod) and the cells are attached to one another end-to-end to form chains.
has exact synonym: streptobacilli
created by: Carrine Blank

streptococcus
type: Class
equivalent class: Class
  intersection of: cell chain
  intersection of: Restriction
    on property: BFO_0000051
    some values from: coccus
IAO_0000119: Wikipedia:Streptococcus Streptococcus is a genus of spherical Gram-positive bacteria belonging to the phylum Firmicutes and the lactic acid bacteria group. Cellular division occurs along a single axis in these bacteria, and thus they grow in chains or pairs, hence the name—from Greek στρεπτος streptos, meaning easily bent or twisted, like a chain (twisted chain). Contrast this with staphylococci, which divide along multiple axes and generate grape-like clusters of cells. Most streptococci are oxidase- and catalase-negative, and many are facultative anaerobes.
has exact synonym: streptococci
created by: Carrine Blank
definition: A multicellular relationship of prokaryotic cells where the shape of the cells is round (forming a coccus) and the cells are attached to one another end-to-end to form chains.

staphylococcus
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: cell cluster
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0001499
  intersection of: Restriction
    on property: BFO_0000051
    some values from: coccus
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001298
definition: A multicellular relationship of prokaryotic cells where the shape of the cells is round (forming a coccus) and the cells are attached to one another end-to-end and side-to-side to form clumps or clusters.
has exact synonym: staphylococci
IAO_0000119: Wikipedia:Staphylococcus Staphylococcus (from the Greek: σταφυλή, staphylē, "grape" and κόκκος, kókkos, "granule") is a genus of Gram-positive bacteria. Under the microscope, they appear round (cocci), and form in grape-like clusters.
created by: Carrine Blank

differentiated filament branching
type: Class
equivalent class: Class
  intersection of: MICRO_0002467
  intersection of: Restriction
    on property: BFO_0000051
    some values from: filament branch
  intersection of: Restriction
    on property: RO_0000086
    some values from: Class
      intersection of: PATO_0000001
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0000402
has exact synonym: branching of filaments
created by: Carrine Blank
has exact synonym: branching
has exact synonym: branches
definition: A differentiated cyanobacterial filament where the filaments are branched.
has exact synonym: branched filaments

false-branched filaments
type: Class
equivalent class: Class
  intersection of: differentiated filament branching
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: necritic cell
      union of: heterocyte
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1150
      union of: NCBITaxon 1161
      union of: NCBITaxon 1189
  intersection of: Restriction
    on property: BFO_0000051
    some values from: false branch
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001295
has exact synonym: commonly false branched
has exact synonym: false branched
has exact synonym: false branching growing usually at first parallel with original trichome, later diverging
created by: Carrine Blank
has related synonym: false branching
definition: Differentiated filament branching, where filaments have "false" branches. Initiated by the interruption of a trichome between two vegetative cells, either at the location of a necridic cell or a heterocyte. Later on, one or both ends of the interrupted trichomes grow aside from the axis of the main trichome. Found in the Oscilaltoriales and Nostocales and Stigonematales.
has exact synonym: pseudobranched
has exact synonym: single false branching
has exact synonym: falsely branched
has exact synonym: false ramification
has exact synonym: pseudobranchings
has exact synonym: lateral false branches
IAO_0000119: http://www.merriam-webster.com/dictionary/false%20branching A branched arrangement of the cells of certain filamentous bacteria and algae resulting from a slipping of the end of one cell past that of another following cell division, from continued growth of the free end of a trichome through the sheath in various blue-green algae, or esp. from continued growth of parts of a filament separated by one or more intervening dead cells or by heterocysts.
has exact synonym: pseudobranchings adpressed with each other and only in the upper parts divaricate

true-branched filaments
type: Class
equivalent class: Class
  intersection of: differentiated filament branching
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1189
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: true branch
      intersection of: Restriction
        on property: has structure
        some values from: PATO_0001667
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      union of: MICRO_0001296
      union of: MICRO_0001297
definition: Differentiated filament branching, where filaments have "true" branches. Formed when one cell occasionally divides longitudinally (with the cell division plane parallel to the plane of the filament axis) or obliquely with respect to the main axis of the filament. Branches remain attached to the main trichome.
has exact synonym: true branching
has exact synonym: true-branching
has exact synonym: true branches
has related synonym: true branching
created by: Carrine Blank
has exact synonym: branching true
has exact synonym: true branched
has related synonym: true-branching filaments
has exact synonym: true branches grow initially perpendicular to the mother trichome
has exact synonym: true-branched
has exact synonym: branches arise after lengthwise cell division

diplobacillus
type: Class
equivalent class: Class
  intersection of: paired cells
  intersection of: Restriction
    on property: BFO_0000051
    some values from: bacillus
disjoint with: diplococcus
definition: A multicellular prokaryotic morphological quality where the shape of the cells are elongated (i.e. bacillus or rod-shaped) and two cells are attached to one another in pairs.
created by: Carrine Blank
IAO_0000119: http://medical-dictionary.thefreedictionary.com/diplobacillus A short, rod-shaped organism occurring in pairs, joined end-to-end; diplobacterium.
has exact synonym: diplobacilli

diplococcus
type: Class
equivalent class: Class
  intersection of: paired cells
  intersection of: Restriction
    on property: BFO_0000051
    some values from: coccus
has exact synonym: dumbbell
has exact synonym: dumbbell-shaped
has exact synonym: diplococci
IAO_0000119: Wikipedia:Diplococcus A diplococcus (plural diplococci) is a round bacterium (a coccus) that typically occurs in the form of two joined cells. Examples are gram-negative Neisseria sp., and gram-positive Streptococcus sp. and Staphylococcus sp.. Its name comes from diplo, meaning double, and coccus, meaning berry.
definition: A multicellular prokaryotic morphological quality where the shape of the cells are round and two cells are attached to one another in pairs.
created by: Carrine Blank

erect filaments
type: Class
equivalent class: Class
  intersection of: spatially differentiated filaments
  intersection of: Restriction
    on property: has position
    some values from: PATO_0000622
subclass of: spatially differentiated filaments
subclass of: Restriction
  on property: has position
  some values from: PATO_0000622
definition: A filament orientation quality where filaments are lying upright (perpendicular) to a substrate or surface.
has related synonym: filaments erect
created by: Carrine Blank

prostrate filaments
type: Class
equivalent class: Class
  intersection of: spatially differentiated filaments
  intersection of: Restriction
    on property: has position
    some values from: PATO_0000631
subclass of: spatially differentiated filaments
subclass of: Restriction
  on property: has position
  some values from: PATO_0000631
created by: Carrine Blank
has related synonym: filaments prostrate
definition: A filament orientation quality where filaments are lying along (parallel to) a substrate or surface.

straight filament
type: Class
equivalent class: Class
  intersection of: distinctively shaped filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0002180
subclass of: distinctively shaped filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0002180
disjoint with: curved filament
disjoint with: coiled filament
disjoint with: bent filament
disjoint with: moniliform filament
has related synonym: filaments straight
created by: Carrine Blank
definition: A filament shape where the filament has a straight appearance (is not bent, curved, coiled, or torulose).
has exact synonym: trichomes straight

curved filament
type: Class
equivalent class: Class
  intersection of: distinctively shaped filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000406
subclass of: distinctively shaped filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0000406
has exact synonym: filaments flexous
has related synonym: filaments curved
created by: Carrine Blank
definition: A filament shape where the filament has a curved appearance along a gradual angle (not straight or bent).
has exact synonym: filaments flexuous
has exact synonym: branches waved
has exact synonym: branches arcuated
has exact synonym: filaments arcuated
has exact synonym: trichomes curved
has exact synonym: trichomes arcuate

coiled filament
type: Class
equivalent class: Class
  intersection of: distinctively shaped filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000404
subclass of: distinctively shaped filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0000404
created by: Carrine Blank
has exact synonym: coiled filaments
has exact synonym: trichomes coiled
definition: A filament shape where the filament has a regularly coiled (helical) appearance.
has related synonym: filaments coiled

bent filament
type: Class
equivalent class: Class
  intersection of: distinctively shaped filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000617
subclass of: distinctively shaped filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0000617
has related synonym: filaments bent
has exact synonym: filaments crooked
has exact synonym: filaments bent in the middle
definition: A filament shape where the filament has an appearance of being bent at an angle.
created by: Carrine Blank

torulose filament
type: Class
equivalent class: Class
  intersection of: moniliform filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0005020
subclass of: moniliform filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0005020
has exact synonym: filaments roughened
has exact synonym: trichomes torulose
definition: A torulose filament shape where the filament has a non-uniformly beaded appearance, where parts of the filament are swollen and constricted.
created by: Carrine Blank
has related synonym: filaments torulose
IAO_0000119: http://www.thefreedictionary.com/torulose Adj. 1. torulose - of a cylindrical or ellipsoid body; swollen and constricted at intervals

moniliform filament
type: Class
equivalent class: Class
  intersection of: distinctively shaped filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001979
subclass of: distinctively shaped filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001979
created by: Carrine Blank
definition: A filament shape where the filament has a uniformly regular, beaded appearance.
IAO_0000119: Wikipedia: Moniliform Having a form resembling a string of beads, where the component parts or segments are more or less uniform in size and are spherical or rounded in shape.
has exact synonym: filaments resembling a string of beads
has exact synonym: trichomes moniliform
has related synonym: filaments moniliform

trichome part
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament part
  intersection of: Restriction
    on property: BFO_0000050
    some values from: trichome
subclass of: cyanobacterial filament part
subclass of: Restriction
  on property: BFO_0000050
  some values from: trichome
created by: Carrine Blank
definition: Any consituent part of a prokaryotic heteropolar filament.

basal heterocyte
type: Class
equivalent class: Class
  intersection of: heterocyte
  intersection of: MICRO_0001285
  intersection of: Restriction
    on property: BFO_0000051
    some values from: heterocyte
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002099
  intersection of: Restriction
    on property: RO_0001025
    some values from: BSPO_0000058
subclass of: heterocyte
subclass of: MICRO_0001285
subclass of: Restriction
  on property: BFO_0000051
  some values from: heterocyte
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002099
subclass of: Restriction
  on property: RO_0001025
  some values from: BSPO_0000058
definition: A trichome part that is comprised of the terminal (basal) cell in a trichome, which has differentiated to form a heterocyte (heterocyst). Found in trichomes with apical-basal polarity that have an erect positionality.
created by: Carrine Blank

tight filament coiling
type: Class
equivalent class: Class
  intersection of: coiled filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001795
subclass of: coiled filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001795
disjoint with: loose filament coiling
has exact synonym: filaments forming tight, regular spirals
definition: A coiled filament shape where the shape of the coiling is tight, having increased coiling.
has exact synonym: densely coiled
created by: Carrine Blank
has related synonym: tight filament coiling

loose filament coiling
type: Class
equivalent class: Class
  intersection of: coiled filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001796
subclass of: coiled filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001796
has related synonym: loose filament coiling
has exact synonym: filaments slightly coiled
definition: A coiled filament shape where the shape of the coiling is loose, having decreased coiling.
has exact synonym: filaments loosely coiled
created by: Carrine Blank

irregular filament coiling
type: Class
equivalent class: Class
  intersection of: coiled filament
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0005020
subclass of: coiled filament
subclass of: Restriction
  on property: has shape
  some values from: PATO_0005020
disjoint with: regular filament coiling
has exact synonym: trichomes irregularly coiled
has related synonym: irregular filament coiling
has exact synonym: trichomes irregularly waved
has exact synonym: trichomes irregularly screw-like or spirally coiled
definition: A coiled filament shape where the shape of the coiling is irregular.
created by: Carrine Blank
has exact synonym: irregularly arranged coiled filaments
has exact synonym: irregularly coiled
has exact synonym: coils irregular
has exact synonym: filaments irregularly spirally coiled

regular filament coiling
type: Class
subclass of: coiled filament
created by: Carrine Blank
has exact synonym: filaments screw-like coiled
definition: A coiled filament shape where the shape of the coiling is regular.
has exact synonym: helical trichomes
has exact synonym: coils regular
has related synonym: regular filament coiling
has exact synonym: screw-like coiled

cyanobacterial thylakoid
type: Class
equivalent class: Class
  intersection of: GO_0030075
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1117
created by: Carrine Blank
definition: Bacterial thylakoid that is present in Cyanobacteria.

differentiated cyanobacterial filament part
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002099
created by: Carrine Blank
definition: A cyanobacterial filament part (e.g. apical cell, meristematic zone) which is differentiated.
has exact synonym: trichome_differentiation

distinctively shaped prokaryotic cell
type: Class
equivalent class: Class
  intersection of: morphologically distinct prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0000052
created by: Carrine Blank
definition: Prokaryotic cell having a distinctive shape.

bacillus
type: Class
equivalent class: Class
  intersection of: bacilloid cell
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: PATO_0001643
      intersection of: PATO_0001873
subclass of: bacilloid cell
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: PATO_0001643
    intersection of: PATO_0001873
has exact synonym: rod-shaped
has exact synonym: rod-like
has exact synonym: bacillus
has exact synonym: rods
created by: Carrine Blank
IAO_0000119: Wikipedia:Bacillus_(shape) The word bacillus (plural bacilli) may be used to describe any rod-shaped bacterium, and such bacilli are found in many different taxonomic groups of bacteria. However, the name Bacillus, capitalized and italicized, refers to a specific genus of bacteria. The name Bacilli, capitalized but not italicized, can also refer to a more specific taxonomic class of bacteria that includes two orders, one of which contains the genus Bacillus. Bacilli are usually solitary, but can combine to form diplobacilli, streptobacilli, and palisades.
has exact synonym: bacilli
has exact synonym: rod shaped
definition: A prokaryotic cell, where one axis (the long axis, the length) of the cell is longer than the other axis (the short axis, the width) of the cell.

coccus
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001499
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001499
created by: Carrine Blank
has exact synonym: coccoidal
has exact synonym: strongly lobed
has exact synonym: spherical
has exact synonym: polygonal-rounded
has exact synonym: spheroids
has exact synonym: isodiametric
has exact synonym: coccoid
has exact synonym: sphere-shaped
has exact synonym: semi-globose
IAO_0000119: Wikipedia:Coccus Coccus (plural cocci or coccuses) can be used to describe any bacterium that has a spherical shape. It is one of the three distinct types of bacteria shapes, the other two being bacillus (rod-shaped) and spirillum (spiral-shaped) cells. Coccus is an English loanword of a Neolatin noun, which in turn stems from the Greek masculine noun kokkos (κόκκος) meaning "berry".
has exact synonym: lobed
has exact synonym: multi-lobed
has exact synonym: coccus
has exact synonym: globose
has exact synonym: sphaerical
has exact synonym: spheroidal
has exact synonym: lobes
has exact synonym: spheres
definition: A prokaryotic cell that is spherical with no apparent long axis.
has exact synonym: cocci

cylindrical cell
type: Class
equivalent class: Class
  intersection of: bacilloid cell
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: cylindrical cell
      intersection of: PATO_0001154
subclass of: bacilloid cell
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: cylindrical cell
    intersection of: PATO_0001154
disjoint with: flattened cell
created by: Carrine Blank
IAO_0000119: Wikipedia:Cylinder_(geometry) A cylinder (from Greek κύλινδρος – kulindros, "roller, tumbler") is one of the most basic curvilinear geometric shapes, the surface formed by the points at a fixed distance from a given line segment, the axis of the cylinder. The solid enclosed by this surface and by two planes perpendicular to the axis is also called a cylinder. The surface area and the volume of a cylinder have been known since deep antiquity.
has exact synonym: cylindrical
has exact synonym: barrel-shaped
has exact synonym: barreliform
definition: A prokaryotic cell, being a bacillus where the long axis of the cell is much longer than the short axis of the cell.

discoid
type: Class
equivalent class: Class
  intersection of: flattened cell
  intersection of: Restriction
    on property: has shape
    some values from: discoid
subclass of: flattened cell
subclass of: Restriction
  on property: has shape
  some values from: discoid
has exact synonym: disk
has exact synonym: disk shaped
has exact synonym: plate-shaped
has exact synonym: discoidal
created by: Carrine Blank
has exact synonym: disc
definition: A flattened prokaryotic cell where the shape is partially spherical.
has exact synonym: discoid
has exact synonym: disc-shaped

flattened cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: flattened cell
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: flattened cell
has exact synonym: flat
has broad synonym: flattened
definition: A prokaryotic cell where one part of the cell has been made flat so that the shape of the cell is asymmetrical or irregular.
has exact synonym: flattened cell
created by: Carrine Blank
has exact synonym: compressed

pear-shaped cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0005002
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0005002
has exact synonym: pear shaped
has exact synonym: flask shaped
has exact synonym: flask
definition: A prokaryotic cell where one end end of the cell are wider than the middle (pear shaped).
has related synonym: flask-like
has related synonym: pear-like
created by: Carrine Blank
has exact synonym: pearshaped
has exact synonym: pear-shaped
has exact synonym: flaskshaped

polygonal cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001977
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001977
has exact synonym: polygonal shape
has exact synonym: polygonal
created by: Carrine Blank
definition: A prokaryotic cell where the surface of the cell is not rounded but is polygonal (has angular edges).

prosthecate cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0005003
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0005003
created by: Carrine Blank
definition: A prokaryotic cell where the cell has appendages or stalks that are extensions of the cell surface (including the cell wall and cell membrane).
has exact synonym: appendaged
has exact synonym: stalked
has exact synonym: prosthecate
IAO_0000119: Wikipedia:Prosthecate_bacteria Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae. These cellular appendages are neither pili nor flagella, as they are extensions of the cellular membrane and contain cytosol. One notable group of prosthecates is the genus Caulobacter.

cuboidal cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001872
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: PATO_0001872
created by: Carrine Blank
has broad synonym: square
definition: A prokaryotic cell where the surface of the cell is polygonal and the angles of the cell meet at right angles forming a box.
IAO_0000119: Wikipedia:Haloquadratum Haloquadratum ("salt square") is a genus of the family Halobacteriaceae. The first species to be identified in this group, Haloquadratum walsbyi, is highly unusual since its cells are shaped like flat, square boxes.
has exact synonym: cuboidal

pyramidal cell
type: Class
equivalent class: Class
  intersection of: distinctively shaped prokaryotic cell
  intersection of: Restriction
    on property: has shape
    some values from: pyramidal cell
subclass of: distinctively shaped prokaryotic cell
subclass of: Restriction
  on property: has shape
  some values from: pyramidal cell
created by: Carrine Blank
has exact synonym: triangles
has exact synonym: pyramidal
definition: A prokaryotic cell where the surface of the cell is polygonal and the angles of the cell meet at angles that are less than 90 degrees giving the cell a triangular or pyramidal appearance.
has related synonym: triangular

hemispherical
type: Class
equivalent class: Class
  intersection of: sub-cylindrical
  intersection of: Restriction
    on property: has shape
    some values from: hemispherical
subclass of: sub-cylindrical
subclass of: Restriction
  on property: has shape
  some values from: hemispherical
created by: Carrine Blank
definition: A sub-cylindrical, flattened prokaryotic cell where the shape is hemispherical (flattened on one side of the sphere).
has exact synonym: hemisphaerical
has exact synonym: hemispherical

nanocytes
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: has size
    some values from: Class
      union of: PATO_0000587
      union of: PATO_0000969
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      intersection of: GO_0051301
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0000912
subclass of: CL_0000520
subclass of: Restriction
  on property: RO_0002354
  some values from: Class
    intersection of: GO_0051301
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0000912
subclass of: Restriction
  on property: has size
  some values from: Class
    union of: PATO_0000587
    union of: PATO_0000969
definition: Prokaryotic cells that are very small formed as a result of rapid cell division.
created by: Carrine Blank

diphtheroid cell
type: Class
equivalent class: Class
  intersection of: bacilloid cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: NCBITaxon 1717
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: cylindrical cell
      intersection of: PATO_0001883
has exact synonym: club-shaped
has exact synonym: shape regularity diptheroid
created by: Carrine Blank
has exact synonym: diphtheroid
definition: A prokaryotic cell, being a bacillus where one one end is wider and more rounded than the other end (i.e. being club-shaped, or cudgel-shaped). The cannonical morphology of Corynebacterium diphtheriae.
has exact synonym: corneform

vibrioid cell
type: Class
equivalent class: Class
  intersection of: bacilloid cell
  intersection of: Restriction
    on property: has shape
    some values from: Class
      intersection of: cylindrical cell
      intersection of: PATO_0001879
subclass of: bacilloid cell
subclass of: Restriction
  on property: has shape
  some values from: Class
    intersection of: cylindrical cell
    intersection of: PATO_0001879
has exact synonym: crooked
created by: Carrine Blank
IAO_0000119: Wikipedia:Vibrio Vibrio is a genus of Gram-negative bacteria possessing a curved rod shape (comma shape), several species of which can cause foodborne infection, usually associated with eating undercooked seafood.
definition: A prokaryotic cell, being a bacillus where the elongated axis of the cells is curved (but not spiral).
has exact synonym: cresent-shaped
has exact synonym: vibrioid
has exact synonym: curved

multiseriate filament
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament
  intersection of: Restriction
    on property: RO_0000053
    some values from: Class
      intersection of: PATO_0000921
      intersection of: Restriction
        on property: has measurement
        some values from: Class
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001295
subclass of: cyanobacterial filament
subclass of: Restriction
  on property: RO_0002354
  some values from: MICRO_0001296
subclass of: Restriction
  on property: RO_0000053
  some values from: Class
    intersection of: PATO_0000921
    intersection of: Restriction
      on property: has measurement
      some values from: Class
        intersection of: Restriction
disjoint with: uniseriate filament
has exact synonym: multiserial
IAO_0000119: Seong-Joo L & Golubic S. 1998. Multi-trichomous cyanobacterial microfossils from the Mesoproterozoic Gaoyuzhuang Formation, China: Paleoecological and taxonomic implications. Lethaia 31:169-184. Multi-trichomous filamentous cyanobacteria of the genera Schizothrix and Microcoleus are the most commonly reported constructive elements in modern microbial mat ecosystems. .... A few specimens within the studied assemblage contain two to several parallel rows of evenly spaced internal bodies within a tube (Fig. 5C, D0, corresponding to a multi-trichomous arrangement.
IAO_0000119: Castenholz, 2001, in Bergey's Manual of Systematic Bacteriology, v. 1, 2nd ed., pg. 473.
has exact synonym: polyseriate
has broad synonym: filaments with 2-3 joined trichomes
has exact synonym: multi-seriate
has exact synonym: multi-trichomous
definition: Cyanobacterial filament with one trichome in the sheath, where the trichome is greater than two cells in width. Arises as a result of cell division occuring in two planes,one perpendicular to the axis of the trichome and one parallel to the axis of the trichome.
has exact synonym: multitrichomous
created by: Carrine Blank

uniseriate filament
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament
  intersection of: Restriction
    on property: RO_0000053
    some values from: Class
      intersection of: PATO_0000921
      intersection of: Restriction
        on property: has measurement
        some values from: Class
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001295
subclass of: cyanobacterial filament
subclass of: Restriction
  on property: RO_0000053
  some values from: Class
    intersection of: PATO_0000921
    intersection of: Restriction
      on property: has measurement
      some values from: Class
        intersection of: Restriction
subclass of: Restriction
  on property: RO_0002354
  some values from: MICRO_0001295
has exact synonym: uniserial
has exact synonym: trichomes uniseriate
definition: Cyanobacterial filament with one trichome in the sheath, where the trichome is one cell in width. Arises as a result of cell division occuring in only one plane.
has exact synonym: sheaths envelop always only one trichome
created by: Carrine Blank
has exact synonym: sheaths containing a single trichome
has exact synonym: trichomes in pairs in one sheath
IAO_0000119: Wiktionary:uniseriate Having one line or series; uniserial, unbranched

distinctively sized prokaryotic cell
type: Class
equivalent class: Class
  intersection of: morphologically distinct prokaryotic cell
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000921
subclass of: morphologically distinct prokaryotic cell
subclass of: Restriction
  on property: has size
  some values from: PATO_0000921
definition: Prokaryotic cell having a distinctive size (width).
created by: Carrine Blank

filterable cell
type: Class
equivalent class: Class
  intersection of: distinctively sized prokaryotic cell
  intersection of: Restriction
    on property: is assayed by
    some values from: MICRO_0001323
subclass of: distinctively sized prokaryotic cell
subclass of: Restriction
  on property: is assayed by
  some values from: MICRO_0001323
has exact synonym: filterable
has exact synonym: pass through a filter
created by: Carrine Blank
definition: A distinctively-sized prokaryotic cell, where the size is small enough to pass through a filter with a defined pore size.
has related synonym: filterability
has exact synonym: pass through filters
has exact synonym: filtered

nanophytoplankton
type: Class
equivalent class: Class
  intersection of: MICRO_0001444
  intersection of: Class
    union of: Restriction
      on property: uses electron donor
      some values from: CHEBI_24835
    union of: Restriction
      on property: uses electron donor
      some values from: CHEBI_50860
  intersection of: Restriction
    on property: RO_0000086
    some values from: MICRO_0002540
  intersection of: Restriction
    on property: RO_0002303
    some values from: MICRO_0001451
  intersection of: Restriction
    on property: uses energy source
    all values from: MICRO_0001441
disjoint with: picoplankton
created by: Carrine Blank
IAO_0000119: From: Wikipedia: Nanophytoplankton Nanophytoplankton are particularly small phytoplankton with sizes between 2 ­and 20 µm. They are the autotrophic part of nanoplankton. Like other phytoplankton, nanophytoplankton are microscopic organisms that obtain energy through the process of photosynthesis and must therefore live in the upper sunlit layer of ocean or other bodies of water. These microscopic free-floating organisms, including algae, protists, and cyanobacteria, fix large amounts of carbon which would otherwise be released as carbon dioxide.
definition: Photosynthetic prokaryotes, or single-celled eukaryotes, that have a cell size between 2 and 20 micrometers in diameter.

picoplankton
type: Class
equivalent class: Class
  intersection of: MICRO_0001444
  intersection of: Restriction
    on property: RO_0000086
    some values from: MICRO_0002539
  intersection of: Restriction
    on property: RO_0002303
    some values from: MICRO_0001451
created by: Carrine Blank
IAO_0000119: From: Wikipedia: Picoplankton Picoplankton is the fraction of plankton composed by cells between 0.2 and 2 μm that can be either : Some species can also be mixotrophic. Picoplankton are responsible for the most primary productivity in oligotrophic gyres, and are distinguished from nanoplankton and microplankton. Because they are small, they have a greater surface to volume ratio, enabling them to obtain the scarce nutrients in these ecosystems. Note that the SI prefix pico- is used quite loosely here, as nanoplankton and microplankton are only 10 and 100 times larger, respectively.
definition: Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter.

heterotrophic picoplankton
type: Class
equivalent class: Class
  intersection of: picoplankton
  intersection of: Restriction
    on property: uses carbon source
    some values from: Class
      intersection of: CHEBI_50860
      intersection of: Restriction
        on property: uses energy source
        some values from: CHEBI_50860
subclass of: Class
  intersection of: picoplankton
  intersection of: Restriction
    on property: uses carbon source
    some values from: Class
      intersection of: CHEBI_50860
      intersection of: Restriction
        on property: uses energy source
        some values from: CHEBI_50860
disjoint with: photosynthetic picoplankton
definition: Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter and that are not photosynthetic, but rather use organic carbon as a source of energy.
IAO_0000119: From: Wikipedia: Heterotrophic_picoplankton Heterotrophic picoplankton is the fraction of plankton composed by cells between 0.2 and 2 μm that do not perform photosynthesis.
created by: Carrine Blank

photosynthetic picoplankton
type: Class
equivalent class: Class
  intersection of: picoplankton
  intersection of: Restriction
    on property: uses energy source
    all values from: MICRO_0001441
subclass of: picoplankton
subclass of: Restriction
  on property: uses energy source
  all values from: MICRO_0001441
has exact synonym: picophytoplankton
IAO_0000119: From: Wikipedia: Photosynthetic_picoplankton Photosynthetic picoplankton is the fraction of the phytoplankton performing photosynthesis composed by cells between 0.2 and 2 µm (picoplankton). It is especially important in the central oligotrophic regions of the world oceans that have very low concentration of nutrients.
definition: Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter and that are photosynthetic (use light as a source of energy).
created by: Carrine Blank

picocyanobacteria
type: Class
equivalent class: Class
  intersection of: photosynthetic picoplankton
  intersection of: Restriction
    on property: BFO_0000050
    some values from: Class
      union of: NCBITaxon 1129
      union of: NCBITaxon 1218
definition: Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter, that are photosynthetic (use light as a source of energy), and that are members of the genus Prochlorococcus and iin some members of the genus Synechococcus (both Cyanobacteria).
created by: Carrine Blank
IAO_0000119: From: Scanlan DJ et al. 2009. Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73(2):249-299. Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production.

septate filaments
type: Class
equivalent class: Class
  intersection of: filament septation
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000936
subclass of: filament septation
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000936
has related synonym: septa
has related synonym: septate
created by: Carrine Blank
definition: Filament septation, where septa separating the individual cells that make up the filament are present.
has related synonym: septum

multi-trichomous filament
type: Class
equivalent class: Class
  intersection of: cyanobacterial filament
  intersection of: Restriction
    on property: RO_0000053
    some values from: Class
      intersection of: PATO_0000921
      intersection of: Restriction
        on property: has measurement
        some values from: Class
  intersection of: Restriction
    on property: RO_0002354
    some values from: MICRO_0001296
subclass of: cyanobacterial filament
subclass of: Restriction
  on property: RO_0000053
  some values from: Class
    intersection of: PATO_0000921
    intersection of: Restriction
      on property: has measurement
      some values from: Class
        intersection of: Restriction
subclass of: Restriction
  on property: RO_0002354
  some values from: MICRO_0001296
definition: Cyanobacterial filament one or more than one trichome in the sheath, with the trichomes oriented parallel to one another, where each trichome is one cell in width. Arises as a result of cell division mostly occurring in only one plane, and occasionally occurring in a second plane.
has broad synonym: filaments contain one or more trichomes placed together and more or less parallel within one sheath
has broad synonym: filaments composed of one to more parallel arranged trichomes
has broad synonym: filaments single or many together
has broad synonym: sheaths enveloping one (rarely 2) trichomes
has broad synonym: sheaths containing 1 to several trichomes
created by: Carrine Blank
has broad synonym: one or more trichomes per filament

tapered trichome
type: Class
equivalent class: Class
  intersection of: heteropolar trichome
  intersection of: Restriction
    on property: has shape
    some values from: PATO_0001500
has exact synonym: taper
definition: A heteropolar trichome that is tapered (has a larger cell diameter at one end of the filament than the other).
created by: Carrine Blank
has exact synonym: tapering
has related synonym: cells tapered

pleomorphic cell
type: Class
equivalent class: Class
  intersection of: irregular cell
  intersection of: Restriction
    on property: has shape
    some values from: pleomorphic cell
subclass of: irregular cell
subclass of: Restriction
  on property: has shape
  some values from: pleomorphic cell
definition: A prokaryotic cell that is irregular in shape, where the shapes of the cells are irregular and variable (pleomorphic). Cell shapes may be variable in size and shape, depending on the environmental conditions.
has broad synonym: pleiomorphic
has broad synonym: polymorphic
has exact synonym: pleomorphic
has broad synonym: polymorphous
created by: Carrine Blank

ZoBell starch agar
type: Class
equivalent class: Class
  intersection of: ZoBell marine agar
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_28017
definition: An organic-rich, mineral-salts, solid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Supplemented with starch. Used for the cultivation of heterotrophic marine microorganisms.
has exact synonym: Starch agar
created by: Carrine Blank
has exact synonym: ZoBell starch agar
IAO_0000119: From: Barbeyron T, L'Haridon S, Corre E, Kloareg B & Potin P. 2001. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. IJSEM 51:985-997. The strain was assayed for amylase activity using starch at a concentration of 0.2 % (w/v) in ZoBell agar or in ZoBell Phytagel plates.

indole assay
type: Class
equivalent class: Class
  intersection of: MICRO_0000849
  intersection of: Restriction
    on property: is an assay using the culture medium
    some values from: Class
      union of: MICRO_0000633
      union of: MICRO_0001173
  intersection of: Restriction
    on property: is an assay using the chemical reagent
    some values from: TEMP_0000189
  intersection of: Restriction
    on property: is an assay for the enzymatic substrate
    some values from: Class
      intersection of: CHEBI_27897
      intersection of: Restriction
        on property: is an assay for the enzymatic substrate
        some values from: ENVO_00002006
  intersection of: Restriction
    on property: is an assay for the enzymatic product
    some values from: Class
      intersection of: CHEBI_35581
      intersection of: Restriction
        on property: is an assay for the enzymatic product
        some values from: Class
  intersection of: Restriction
    on property: is an assay for the enzymatic activity of
    some values from: GO_0009034
subclass of: MICRO_0000849
subclass of: Restriction
  on property: is an assay for the enzymatic activity of
  some values from: GO_0009034
subclass of: Restriction
  on property: is an assay using the chemical reagent
  some values from: TEMP_0000189
subclass of: Restriction
  on property: is an assay for the enzymatic product
  some values from: Class
    intersection of: CHEBI_35581
    intersection of: Restriction
      on property: is an assay for the enzymatic product
      some values from: Class
        intersection of: CHEBI_15361
        intersection of: Restriction
subclass of: Restriction
  on property: is an assay for the enzymatic substrate
  some values from: Class
    intersection of: CHEBI_27897
    intersection of: Restriction
      on property: is an assay for the enzymatic substrate
      some values from: ENVO_00002006
subclass of: Restriction
  on property: is an assay using the culture medium
  some values from: Class
    union of: MICRO_0000633
    union of: MICRO_0001173
database cross reference: Wikipedia:Indole_test
has exact synonym: indole test
created by: Carrine Blank
has related synonym: Indole formed
has related synonym: indole test positive
has related synonym: tryptophanase
has exact synonym: IND
has related synonym: Kovac's reagent
definition: Metabolic test for tryptophanase [L-tryptophan indole-lyase (deaminating)] activity. Measures the formation of indole from tryptophan using the enzyme Tryptophanase. Indole is detected by the addition of Kovac's reagent (isoamy alchohol, para-dimethylaminobenzaldehyde, and concentrated HCl). Indole forms a complex with para-dimethylaminobenzaldehyde, resulting a red color. A negative result is yellow. In some API tests, James' reagent (a proprietary mixture of HCl, water, and 2-methoxy-4-dimethylamino benzaldehyde) is used instead of Kovac's reagent, as it has a longer shelf life. Tryptophanase catalyzes the following reaction: Tryptophan + H2O <=> indole + pyruvate + ammonia
has exact synonym: TRP
has related synonym: Kovacs reagent
has related synonym: indole
has related synonym: indole production

prokaryotic cell wall lysis susceptibility
type: Class
equivalent class: Class
  intersection of: prokaryotic cell part quality
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005618
      intersection of: Restriction
        on property: RO_0000053
        some values from: Class
definition: Prokaryotic cell wall quality that defines how susceptible the cell wall is to lysis when the cell is placed in the presence of an environment with an altered chemical composition (detergent, water, hypotonic solution).
created by: Carrine Blank

susceptibile to lysis by detergent
type: Class
equivalent class: Class
  intersection of: susceptibility to lysis by detergent
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005618
      intersection of: Restriction
        on property: RO_0000053
        some values from: Class
has exact synonym: sensitive to SDS
has exact synonym: lyse rapdily in SDS
has exact synonym: susceptible to lysis by SDS
has exact synonym: cell wall is SDS sensitive
created by: Carrine Blank
has exact synonym: easily lysed by detergent
has exact synonym: sensitive to lysis by detergent
has exact synonym: SDS-sensitive
has exact synonym: susceptible to lysis by sodium dodecyl sulfate
has exact synonym: Disintegrated by SDS
has exact synonym: lysis in SDS
has exact synonym: lysis with SDS
has exact synonym: sensitive to sodium dodecyl sulfate
has exact synonym: lysed on addition of SDS
has exact synonym: sensitive to lysis by SDS
has exact synonym: lysed by sodium dodecyl sulfate
has exact synonym: lyse in SDS
has exact synonym: lyse completely in SDS
has exact synonym: lyse completely in sodium dodecyl sulfate
has exact synonym: SDS-soluble
definition: Susceptibility to lysis by detergent where the cell shows increased susceptibility toward lysis by detergent.
has exact synonym: lysis by SDS
has exact synonym: sensistive to lysis by sodium dodecyl sulfate
has exact synonym: lysed in SDS
has exact synonym: lysed with sodium dodecyl sulfate
has exact synonym: lysed by SDS

susceptibile to lysis by hypotonic solution
type: Class
equivalent class: Class
  intersection of: susceptibility to lysis by hypotonic solution
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005618
      intersection of: Restriction
        on property: RO_0000053
        some values from: Class
has exact synonym: lysis occurs in hypotonic solution
has exact synonym: lysed by hypotonic solution
has exact synonym: osmotically fragile
created by: Carrine Blank
has exact synonym: lyse in hypotonic distilled water
has exact synonym: lyse rapidly in hypotonic solution
definition: Susceptibility to lysis by hypotonic solution where the cell shows increased susceptibility toward lysis by hypotonic solution.
has exact synonym: lysed in low osmolal solutions
has exact synonym: susceptible to lysis by hypotonic solution
has broad synonym: lyse in hypotonic distilled water

susceptible to lysis by water
type: Class
equivalent class: Class
  intersection of: MICRO_0001278
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005618
      intersection of: Restriction
        on property: RO_0000053
        some values from: Class
has exact synonym: lyse immediately in distilled water
has exact synonym: lyse after transfer into demineralized water
has exact synonym: lyse in distilled water
has exact synonym: lyse rapidly in water
has exact synonym: lyse completely in distilled water
has exact synonym: lyse in water
created by: Carrine Blank
has exact synonym: sensitive to distilled water
has exact synonym: lysis in distilled water
has exact synonym: lysed in H2O
has exact synonym: lysed in distilled water
has exact synonym: lysed on addition of freshwater
has exact synonym: lyse rapidly in distilled water
has exact synonym: lysed in water
definition: Susceptibility to lysis by water where the cell shows increased susceptibility toward lysis by water.

DNA Guanosine and Cytidine Content
type: Class
subclass of: prokaryotic nucleobase quality
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_17172
subclass of: Restriction
  on property: BFO_0000051
  some values from: CHEBI_15698
definition: The molar percentage of guanosine and cytidine nucleobases ([molG+molC]/[molG+molC+molA+molT)) in the DNA of a prokaryotic chromosome and/or plasmid.
has exact synonym: mol% guanine plus cytosine
has exact synonym: mol% GC
has exact synonym: DNA base composition
has exact synonym: mol% G+C
has broad synonym: G+C
has broad synonym: content of the DNA
has broad synonym: moles guanine+cytosine
has exact synonym: mol % G+C
has exact synonym: GC content
has exact synonym: G+C mol %
created by: Carrine Blank
has exact synonym: mol % guanine plus cytosine
has exact synonym: G+C content
has exact synonym: DNA mol G+C content
has exact synonym: guanine plus cytosine content
has exact synonym: guanine-plus-cytosine content

nitrate reduction
type: Class
subclass of: GO_0071941
definition: The process in which nitrite is reduced to more reduced nitrogen compounds, including nitrite, nitric oxide, nitrous oxide, and dinitrogen.
created by: Carrine Blank

gliding motility
type: Class
subclass of: GO_0071976
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: CL_0000520
    intersection of: Restriction
      on property: BFO_0000051
      all values from: Class
        complement of: GO_0009288
has exact synonym: twitching
has exact synonym: gliding
has exact synonym: bacterial gliding
definition: Cell gliding, characterized by bacterial movement that does not involve use of a flagellum. Gliding is typically observed when a particular genus or species of microorganism encounters a surface.
has exact synonym: twitching motility
IAO_0000119: Wikipedia:bacterial_gliding
created by: Carrine Blank

nitrite reduction
type: Class
subclass of: GO_0071941
definition: The process in which nitrite is reduced to more reduced nitrogen compounds, including nitric oxide, nitrous oxide, and dinitrogen.
created by: Carrine Blank

anaerobic respiration, using tetrathionate as electron acceptor
type: Class
equivalent class: Class
  intersection of: GO_0009061
  intersection of: Restriction
    on property: uses electron acceptor
    some values from: CHEBI_26936
subclass of: GO_0009061
subclass of: Restriction
  on property: uses electron acceptor
  some values from: CHEBI_26936
created by: Carrine Blank
definition: The process of anaerobic respiration, through the reduction of tetrathionate to thiosulfate, elemental sulfur, or hydrogen sulfide.

Berkefeld W filter
type: Class
equivalent class: Class
  intersection of: Berkefeld filter candle
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000600
subclass of: Berkefeld filter candle
subclass of: Restriction
  on property: has size
  some values from: PATO_0000600
definition: A gravity-driven water filter made by the British Berkefeld® company, with a wider pore size W (for Wenig). Pore sizes average 0.45 microns in diameter.
created by: Carrine Blank

prokaryote cytopathogenicity
type: Class
subclass of: IDO_0000405
has broad synonym: cytopathogenic
created by: Carrine Blank
definition: Pathogen role of a pathogenic prokaryotic cell.
database cross reference: http://www.merriam-webster.com/dictionary/cytopathogenic

Berkefeld V filter
type: Class
equivalent class: Class
  intersection of: Berkefeld filter candle
  intersection of: Restriction
    on property: has size
    some values from: PATO_0000599
subclass of: Berkefeld filter candle
subclass of: Restriction
  on property: has size
  some values from: PATO_0000599
created by: Carrine Blank
definition: A gravity-driven water filter made by the British Berkefeld® company, with a narrow pore size V (for Viel). Pore sizes average 0.38 microns in diameter. This is the most common filter size used to study the filterability of microorganisms.

intracellular storage of carbon
type: Class
subclass of: GO_0044710
definition: Single-organism metabolic process, where the prokaryotic microorganism uses enzymes to synthesize a storage molecule (usually a polymer) inside the cell that is used to store carbon.
created by: Carrine Blank

microbiological reactivity to lymphatic materials assay
type: Class
subclass of: OBI_0000070
subclass of: Restriction
  on property: is an assay using the material entity
  some values from: Class
    union of: CL_0000232
    union of: CL_0000738
    union of: ENVO_02000027
    union of: UBERON_0000178
subclass of: Restriction
  on property: is an assay using the material entity
  some values from: MICRO_0001591
definition: An assay to determine if a particular microbial taxon or isolate has reactivity towards blood, blood plasma, or blood cells (including clotting).
created by: Carrine Blank

intracellular storage of nitrogen
type: Class
subclass of: GO_0044710
definition: Single-organism metabolic process, where the prokaryotic microorganism uses enzymes to synthesize a storage molecule (usually a polymer) inside the cell that is used to store nitrogen.
created by: Carrine Blank

egg yolk emulsion
type: Class
equivalent class: Class
  intersection of: homogenized chicken egg
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31823
IAO_0000119: From: McClung-Toabe Agar (Atlas, The Handbook of Microbiological Media for the Examination of Food, 2nd ed., pgs 221-222) Egg Yolk Emulsion, 50%: Composition per 100.0 mL: Chicken egg yolks 11 Whole chicken egg 1 NaCl (0.9% solution) 50.0 mL Preparation of Egg Yolk Emulsion, 50%: Soak eggs with 1:100 dilution of saturated mercuric chloride solution for 1 min. Crack eggs and separate yolks from whites. Mix egg yolks with 1 chicken egg. Measure 50.0 mL of egg yolk emulsion and add to 50.0 mL of 0.9% NaCl solution. Mix thoroughly. Filter sterilize. Warm to 45-50˚C.
created by: Carrine Blank
definition: An emulsion of chicken egg and chicken egg yolks, created by heating an homogenized mixture of egg and egg yolks with sodium chloride.

erythrocyte hemadsorption assay
type: Class
equivalent class: Class
  intersection of: MICRO_0001421
  intersection of: Restriction
    on property: is an assay for the biological process of
    some values from: GO_0034113
subclass of: MICRO_0001421
subclass of: Restriction
  on property: is an assay for the biological process of
  some values from: GO_0034113
has related synonym: hamadsorption
has related synonym: haemadsorb
definition: A microbiological assay for binding to blood cells, where the cell of a microorganism adheres to red blood cells.
has related synonym: hemadsorb
has exact synonym: HAd
has related synonym: haemadsorption
IAO_0000119: http://medical-dictionary.thefreedictionary.com/hemadsorption\ hemadsorption /he·mad·sorp·tion/ (hem″ad-sorp´shun) the adherence of red cells to other cells, particles, or surfaces.hemadsor´bent
created by: Carrine Blank

hemolysis assay
type: Class
equivalent class: Class
  intersection of: MICRO_0001418
  intersection of: Restriction
    on property: is an assay using the culture medium
    some values from: microbiological culture medium containing blood
  intersection of: Restriction
    on property: is an assay for the biological process of
    some values from: MICRO_0001422
subclass of: MICRO_0001418
subclass of: Restriction
  on property: is an assay for the biological process of
  some values from: MICRO_0001422
subclass of: Restriction
  on property: is an assay using the culture medium
  some values from: microbiological culture medium containing blood
definition: A microbiological assay of lysis of blood cells, where the assay is for cytolysis of red blood cells. Hemolysis assays are carried out using some formulation of blood agar, and the assay involves determination of whether lysis has occured and the nature of the lysis.
created by: Carrine Blank
has related synonym: hemolysis
has related synonym: serum digestion
has related synonym: liquifaction of coagulated serum

alpha-hemolysis assay
type: Class
equivalent class: Class
  intersection of: hemolysis assay
  intersection of: Restriction
    on property: is an assay for the metabolic product
    some values from: Class
      intersection of: CHEBI_17033
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0000320
  intersection of: Restriction
    on property: is an assay for the biological process of
    some values from: MICRO_0001423
subclass of: hemolysis assay
subclass of: Restriction
  on property: is an assay for the metabolic product
  some values from: Class
    intersection of: CHEBI_17033
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0000320
subclass of: Restriction
  on property: is an assay for the biological process of
  some values from: MICRO_0001423
has related synonym: alpha-haemolysis
has related synonym: alpha hemolysis
has related synonym: green hemolysis
has related synonym: incomplete hemolysis
has related synonym: viridands-type hemolysis
IAO_0000119: Wikipedia:hemolysis_(microbiology) Alpha-haemolysis occurs when an organism secretes alpha-haemolysin, a protein which forms a pore in the membranes of red blood cells. This leads to the formation of colonies on blood agar that have a dark greenish appearance. The green color is caused by peroxidation of hemoglobin (presence of biliverdin).
definition: A hemolysis assay for the process of alpha-hemolysis, where a protein secreted by a microorganism results in the formation of a pore in the membranes of erythrocytes (red blood cells) and thus causing the cells to lyse. Alpha hemolysis partially breaks down the red blood cells leaving a greenish color due to the presence of biliverdin, a by-product of hemoglobin.
has related synonym: partial hemolysis
created by: Carrine Blank
has related synonym: viridans type haemolysis
has related synonym: green haemolysis
has related synonym: incomplete haemolysis
has related synonym: alpha-hemolysis
has related synonym: partial haemolysis

beta-hemolysis assay
type: Class
equivalent class: Class
  intersection of: hemolysis assay
  intersection of: Restriction
    on property: is an assay for the biological process of
    some values from: MICRO_0001424
  intersection of: Restriction
    on property: is an assay for the metabolic product
    all values from: Class
      intersection of: Class
        complement of: CHEBI_17033
      intersection of: Restriction
        on property: RO_0000086
        some values from: PATO_0000337
subclass of: hemolysis assay
subclass of: Restriction
  on property: is an assay for the biological process of
  some values from: MICRO_0001424
subclass of: Restriction
  on property: is an assay for the metabolic product
  all values from: Class
    intersection of: Class
      complement of: CHEBI_17033
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0000337
has related synonym: beta hemolysis
created by: Carrine Blank
has related synonym: beta-haemolysis
has related synonym: complete haemolysis
definition: A hemolysis assay for the process of beta-hemolysis, where a protein (beta-haemolysin) secreted by a microorganism results in the hyrolysis of sphingomyelin in erythrocytes (red blood cells) and thus causing the cells to lyse. Beta-hemolysis breaks down the red blood cells and hemoglobin completely, leaving a clear zone in the agar around the growing cells or colonies.
has related synonym: complete hemolysis
has related synonym: betahemolysis
IAO_0000119: Wikipedia:hemolysis_(microbiology) Beta hemolysis (β-hemolysis), is caused by the secretion of beta-hemolysin by a pathogenic bacterium. Beta-hemolysin is a protein which catalyzes the hydrolysis of sphingomyelin, releasing phosphoryl choline and resulting in lysis fo the red blood cell. The result are colonies on blood agar that are surrounded by a yellow, transparent zone.

gamma-hemolysis assay
type: Class
equivalent class: Class
  intersection of: hemolysis assay
  intersection of: Restriction
    on property: is an assay for the biological process of
    some values from: MICRO_0001425
  intersection of: Restriction
    on property: is an assay for the metabolic product
    all values from: Class
      intersection of: Class
        complement of: CHEBI_17033
      intersection of: Restriction
        on property: RO_0000086
        all values from: Class
subclass of: hemolysis assay
subclass of: Restriction
  on property: is an assay for the metabolic product
  all values from: Class
    intersection of: Class
      complement of: CHEBI_17033
    intersection of: Restriction
      on property: RO_0000086
      all values from: Class
        complement of: PATO_0000337
subclass of: Restriction
  on property: is an assay for the biological process of
  some values from: MICRO_0001425
created by: Carrine Blank
definition: A hemolysis assay for the process of gamma-hemolysis, where a protein (beta-haemolysin) secreted by a microorganism results in the hydrolysis of sphingomyelin in erythrocytes (red blood cells) and thus causing the cells to lyse. Gamma-hemolysis does not break dow the red blood cells, and thus no clearing is seen.
IAO_0000119: Wikipedia:hemolysis_(microbiology) Gamma hemolysis, caused by the secretion of gamma-hemolysin, results in the lysis of leucocytes (white blood cells). Red blood cells are unaffected, and therefore do not show hemolytic activity on blood agar plates.

erythrocyte hemagglutination assay
type: Class
equivalent class: Class
  intersection of: MICRO_0001421
  intersection of: Restriction
    on property: is an assay for the biological process of
    some values from: GO_0034117
subclass of: MICRO_0001421
subclass of: Restriction
  on property: is an assay for the biological process of
  some values from: GO_0034117
has exact synonym: HA
has related synonym: haemagglutinated
created by: Carrine Blank
IAO_0000119: Wikipedia:hemagglutination Hemagglutination, or haemagglutination, is a specific form of agglutination that involves red blood cells (RBCs). It has two common uses in the laboratory: blood typing and the quantification of virus dilutions.
has related synonym: hemagglutinated
definition: A microbiological assay for binding to blood cells, where a microorganism causes red blood cells to clump (agglutinate).
has related synonym: haemagglutinates
has related synonym: hemagglutinates
has related synonym: haemagglutination

cytadsorption
type: Class
subclass of: GO_0034113
has exact synonym: cytadherence
definition: Heterotypic cell-cell adhesion where a prokaryotic cell is able to adhere to another cell.
created by: Carrine Blank

Staley vitamin solution
type: Class
equivalent class: Class
  intersection of: vitamin solution
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15956
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16709
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17015
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17154
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_27470
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30411
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31345
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_49105
IAO_0000119: From: Staley JT. 1981. The genera Prosthecomicrobium and Ancalomicrobium. In: Starr MP, Stolp H, Truper HG, Balows A,Schlegel HG, (eds). The prokaryotes. Berlin: Springer-Verlag. Pg 68. Vitamin Solution B12 0.1 mg Biotin 2 mg Calcium pantothenate 5 mg Folic acid 2 mg nicotinamide 5 mg pyridoxine HCl 10 mg riboflavin 5 mg thiamine HCL 5 mg Add distilled water up to 1 L and store in 4˚C in a dark container.
definition: A solution of B vitamins including cobalamin (B12), biotin (B7), pantothenic acid (B5), folic acid (B9), nicotinamide (B3), pyridoxine (B6), riboflavin (B2), and thiamine (B1). Used to support the growth of microorganisms.
created by: Carrine Blank

trace elements solution
type: Class
subclass of: defined inorganic chemical mixture
subclass of: Restriction
  on property: has ingredient
  some values from: ENVO_00002006
created by: Carrine Blank
definition: A solution of trace elements (or trace metals), sometimes also having an organic chelator of metal ions (such as EDTA or nitrilotriacetic acid). Used to support the growth of microorganisms.

trace metals 44
type: Class
equivalent class: Class
  intersection of: trace elements solution
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31440
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_38892
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_64734
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_75836
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86214
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86364
has broad synonym: metals "44"
has broad synonym: metals 44
definition: A trace elements solution containing disodium EDTA, zinc sulfate, ferrous sulfate, manganese sulfate, copper sulfate, cobalt nitrate, and sodium tetraborate.
created by: Carrine Blank
IAO_0000119: From http://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=149 Metals ''44'': EDTA·2Na 250.0 mg ZnSO4·7H2O 1095.0 mg FeSO4·7H2O 500.0 mg MnSO4·xH2O 154.0 mg CuSO4·5H2O 39.2 mg Co(NO3)2·6H2O 24.8 mg Na2B4O7·10H2O 17.7 mg Distilled water 1.0 L

soil extract
type: Class
equivalent class: Class
  intersection of: MICRO_0001370
  intersection of: Restriction
    on property: is an aqueous extract derived from
    some values from: ENVO_00001998
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15377
  intersection of: Restriction
    on property: RO_0002354
    some values from: CHMO_0002846
created by: Carrine Blank
definition: A water extract of soil. Soil extract is often prepared by sieving air dried soil through a coarse sieve and autoclaving distilled water. Used to support the growth of microorganisms.

chopped lean ground beef
type: Class
equivalent class: Class
  intersection of: MICRO_0000611
  intersection of: Restriction
    on property: RO_0002354
    some values from: CHMO_0001652
  intersection of: Restriction
    on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
    all values from: Class
      intersection of: NCBITaxon 9913
      intersection of: Restriction
        on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
        some values from: UBERON_0002385
definition: Chopped and ground meat (muscle tissue) containing a low fat content from beef (Bos taurus). Used to culture microorganisms.
has broad synonym: lean ground beef
created by: Carrine Blank

microbiological gelling agent
type: Class
subclass of: CHEBI_33232
subclass of: Restriction
  on property: is an ingredient of
  some values from: solid microbiological culture medium
definition: A polymeric organic compound or mix of organic compounds which are liquid under autoclave conditions but solidify under the growth conditions used to cultivate a microorganism. Used to make solid microbiological culture media.
created by: Carrine Blank

vitamin solution
type: Class
subclass of: MICRO_0001650
subclass of: Restriction
  on property: has ingredient
  some values from: ENVO_00002006
definition: Defined organic solution comprised of a mixture of vitamins (used as enzyme co-factors) added in small amounts to microbiological culture medium. Used to support the growth of microorganisms.
created by: Carrine Blank

homogenized chicken egg
type: Class
equivalent class: Class
  intersection of: MICRO_0001777
  intersection of: Restriction
    on property: RO_0002354
    some values from: CHMO_0002020
definition: Microbiological medium ingredient, derived from chicken egg, where the chicken egg has been homogenized (mixed).
created by: Carrine Blank

fish peptone
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of protein
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: Class
      intersection of: NCBITaxon 7898
      intersection of: Restriction
        on property: is an enzymatic hydrolytic extract derived from
        some values from: UBERON_0002385
definition: An enzymatic hydrolysis of protein derived from fish (of unspecified origin), used for the cultivation of microorganisms.
created by: Carrine Blank

microbiological medium ingredient, derived from enzymatic hydrolysis of mammalian protein
type: Class
subclass of: microbiological medium ingredient, derived from enzymatic hydrolysis of protein
subclass of: Class
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: NCBITaxon_40674
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: UBERON_0002385
created by: Carrine Blank
definition: Protein hydrolysates, also called peptones, are the result of the enzymatic hydrolysis of animal protein (mammal meat, muscle tissue).

heart pancreatic digest
type: Class
equivalent class: Class
  intersection of: proteose peptone
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: Class
      intersection of: NCBITaxon_40674
      intersection of: Restriction
        on property: is an enzymatic hydrolytic extract derived from
        some values from: UBERON_0000948
created by: Carrine Blank
definition: A pancreatic digest of heart tissue derived from animal (mammalian) tissue, used for the culturing of microorganisms.

microbiological medium ingredient, derived from enzymatic hydrolysis of milk protein
type: Class
subclass of: microbiological medium ingredient, derived from enzymatic hydrolysis of protein
subclass of: Restriction
  on property: is an enzymatic hydrolytic extract derived from
  some values from: Class
    intersection of: NCBITaxon 9913
    intersection of: Restriction
      on property: is an enzymatic hydrolytic extract derived from
      some values from: ENVO_0010129
subclass of: Restriction
  on property: is an enzymatic hydrolytic extract derived from
  some values from: MICRO_0001242
definition: Protein hydrolysates, also called peptones, are the result of the enzymatic hydrolysis of milk proteins (such as casein or lactalbumin).
created by: Carrine Blank
has exact synonym: peptone from casein

pancreatic digest of gelatin
type: Class
equivalent class: Class
  intersection of: microbiological medium ingredient, derived from enzymatic hydrolysis of mammalian protein
  intersection of: Restriction
    on property: is an enzymatic hydrolytic extract derived from
    some values from: Class
      intersection of: NCBITaxon_40674
      intersection of: Restriction
        on property: is an enzymatic hydrolytic extract derived from
        some values from: CHEBI 5291
has broad synonym: pancreatic digest of gelatin peptone
has broad synonym: gelatine peptone
definition: A pancreatic digest of gelatin, extracted from collagen derived from bone, cartilage, and connective tissue (of unspecified origin).
created by: Carrine Blank
has broad synonym: gelatin peptone
has broad synonym: gelatine peptone, pancreatic
has exact synonym: Gelysate(TM) peptone

microbiological culture medium, promotes growth of autotrophs
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Class
    complement of: microbiological culture medium, promotes growth of heterotrophs
disjoint with: microbiological culture medium, promotes growth of heterotrophs
definition: A microbiological culture medium that lacks organic carbon compounds and therefore promotes the growth of autotrophic microorganisms.
created by: Carrine Blank
has related synonym: mineral salts media
has related synonym: Mineral salts growth medium

microbiological culture medium, promotes growth of heterotrophs
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: CHEBI_16646
      union of: CHEBI_29067
      union of: CHEBI_32138
      union of: CHEBI_32954
      union of: CHEBI_50144
      union of: CHEBI_53258
      union of: CHEBI_75228
      union of: undefined organic chemical mixture
subclass of: microbiological culture medium
definition: A microbiological culture medium that contains organic carbon compounds and therefore promotes the growth of heterotrophic microorganisms.
created by: Carrine Blank

Carboxymethyl cellulose agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_62982
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_85146
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: A mineral-salts, solid microbiological culture medium with yeast extract, ammonium phosphate, and carboxymethyl cellulose. Used for the cultivation of microorganisms capable of metabolizing cellulose.
has exact synonym: CMC-containing plates
IAO_0000119: From: BugwoodWiki:CMCA (Carboxymethylcellulose agar) Medium contains: Part 1: Distilled water, 1 L NH4H2PO4, 1 g KCl, 0.2 g MgSO4*7H2O, 1 g Yeast extract, 1 g Part 2: Carboxymethyl cellulose, 26 g Agar, 3g Mix ingredients from Part 1 and add ingredients from Part 2 while stirring Autoclave 20 minutes.
has exact synonym: cellulose gum agar
created by: Carrine Blank
has exact synonym: carboxymethylcellulose plates
has exact synonym: CMC plates
has exact synonym: CMCA

agar plate medium
type: Class
subclass of: solid microbiological culture medium
created by: Carrine Blank
definition: A solid microbiological culture medium that has been solidified by agar and poured into a flat surface in a Petri dish.

hypersaline microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001293
definition: A microbiological culture medium that has a salinity of greater than 5% salt.
created by: Carrine Blank

marine microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
created by: Carrine Blank
definition: A microbiological culture medium that has a salinity of 3-5 % salts.

brackish microbiological culture medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
created by: Carrine Blank
definition: A microbiological culture medium that has a salinity of greater than 0.05 % salts and less than 3% salts.

prokaryotic physiological quality
type: Class
equivalent class: Class
  intersection of: prokaryotic quality
  intersection of: Restriction
    on property: is prokaryotic physiological quality of
    some values from: MICRO_0001541
subclass of: prokaryotic quality
subclass of: Restriction
  on property: is prokaryotic physiological quality of
  some values from: MICRO_0001541
created by: Carrine Blank
definition: A prokaryotic quality relating the optimal physiological preference (pressure, salinity, temperature) of a particular strain of prokaryotes. When these preferred conditions are met, the organism will exhibit cell division.

barophilic
type: Class
equivalent class: Class
  intersection of: MICRO_0001317
  intersection of: Restriction
    on property: is prokaryotic physiological quality of
    some values from: MICRO_0001359
subclass of: MICRO_0001317
subclass of: Restriction
  on property: is prokaryotic physiological quality of
  some values from: MICRO_0001359
disjoint with: barotolerant
IAO_0000119: Wikipedia:piezophile Barophilic microorganisms grow at high pressures. They are typically isolated from deep subsurface or deep sea habitats.
definition: Pressure optimum quality, where growth rates at elevated pressures are higher than growth rates at atmospheric pressure. Generally a characteristic of prokaryotic microorganisms that grow in the deep oceans.
has exact synonym: piezophile
created by: Carrine Blank
has exact synonym: piezophilic
has exact synonym: barophile

requires magnesium for growth
type: Class
equivalent class: Class
  intersection of: MICRO_0000690
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_33975
has exact synonym: Magnesium required
has exact synonym: Magnesium is required
has exact synonym: Mg2+ required
definition: Magnesium (II) ions are required to be present in order for growth of a particular microorganism to occur.
created by: Carrine Blank

microbiological diagnostic assay
type: Class
equivalent class: Class
  intersection of: OBI_0000070
  intersection of: Restriction
    on property: is an assay using the material entity
    some values from: MICRO_0001591
subclass of: OBI_0000070
subclass of: Restriction
  on property: is an assay using the material entity
  some values from: MICRO_0001591
definition: An assay used to identify or characterize a microorganism. Is used to determine the biological process, quality, cellular component, molecular function, or a chemical entity that is associated with the particular microorganism.
created by: Carrine Blank

urease assay
type: Class
equivalent class: Class
  intersection of: MICRO_0000795
  intersection of: Restriction
    on property: is an assay for the enzymatic substrate
    some values from: Class
      intersection of: CHEBI_16199
      intersection of: Restriction
        on property: is an assay for the enzymatic substrate
        some values from: ENVO_00002006
  intersection of: Restriction
    on property: is an assay for the enzymatic product
    some values from: Class
      intersection of: CHEBI_16526
      intersection of: Restriction
        on property: is an assay for the enzymatic product
        some values from: CHEBI_16134
  intersection of: Restriction
    on property: is an assay for the enzymatic activity of
    some values from: GO_0009039
subclass of: MICRO_0000795
subclass of: Restriction
  on property: is an assay for the enzymatic product
  some values from: Class
    intersection of: CHEBI_16526
    intersection of: Restriction
      on property: is an assay for the enzymatic product
      some values from: CHEBI_16134
subclass of: Restriction
  on property: is an assay for the enzymatic activity of
  some values from: GO_0009039
subclass of: Restriction
  on property: is an assay for the enzymatic substrate
  some values from: Class
    intersection of: CHEBI_16199
    intersection of: Restriction
      on property: is an assay for the enzymatic substrate
      some values from: ENVO_00002006
has related synonym: urease
has exact synonym: URE
has related synonym: urea hydrolysis
has exact synonym: urease test
definition: An enzymatic assay which tests for the presence of urease in a microorganism. Urease hydrolyzes urea to produce CO2 and ammonia, which increases the pH of the media: (NH2)2CO + H2O -> CO2 + 2 NH3 The urease test uses phenol red as a pH indicator. An increase in alkalinity results in a color from yellow to pink/red. A positive result is pink/orange/red; a negative test result is yellow. The test employs either Christensen's Urea Agar or Stuart's Urea Broth.
database cross reference: http://www.microbelibrary.org/library/laboratory-test/3223-urease-test-protocol
created by: Carrine Blank

barotolerant
type: Class
equivalent class: Class
  intersection of: MICRO_0001317
  intersection of: Restriction
    on property: is prokaryotic physiological quality of
    some values from: MICRO_0001364
subclass of: MICRO_0001317
subclass of: Restriction
  on property: is prokaryotic physiological quality of
  some values from: MICRO_0001364
IAO_0000119: Wikipedia:piezophlie Barotolerant microorganisms are able to grow or survive at high pressures, but can also grow and survive at atmospheric pressures.
definition: Pressure optimum quality, where some growth occurs at elevated pressures, but growth is fastest at atmospheric pressures.
has exact synonym: facultative barophile
has exact synonym: piezotolerant
created by: Carrine Blank
has exact synonym: facultatively barophilic

obligately barophilic
type: Class
equivalent class: Class
  intersection of: barophilic
  intersection of: Restriction
    on property: is prokaryotic physiological quality of
    some values from: MICRO_0001361
subclass of: barophilic
subclass of: Restriction
  on property: is prokaryotic physiological quality of
  some values from: MICRO_0001361
definition: Barophilic, and can only grow at elevated pressures. These organisms require elevated pressure to grow and survive.
IAO_0000119: Wikipedia:piezophile
created by: Carrine Blank
has exact synonym: obligate piezophile

aerophilicity
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: MICRO_0001488
    intersection of: Restriction
      on property: BFO_0000051
      some values from: CHEBI_15379
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001513
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001526
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001513
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001526
subclass of: Class
  intersection of: MICRO_0001488
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CHEBI_15379
definition: The metabolic quality of a microorganism with respect to its relationship to oxygen.
created by: Carrine Blank
has exact synonym: aerobicity

fermentation metabolic process
type: Class
equivalent class: Class
  intersection of: prokaryotic metabolic process
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0006113
      intersection of: Restriction
        on property: BFO_0000051
        some values from: Class
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001496
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001490
  intersection of: Restriction
    on property: uses electron donor
    all values from: Class
      intersection of: CHEBI_50860
      intersection of: Restriction
        on property: uses energy source
        all values from: Class
subclass of: prokaryotic metabolic process
subclass of: Restriction
  on property: uses electron donor
  all values from: Class
    intersection of: CHEBI_50860
    intersection of: Restriction
      on property: uses energy source
      all values from: Class
        intersection of: CHEBI_50860
        intersection of: Restriction
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001490
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001496
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: GO_0006113
    intersection of: Restriction
      on property: BFO_0000051
      some values from: Class
        complement of: GO_0045333
created by: Carrine Blank
has exact synonym: fermentation
has exact synonym: fermenter
has exact synonym: ferment
has exact synonym: ferments
has exact synonym: fermentatively
has exact synonym: fermentative
IAO_0000119: Wikipedia:fermentation Fermentation is a metabolic process of microorganisms which converts a carbohydrate carbon and energy substrate into acids, gases, and/or alcohols.
has exact synonym: fermenting
has exact synonym: fermented
has exact synonym: fermentable
definition: A prokaryotic metabolic process where the carbon and energy sources are organic compounds. Is an anaerobic process which does not require an electron transport system.

respiratory metabolic process
type: Class
equivalent class: Class
  intersection of: prokaryotic metabolic process
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0045333
      intersection of: Class
        complement of: Restriction
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001455
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001489
  intersection of: Restriction
    on property: uses energy source
    all values from: Class
      union of: CHEBI_24431
      union of: MICRO_0001441
subclass of: prokaryotic metabolic process
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001489
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: GO_0045333
    intersection of: Class
      complement of: Restriction
        on property: BFO_0000051
        some values from: GO_0006113
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001455
subclass of: Restriction
  on property: uses energy source
  all values from: Class
    union of: CHEBI_24431
    union of: MICRO_0001441
definition: A prokaryotic metabolic process which involves the oxidation and reduction of chemical compounds and involves an electron transport chain.
created by: Carrine Blank

aerobic
type: Class
equivalent class: Class
  intersection of: aerophilicity
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001514
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001531
subclass of: aerophilicity
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001531
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001514
created by: Carrine Blank
IAO_0000119: Wikipedia:aerobic organism An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. Facultative anaerobes grow and survive in an oxygenated environment and so do aerotolerant anaerobes.
has exact synonym: aerobic
definition: A prokaryotic metabolic quality where the organism grows in the presence of oxygen.
has exact synonym: aerobically

anaerobic
type: Class
equivalent class: Class
  intersection of: aerophilicity
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001517
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001528
subclass of: aerophilicity
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001517
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001528
has exact synonym: anoxic
created by: Carrine Blank
has exact synonym: anaerobic
IAO_0000119: Wikipedia:anaerobic_organism An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if oxygen is present, which means that it can perform its bodily functions better in the absence of oxygen. An anaerobic organism may be unicellular or multicellular (like metazoa or more complex organisms like deep sea worms). A few parasites like Trichinella spiralis (pork worm) respire anaerobically in nurse cells (infected cell playing host to the juvenile parasite). Some largely unicellular anaerobic microbes are protozoans, but most of the anaerobic microbes are bacteria or Archaea. For practical purposes there are three categories: obligate anaerobes, which are harmed by the presence of oxygen aerotolerant organisms, which cannot use oxygen for growth, but tolerate the presence of it facultative anaerobes, which can grow without oxygen but can utilize oxygen if it is present
has exact synonym: anaerobically
definition: A prokaryotic metabolic quality where the organism grows in the absence of oxygen.

chemotrophy
type: Class
equivalent class: Class
  intersection of: respiratory metabolic process
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001494
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001458
  intersection of: Restriction
    on property: uses energy source
    all values from: CHEBI_24431
subclass of: respiratory metabolic process
subclass of: Restriction
  on property: uses energy source
  all values from: CHEBI_24431
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001458
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001494
IAO_0000119: Wikipedia:Chemotroph Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic (chemolithotrophs). The chemotroph designation is in contrast to phototrophs, which utilize solar energy. Chemotrophs can be either autotrophic or heterotrophic.
definition: A prokaryotic respiratory metabolic process where the oxidation and reduction of chemical compounds is the energy source.
created by: Carrine Blank

mixotrophy
type: Class
equivalent class: Class
  intersection of: respiratory metabolic process
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: phototrophy
      intersection of: Restriction
        on property: BFO_0000051
        some values from: MICRO_0001442
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001454
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001475
subclass of: respiratory metabolic process
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001475
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: phototrophy
    intersection of: Restriction
      on property: BFO_0000051
      some values from: MICRO_0001442
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001454
IAO_0000119: Wikipedia:Mixotroph A mixotroph is an organism that can use a mix of different sources of energy and carbon. Possible alternations are between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of it. Mixotrophs can be either eukaryotic or prokaryotic. They can take advantage of different environmental conditions. If a trophic mode is obligate, then it is always necessary for sustaining growth and maintenance; if facultative, it can be used as a supplemental source. Some organisms have incomplete Calvin cycles, so they are incapable of fixing carbon dioxide and must use organic carbon sources.
definition: A prokaryotic respiratory metabolic process where phototrophy and heterotrophy co-occur at the same instance in time.
created by: Carrine Blank

phototrophy
type: Class
equivalent class: Class
  intersection of: respiratory metabolic process
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0009853
      intersection of: Restriction
        on property: BFO_0000051
        some values from: GO_0015979
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001452
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001457
  intersection of: Restriction
    on property: uses energy source
    all values from: MICRO_0001441
subclass of: respiratory metabolic process
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001452
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001457
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: GO_0009853
    intersection of: Restriction
      on property: BFO_0000051
      some values from: GO_0015979
subclass of: Restriction
  on property: uses energy source
  all values from: MICRO_0001441
definition: A prokaryotic respiratory metabolic process where light is the energy source.
created by: Carrine Blank
IAO_0000119: Wikipedia:Phototroph Phototrophs are the organisms that carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. Most of the well-recognized phototrophs are autotrophs, also known as photoautotrophs, and can fix carbon.

photolithotrophy
type: Class
equivalent class: Class
  intersection of: phototrophy
  intersection of: Restriction
    on property: uses electron donor
    some values from: CHEBI_24835
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001507
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001482
subclass of: phototrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001507
subclass of: Restriction
  on property: uses electron donor
  some values from: CHEBI_24835
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001482
definition: A prokaryotic respiratory metabolic process where light is the energy source, and the electron donor is an inorganic compound.
IAO_0000119: Wikipedia:Lithotroph Photolithotrophs obtain energy from light and therefore use inorganic electron donors only to fuel biosynthetic reactions (e.g., carbon dioxide fixation in lithoautotrophs). These bacteria are photosynthetic; photolithotrophic bacteria are found in the purple bacteria (e. g., Chromatiaceae), green bacteria (Chlorobiaceae and Chloroflexi) and Cyanobacteria. Purple and green bacteria oxidize sulfide, sulfur, sulfite, iron or hydrogen. Cyanobacteria extract reducing equivalents from water, i.e., they oxidise water to oxygen. The electrons obtained from the electron donors are not used for ATP production (as long as there is light); they are used in biosynthetic reactions. Some photolithotrophs shift over to chemolithotrophic metabolism in the dark.
created by: Carrine Blank

photolithoautotrophy
type: Class
equivalent class: Class
  intersection of: photolithotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_16526
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001508
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001483
subclass of: photolithotrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001483
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_16526
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001508
created by: Carrine Blank
IAO_0000119: Wikipedia:Microbial metabolism Photolithoautotrophs obtain energy from light and carbon from the fixation of carbon dioxide, using reducing equivalents from inorganic compounds. Examples: Cyanobacteria (water (H2O) as reducing equivalent donor), Chlorobiaceae, Chromatiaceae (hydrogen sulfide (H2S) as reducing equivalent donor), Chloroflexus (hydrogen (H2) as reducing equivalent donor).
definition: A prokaryotic respiratory metabolic process where light is the energy source, the electron donor is an inorganic compound, and the carbon source is carbon dioxide

photofermentation
type: Class
equivalent class: Class
  intersection of: fermentation metabolic process
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001498
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001493
  intersection of: Restriction
    on property: is prokaryotic metabolic process carried out in the presence of
    all values from: MICRO_0001441
subclass of: fermentation metabolic process
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001493
subclass of: Restriction
  on property: is prokaryotic metabolic process carried out in the presence of
  all values from: MICRO_0001441
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001498
definition: A prokaryotic metabolic process that involves fermentation in the light. Is carried out by photosynthetic prokaryotic microorganisms.
created by: Carrine Blank
IAO_0000119: Wikipedia: Photofermentation Photofermentation is the fermentative conversion of organic substrate to biohydrogen manifested by a diverse group of photosynthetic bacteria by a series of biochemical reactions involving three steps similar to anaerobic conversion. Photofermentation differs from dark fermentation because it only proceeds in the presence of light. For example photo-fermentation with Rhodobacter sphaeroides SH2C (or many other purple non-sulfur bacteria[1]) can be employed to convert small molecular fatty acids into hydrogen[2] and other products.
has exact synonym: photofermentative

aerotolerant
type: Class
equivalent class: Class
  intersection of: aerophilicity
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001416
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001529
subclass of: aerophilicity
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001416
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001529
IAO_0000119: Wikipedia:anaerobic_organism An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. For practical purposes there are three categories: obligate anaerobes, which are harmed by the presence of oxygen aerotolerant organisms, which cannot use oxygen for growth, but tolerate the presence of it facultative anaerobes, which can grow without oxygen but can utilize oxygen if it is present
created by: Carrine Blank
definition: A prokaryotic metabolic quality where the organism grows in the absence of oxygen. Can grow or live in the presence of oxygen.

facultatively anaerobic
type: Class
equivalent class: Class
  intersection of: aerophilicity
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001520
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001527
subclass of: aerophilicity
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001527
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001520
has exact synonym: facultative anaerobe
has exact synonym: facultatively anaerobic
has exact synonym: facultatively aerobic
IAO_0000119: Wikipedia:facultative_anaerobic_organism A facultative anaerobic organism is an organism, usually a bacterium, that makes ATP by aerobic respiration if oxygen is present but is also capable of switching to fermentation. In contrast, obligate anaerobes die in the presence of oxygen.
created by: Carrine Blank
has related synonym: facultative anaerobe
definition: A prokaryotic metabolic quality where the organism grows in the presence of oxygen or in the absence of oxygen.
has exact synonym: facultative aerobe

obligately anaerobic
type: Class
equivalent class: Class
  intersection of: anaerobic
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001519
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001530
subclass of: anaerobic
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001530
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001519
has exact synonym: obligate anaerobic
IAO_0000119: Wikipedia:obligate_anaerobe Obligate anaerobes are microorganisms that live and grow in the absence of molecular oxygen; some of these are killed by oxygen.
has exact synonym: strictly anoxic
has exact synonym: strictly anaerobic
has exact synonym: obligately anaerobic
definition: A prokaryotic metabolic quality where the organism grows in the absence of oxygen. Cannot grow or live in the presence of oxygen.
has exact synonym: obligatory anaerobic
created by: Carrine Blank

chemolithotrophy
type: Class
equivalent class: Class
  intersection of: chemotrophy
  intersection of: Restriction
    on property: uses electron donor
    some values from: CHEBI_24835
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001499
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001476
subclass of: chemotrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001499
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001476
subclass of: Restriction
  on property: uses electron donor
  some values from: CHEBI_24835
created by: Carrine Blank
definition: A prokaryotic respiratory metabolic process where the oxidation and reduction of chemical compounds is the energy source, and the electron donor is an inorganic compound.
IAO_0000119: Wikipedia:Lithotroph A chemolithotroph (named after the process of chemolithotropy) is a type of extremophile that is able to use inorganic reduced compounds as a source of energy. This process is accomplished through oxidation and ATP synthesis. Most chemolithotrophs are able to fix carbon dioxide (CO2) through the Calvin Cycle, a metabolic pathway in which carbon enters as CO2 and leaves as glucose. This group of organisms includes sulfur oxidizers, nitrifying bacteria, iron oxidizers, and hydrogen oxidizers. The term chemolithotropy refers to a cell’s acquisition of energy from the oxidation of inorganic compounds, also known as electron donors, in the absence of light. Chemolithotropy is a form of metabolism, and the extreme conditions under which it can take place leads to its classification as a branch of the extremophiles. This process only occurs in prokaryotes, and was first characterized by the Russian microbiologist Sergej Winogradsky.

chemoorganotrophy
type: Class
equivalent class: Class
  intersection of: chemotrophy
  intersection of: Restriction
    on property: uses electron donor
    some values from: CHEBI_50860
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001504
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001479
subclass of: chemotrophy
subclass of: Restriction
  on property: uses electron donor
  some values from: CHEBI_50860
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001479
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001504
definition: A prokaryotic respiratory metabolic process where the oxidation and reduction of chemical compounds is the energy source, and the electron donor is an organic compound.
IAO_0000119: Wikipedia:Primary nutritional groups Chemoorganotrophs are organisms which oxidize the chemical bonds in organic compounds as their energy source. Chemoorganotrophs also attain the carbon molecules that they need for cellular function from these organic compounds. The organic compounds that they oxidize include sugars (i.e. glucose), fats and proteins).[2]
created by: Carrine Blank

photolithoheterotrophy
type: Class
equivalent class: Class
  intersection of: photolithotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_50860
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001509
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001484
subclass of: photolithotrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001484
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_50860
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001509
created by: Carrine Blank
definition: A prokaryotic respiratory metabolic process where light is the energy source, the electron donor is an inorganic compound, and the carbon source is an organic compound.

photoorganotrophy
type: Class
equivalent class: Class
  intersection of: phototrophy
  intersection of: Restriction
    on property: uses electron donor
    some values from: CHEBI_50860
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001510
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001485
subclass of: phototrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001485
subclass of: Restriction
  on property: uses electron donor
  some values from: CHEBI_50860
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001510
definition: A prokaryotic respiratory metabolic process where light is the energy source, and the electron donor is an organic compound.
has exact synonym: photoheterotroph
IAO_0000119: Wikipedia:Photoheterotroph Photoheterotrophs are heterotrophic organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source. Consequently, they use organic compounds from the environment to satisfy their carbon requirements; these compounds include carbohydrates, fatty acids, and alcohols. Examples of photoheterotrophic organisms include purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria.
created by: Carrine Blank

photoorganoautotrophy
type: Class
equivalent class: Class
  intersection of: photoorganotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_16526
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001511
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001486
subclass of: photoorganotrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001486
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_16526
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001511
created by: Carrine Blank
definition: A prokaryotic respiratory metabolic process where light is the energy source, the electron donor is an organic compound, and the carbon source is an carbon dioxide.

photoorganoheterotrophy
type: Class
equivalent class: Class
  intersection of: photoorganotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_50860
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001512
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001487
subclass of: photoorganotrophy
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_50860
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001512
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001487
IAO_0000119: Wikipedia:Microbial metabolism Photoorganoheterotrophs obtain energy from light, carbon and reducing equivalents for biosynthetic reactions from organic compounds. Some species are strictly heterotrophic, many others can also fix carbon dioxide and are mixotrophic. Examples: Rhodobacter, Rhodopseudomonas, Rhodospirillum, Rhodomicrobium, Rhodocyclus, Heliobacterium, Chloroflexus (alternatively to photolithoautotrophy with hydrogen).
created by: Carrine Blank
definition: A prokaryotic respiratory metabolic process where light is the energy source, the electron donor is an organic compound, and the carbon source is an organic compound.

chemolithoautotrophy
type: Class
equivalent class: Class
  intersection of: chemolithotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_16526
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001500
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001477
subclass of: chemolithotrophy
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_16526
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001500
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001477
IAO_0000119: Wikipedia:Microbial metabolism Chemolithoautotrophs obtain energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide. Examples: Nitrifying bacteria, Sulfur-oxidizing bacteria, Iron-oxidizing bacteria, Knallgas-bacteria.
created by: Carrine Blank
definition: A prokaryotic respiratory metabolic process where the oxidation and reduction of chemical compounds is the energy source, the electron donor is an inorganic compound, and the carbon source is carbon dioxide.

chemolithoheterotrophy
type: Class
equivalent class: Class
  intersection of: chemolithotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_50860
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001503
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001478
subclass of: chemolithotrophy
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_50860
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001503
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001478
IAO_0000119: Wikipedia:Microbial metabolism Chemolithoheterotrophs obtain energy from the oxidation of inorganic compounds, but cannot fix carbon dioxide (CO2). Examples: some Thiobacillus, some Beggiatoa, some Nitrobacter spp., Wolinella (with H2 as reducing equivalent donor), some Knallgas-bacteria, some sulfate-reducing bacteria.
created by: Carrine Blank
definition: A prokaryotic respiratory metabolic process where the oxidation and reduction of chemical compounds is the energy source, the electron donor is an inorganic compound, and the carbon source is an organic compound.

chemoorganoautotrophy
type: Class
equivalent class: Class
  intersection of: chemoorganotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_16526
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001505
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001480
subclass of: chemoorganotrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001505
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_16526
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001480
definition: A prokaryotic respiratory metabolic process where the oxidation and reduction of chemical compounds is the energy source, the electron donor is an organic compound, and the carbon source is carbon dioxide.
created by: Carrine Blank

chemoorganoheterotrophy
type: Class
equivalent class: Class
  intersection of: chemoorganotrophy
  intersection of: Restriction
    on property: uses carbon source
    some values from: CHEBI_50860
  intersection of: Restriction
    on property: is prokaryotic metabolic process occuring in
    some values from: MICRO_0001506
  intersection of: Restriction
    on property: is prokaryotic metabolic process which makes a cell
    some values from: MICRO_0001481
subclass of: chemoorganotrophy
subclass of: Restriction
  on property: is prokaryotic metabolic process which makes a cell
  some values from: MICRO_0001481
subclass of: Restriction
  on property: uses carbon source
  some values from: CHEBI_50860
subclass of: Restriction
  on property: is prokaryotic metabolic process occuring in
  some values from: MICRO_0001506
definition: A prokaryotic respiratory metabolic process where the oxidation and reduction of chemical compounds is the energy source, the electron donor is an organic compound, and the carbon source is an organic compound.
created by: Carrine Blank
IAO_0000119: Wikipedia:Primary nutritional groups A chemoorganoheterotrophic organism is one that requires organic substrates to get its carbon for growth and development, and that produces its energy from oxido-reduction of an organic compound. This group of organisms may be further subdivided according to what kind of organic substrate and compound they use. Decomposers are examples of Chemoorganoheterotrophs which obtain carbon and electron reactions from dead organic matter. Herbivores and carnivores are examples of organisms that obtain carbon and electron reactions from living organic matter.
has exact synonym: heterotroph

microaerophilic
type: Class
equivalent class: Class
  intersection of: aerobic
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001515
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001533
subclass of: aerobic
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001515
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001533
definition: A prokaryotic metabolic quality where the organism grows in the presence of oxygen, where the oxygen concentration is less than atmospheric levels.
IAO_0000119: Wikipedia:microaerophile A microaerophile is a microorganism that requires oxygen to survive, but requires environments containing lower levels of oxygen than are present in the atmosphere (~20% concentration). Many microphiles are also capnophiles, as they require an elevated concentration of carbon dioxide. In the laboratory they can be easily cultivated in a candle jar. A candle jar is a container into which a lit candle is introduced before sealing the container's airtight lid. The candle's flame burns until extinguished by oxygen deprivation, which creates a carbon dioxide-rich, oxygen-poor atmosphere in the jar.
has exact synonym: microaerobically
has exact synonym: Microaerophilically
has exact synonym: microaerobic
has exact synonym: microaerophilic
created by: Carrine Blank
has exact synonym: microoxic

obligately aerobic
type: Class
equivalent class: Class
  intersection of: aerobic
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of
    some values from: MICRO_0001516
  intersection of: Restriction
    on property: is prokaryotic metabolic quality of a cell carrying out the process
    some values from: MICRO_0001532
subclass of: aerobic
subclass of: Restriction
  on property: is prokaryotic metabolic quality of a cell carrying out the process
  some values from: MICRO_0001532
subclass of: Restriction
  on property: is prokaryotic metabolic quality of
  some values from: MICRO_0001516
definition: A prokaryotic metabolic quality where the organism grows in the presence of oxygen. Is incapable of anaerobic growth (growth in the absence of oxygen).
IAO_0000119: Wikipedia:obligate_aerobe An obligate aerobe is an aerobic organism that requires oxygen to grow. Through cellular respiration, these organisms use oxygen to oxidize substances, like sugars or fats, in order to obtain energy. During respiration, they use oxygen as the terminal electron acceptor. They have the advantage of yielding more energy than obligate anaerobes, but face high levels of oxidative stress.
has exact synonym: obligatory aerobic
has exact synonym: obligately aerobic
created by: Carrine Blank
has exact synonym: strictly aerobic

microbiological medium ingredient, derived from extracts of plants
type: Class
subclass of: MICRO_0001370
subclass of: Restriction
  on property: is an aqueous extract derived from
  some values from: NCBITaxon 3193
subclass of: Restriction
  on property: has ingredient
  some values from: CHEBI_15377
definition: Undefined mixtures of complex organic compounds deriving from the aqueous extraction (an extraction using water, such as hot water or steam) of macroscopic plants. Used in the cultivation of microorganisms.
created by: Carrine Blank

defined organic chemical mixture
type: Class
subclass of: organic chemical mixture
definition: Organic compounds or mixtures of organic compounds added to culture media to support growth or metabolism of a microorganism. Because the exact composition of the mixture is known, it is referred to as "defined".
created by: Carrine Blank

clarified rumen fluid
type: Class
equivalent class: Class
  intersection of: undefined organic chemical mixture
  intersection of: Class
    intersection of: Restriction
      on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
      some values from: NCBITaxon 9913
    intersection of: Restriction
      on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
      some values from: UBERON_0010228
  intersection of: Restriction
    on property: has chemical composition
    some values from: UBERON_0010228
  intersection of: Restriction
    on property: RO_0002354
    some values from: Class
      intersection of: CHMO_0002846
      intersection of: Restriction
        on property: RO_0002354
        some values from: OBI_0302886
definition: Undefined organic chemical mixture, comprised of ruminal fluid derived from the rumen of a cow, which has been clarified (through the processes of heating/autoclaving and then centrifugation). Used to cultivate microorganisms.
has exact synonym: rumen fluid
has exact synonym: Tureen fluid
created by: Carrine Blank

sludge fluid
type: Class
subclass of: undefined organic chemical mixture
subclass of: Restriction
  on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
  some values from: ENVO_00002044
IAO_0000119: From Wikipedia:Sludge: Sludge is a semi-solid slurry and can be produced as sewage sludge from wastewater treatment processes or as a settled suspension obtained from conventional drinking water treatment and numerous other industrial processes.
created by: Carrine Blank
definition: Fluid derived from the liquid component of municipal sludge, used for the cultivation of microorganisms.

Yeastolate
type: Class
equivalent class: Class
  intersection of: yeast extract
  intersection of: Restriction
    on property: RO_0002354
    some values from: GO_0001896
created by: Carrine Blank
definition: The water-soluble portion of autolyzed yeast (Saccharomyces cereviseiae), used to support the growth of microorganisms. Yeastolate is a branch name for a yeast extract sold by BD.
has narrow synonym: TC Proteose Yeastolate
IAO_0000119: From BD Bionutrients Technical Manual (3rd edition revised): TC Yeastolate products are animal-free and water-soluble portions of autolyzed yeast or Saccharomyces cerevisiae. TC Yeastolate is a mixture of peptides, amino acids, carbohydrates, simple and complex as well as vitamins. Ash content is 11.7% NaCl content is 0.6%
has narrow synonym: Bacto(TM) TC Yeastolate

multicellular prokaryote
type: Class
equivalent class: Class
  intersection of: prokaryotic cell having distinct cell arrangement
  intersection of: Restriction
    on property: has organismal quality
    some values from: PATO_0001993
subclass of: prokaryotic cell having distinct cell arrangement
subclass of: Restriction
  on property: has organismal quality
  some values from: PATO_0001993
created by: Carrine Blank
has broad synonym: multicellular
definition: A prokaryotic cellularity where cells are physically attached, or connected, to one another after cell division occurs. Septation may or may not occur. The connections between the cells may be loose and transient, or may be long-lasting and permanent.

chocolatized defibrinated blood
type: Class
subclass of: MICRO_0001233
subclass of: Restriction
  on property: RO_0002354
  some values from: CHMO_0002770
subclass of: Restriction
  on property: BFO_0000051
  all values from: Class
    complement of: Class
      union of: CHEBI 5054
      union of: GO_0005577
created by: Carrine Blank
IAO_0000119: From: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/AnimalBloodProd.htm Chocolatized Defibrinated Blood is defibrinated blood that has been heated to release additional growth factors that would otherwise remain unavailable within intact red blood cells. Heat stable hemin (X-factor) and heat labile nicotinamide adenine dinucleotide (V-factor) are the growth factors readily available in chocolatized media.
definition: Blood medium ingredient comprised of defibrinated blood that has been heated. Used in the cultivation of microorganisms.

inspissated serum
type: Class
equivalent class: Class
  intersection of: MICRO_0001236
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0001801
  intersection of: Restriction
    on property: RO_0002354
    some values from: CHMO_0001574
definition: Serum medium ingredient comprised of blood serum from a mammal that has been inspissated (dehydrated, i.e. has a decreased water composition). Used to support the growth of microorganisms which need inspissated blood serum to grow.
IAO_0000119: From Wikipedia:Inspissation: Inspissation is the process of thickening by dehydration.
created by: Carrine Blank
has exact synonym: Spissated serum

prokaryotic differentiated cell
type: Class
equivalent class: Class
  intersection of: CL_0000520
  intersection of: Restriction
    on property: RO_0000086
    some values from: PATO_0002099
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030154
subclass of: CL_0000520
subclass of: Restriction
  on property: RO_0000086
  some values from: PATO_0002099
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030154
created by: Carrine Blank
definition: Prokaryotic cells which have a morphological shape and a role that is different from vegetative (undifferentiated cells).

prokaryotic differentiated cell, specialized for nitrogen fixation
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0009399
subclass of: prokaryotic differentiated cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0009399
definition: Prokaryotic differentiated cell that has a role in the fixation of gaseous dinitrogen (N2) into ammonia and thus enhance survival in nitrogen-deficient environments.
created by: Carrine Blank

prokaryotic differentiated cell, specialized for asexual reproduction
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0019954
subclass of: prokaryotic differentiated cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0019954
IAO_0000119: Prokaryotic differentiated cell that has a role in asexual reproduction.
created by: Carrine Blank

prokaryotic differentiated cell, specialized for dormancy
type: Class
equivalent class: Class
  intersection of: prokaryotic differentiated cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: Class
      intersection of: GO_0022611
      intersection of: GO_0052386
  intersection of: Restriction
    on property: RO_0002354
    some values from: GO_0043936
subclass of: prokaryotic differentiated cell
subclass of: Restriction
  on property: RO_0002354
  some values from: GO_0043936
subclass of: Restriction
  on property: RO_0002215
  some values from: Class
    intersection of: GO_0022611
    intersection of: GO_0052386
definition: Prokaryotic differentiated cell which contributes to enhanced dormancy and thus survival during times unsuitable for growth.

Shioi marine medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17754
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32149
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86345
  intersection of: Restriction
    on property: has ingredient
    some values from: polypeptone
  intersection of: Restriction
    on property: has ingredient
    some values from: casamino acids
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: An organic-rich, marine, liquid microbiological culture medium containing yeast extract, polypeptone, casamino acids, and glycerol in an artificial sea water base. Used for the growth Erythrobacter.
IAO_0000119: Shioi Y. 1986. Growth characteristics and substrate specificity of aerobic photosynthetic bacterium, Erythrobacter sp. Och-114. Plant Cell Physiol 27:567-572. Shioi (1986) used a medium which contains in 1 liter of distilled water: 20 g NaCl, 5.0 g MgCl2x6H2O, 2.0 g Na2SO4, 0.5 g KCl, 0.5 g CaCl2x2H2O, 0.2 g NaHCO3, 0.1 g ferric citrate, 2.0 g yeast extract (Difco), 1.0 g polypeptone, 1.0 g Casamino acids, and 1.0 mL glycerol.
IAO_0000232: The pH is not in any available references online or in Bergey's Manual. However is likely slightly alkaline due to the buffering of sodium bicarbonate.
has exact synonym: Shioi's marine medium
has exact synonym: SMM medium
created by: Carrine Blank
has exact synonym: SMM media
IAO_0000119: Shiba T & Imhoff JF. 2005. Genus XVIII. Roseobacter in Bergey's Manual of Systematic Bacteriology, 2nd Ed. Vol 2, Part C, p. 213.

SM medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31206
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63036
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001404
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
IAO_0000119: From: http://cshprotocols.cshlp.org/content/2008/12/pdb.rec11558.full?text_only=true SM Broth Composition: Reagent Quantity (for 1 L) Final concentration Glucose 10 g 56 mM KH2PO4 1.9 g 14 mM K2HPO4 0.6 g 3.4 mM NH4Cl 1 g 20 mM Proteose peptone 2 ( Difco 212120) 10 g 1% Yeast extract (Oxoid LP0021) 1 g 0.1% Dissolve in 1 L of H2O. Adjust the pH to 6.0–6.4 with KOH.
has exact synonym: SM broth
definition: A liquid microbiological culture medium containing gelatin, magnesium sulfate, and sodium chloride. Used for the storage and dilution of Escherichia coli bacteriophage lambda.

CMRL-1066 medium with glutamine
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_13389
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15346
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15354
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15428
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15603
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15713
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15940
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15956
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_15971
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16015
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16113
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16238
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16283
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16414
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16467
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16643
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16709
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16828
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16856
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16857
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16977
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17015
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17053
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17115
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17154
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17191
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17203
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17268
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17295
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17310
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17895
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_18019
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_18050
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_18095
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_18290
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_25523
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26948
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_27470
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_30753
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32599
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32954
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_37585
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4178
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53426
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_60173
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_68472
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 7916
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_91248
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: CHEBI_22652
      union of: CHEBI_38290
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Datasheet/c0422dat.pdf CMRL-1066 With L-Glutamine, Without Sodium Bicarbonate Components g/L L-Alanine 0.025 L-Arginine 0.05787 L-Aspartic Acid 0.03 L-Cysteine•HCl• H2O 0.26 L-Cystine 0.02 L-Glutamic Acid 0.075 L-Glutamine 0.1 Glycine 0.05 L-Histidine HCl• H2O 0.02 Trans-4-Hydroxy-L-Proline 0.01 L-Isoleucine 0.02 L-Leucine 0.06 L-Lysine•HCl 0.07 L-Methionine 0.015 L-Phenylalanine 0.025 L-Proline 0.04 L-Serine 0.025 L-Threonine 0.03 L-Tryptophan 0.01 L-Tyrosine 0.04 L-Valine 0.025 L-Ascorbic Acid 0.05 PABA 0.00005 D-Biotin 0.00001 Choline Chloride 0.0005 Coenzyme A•Na 0.0025 Cocarboxylase 0.001 2'-Deoxyadenosine 0.01 2'-Deoxyguanosine 0.01 2'-Deoxycytidine•HCl 0.0116 Flavin Aadenine Dinucleotide•2Na 0.000106 Folic Acid 0.00001 myo-Inositol 0.00005 5-Methyldeoxycytidine 0.0001 beta-NAD 0.007 beta-NADP•Na 0.001 Niacinamide 0.000025 Nicotinic Acid 0.000025 D-Pantothenic Acid [hemicalcium] 0.00001 Pyridoxal•HCl 0.000025 Pyridoxine•HCl 0.000025 Riboflavin 0.00001 Thiamine•HCl 0.00001 Thymidine 0.01 Uridine-5-Triphosphate•Na 0.001 Calcium Chloride [Anhydrous] 0.2 Magnesium Sulfate [Anhydrous] 0.09769 Potassium Chloride 0.4 Sodium Acetate [Anhydrous] 0.05 Sodium Chloride 6.8 Sodium Phosphate Monobasic [Anhydrous] 0.122 D-Glucose 1.0 Phenol Red•Na 0.02124 Glutathione 0.01 D-Glucuronic Acid•Na 0.00388 Cholesterol 0.0002 Tween 80 0.005 Sodium bicarbonate is added during the preparation step and the pH is adjusted to 7.0 ± 0.3.
definition: A defined liquid microbiological culture medium containing glucose, a pH indicator, a mixture of amino acids, vitamins, co-factors, and organic micronutrients. Used for tissue cell culture.

skim milk medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001241
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001404
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Skim Milk Medium (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Skim Milk Medium may be used for the cultivation and differentiation of microorganisms based on the coagulation and proteolysis of casein. Principles of the Procedure Skim Milk is a source of lactose and casein and other nutrients required for the growth of lactobacilli.4 Clostridial species can be differentiated based on their ability to enzymatically degrade proteins to peptones (peptonization) or coagulate milk.5 It may be used to detect the stormy fermentation produced by Clostridium perfringens. Formula Difco(TM) Skim Milk Approximate Formula* Per Liter Skim Milk Powder 100.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 6.3 ± 0.2
created by: Carrine Blank
definition: An organic-rich, liquid microbiological culture medium containing skim milk powder. Used to cultivate microorganisms that can metabolize casein.

skim milk agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001241
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001404
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Skim Milk Medium (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Skim Milk Medium may be used for the cultivation and differentiation of microorganisms based on the coagulation and proteolysis of casein. Principles of the Procedure Skim Milk is a source of lactose and casein and other nutrients required for the growth of lactobacilli.4 Clostridial species can be differentiated based on their ability to enzymatically degrade proteins to peptones (peptonization) or coagulate milk.5 It may be used to detect the stormy fermentation produced by Clostridium perfringens. Formula Difco(TM) Skim Milk Approximate Formula* Per Liter Skim Milk Powder 100.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 6.3 ± 0.2
definition: An organic-ric, solid microbiological culture medium containing skim milk powder. Used to cultivate microorganisms that can metabolize casein.
definition: Skim milk media containing agar.

Columbia sheep blood agar
type: Class
equivalent class: Class
  intersection of: Columbia Agar Base
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001230
created by: Carrine Blank
has exact synonym: Sheep blood agar
has exact synonym: Columbia blood agar
has exact synonym: CSB agar
has exact synonym: CBA
has exact synonym: Columba-based sheep blood agar
definition: An organic-rich, solid microbiological culture medium, containing peptones, starch, and sheep blood. Used for the growth of heterotrophic microorganisms that require blood.
has exact synonym: Heart infusion agar supplemented with sheep blood
has exact synonym: CSB
IAO_0000119: From: Columbia Agar with 5% Sheep Blood (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Columbia Agar Base, without or with the addition of 5% (or 10%) sheep blood, is a highly nutritious, general-purpose medium for the isolation and cultivation of nonfastidious and fastidious microorganisms from a variety of clinical and nonclinical materials. Difco™ Columbia Blood Agar Base Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 10.0 g Proteose Peptone No. 3................................................ 5.0 g Yeast Extract................................................................ 5.0 g Beef Heart, Infusion from 500 g................................... 3.0 g Corn Starch.................................................................. 1.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 15.0 g Directions for Preparation from Dehydrated Product 1. Suspend the powder in 1 L of purified water: Difco™ Columbia Blood Agar Base – 44 g; BBL™ Columbia Agar Base – 42.5 g; Difco™ Columbia Blood Agar Base EH – 39 g. Mix thoroughly. 2. Heat with frequent agitation and boil for 1 minute to completely dissolve the powder. 3. Autoclave at 121°C for 15 minutes. 4. For preparation of blood agar, cool the base to 45-50°C and add 5% sterile, defibrinated blood. Mix well. 5. Test samples of the finished product for performance using stable, typical control cultures.

Columbia Agar Base
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_28017
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: heart pancreatic digest
  intersection of: Restriction
    on property: has ingredient
    some values from: pancreatic digest of gelatin
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: An organic-rich, solid microbiological culture medium, containing peptones and starch. Used for the growth of heterotrophic microorganisms.
created by: Carrine Blank
IAO_0000119: From: Columbia Agar Base (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Columbia Agar Base, without or with the addition of 5% (or 10%) sheep blood, is a highly nutritious, general-purpose medium for the isolation and cultivation of nonfastidious and fastidious microorganisms from a variety of clinical and nonclinical materials. Principles of the Procedure Columbia Agar Base supplemented with sheep, rabbit or horse blood derives its superior growth-supporting properties from the combination of peptones prepared from pancreatic digest of casein, meat peptic digest and heart pancreatic digest. Yeast extract and corn starch are also included in the formulation and serve as energy sources with yeast extract being a supplier of the B-complex vitamins. Sodium chloride maintains osmotic balance in the medium. It should be noted that Columbia Sheep Blood Agar has a relatively high carbohydrate content and, therefore, beta-hemolytic streptococci may produce a greenish hemolytic reaction that may be mistaken for alpha hemolysis. Fildes enrichment is prepared by the action of the enzyme pepsin on defibrinated sheep blood. Bacitracin is a polypeptide antibiotic that is active mainly against gram-positive bacteria. BBL™ Columbia Agar Base Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 10.0 g Meat Peptic Digest....................................................... 5.0 g Yeast Extract................................................................ 5.0 g Heart Pancreatic Digest................................................ 3.0 g Corn Starch.................................................................. 1.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 13.5 g pH 7.3 ± 0.2

seawater agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: beef extract
  intersection of: Restriction
    on property: has ingredient
    some values from: Class
      union of: ENVO_00002149
      union of: MICRO_0001715
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: Humphry DR, George A, Black GW & Cummings SP. 2001. Flavobacteirum frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminariolytic bacterium from Antarctica. IJSEM 51:1235-1243.
IAO_0000119: From: http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium246.pdf DSMZ Medium 246 246. SEA WATER AGAR Beef extract 10.0 g Peptone 10.0 g Agar 20.0 g Tap water 250.0 ml Sea water* 750.0 ml Dissolve beef extract and peptone by heating in tap water, adjust pH to 7.8 and boil for 10 min. Readjust pH to 7.3. Add agar and autoclave at 121°C for 20 min. Directly after autoclaving, add warm (55°C) sterile sea water. Liquid medium without agar should be combined when cooled to room temperature. *Natural sea water is stored in the dark for at least three weeks to "age". If natural sea water is not available use artificial sea water. Artificial sea water: NaCl 28.13 g KCl 0.77 g CaCl2 x 2 H2O 1.60 g MgCl2 x 6 H2O 4.80 g NaHCO3 0.11 g MgSO4 x 7 H2O 3.50 g Distilled water 1000.0 ml © 2007 DSMZ GmbH - All rights reserved
definition: An organic-rich, marine, solid microbiological culture medium containing beef extract and peptone, in a diluted artificial sea water base. Used for the growth of marine Flavobacterium.
created by: Carrine Blank

ZoBell medium, NaCl-free
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Class
    intersection of: Restriction
      on property: has ingredient
      some values from: CHEBI_26710
    intersection of: Restriction
      on property: RO_0000086
      some values from: PATO_0001163
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_132769
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32030
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32139
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_33118
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 3312
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_34683
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_36383
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 4991
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_60720
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63038
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 6636
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_76208
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: Class
      union of: MICRO_0001290
      union of: MICRO_0001291
      union of: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001403
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Yi H, Cho J-C, & Chun J. 2012. Flavivirga jejuensis gen. nov., sp. nov., and Flavivirga amylovorans sp. nov., new members of the family Flavobacteriaceae isolated from seawater, and emended descriptions of the genera Psychroserpens and Lacinutrix. IJSEM 62:1061-1068. Growth in synthetic ZoBell broth was tested at 5-50˚C (at 5˚C intervals) and in the presence of 0, 0.5, 1, 2, 3, 4, 5, 7, 10, 12, 15 and 20% (w/v) NaCl or sea salts (Sigma).
has exact synonym: Sea salts-free Zobell's medium
definition: An organic-rich, mineral-salts, liquid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Made without sodium chloride. Used to test the salinity preference of marine heterotrophic microorganisms.
created by: Carrine Blank

rabbit laked blood agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_16236
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26709
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_28384
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32145
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50385
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001228
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001387
definition: An organic-rich, solid microbiological culture medium containing peptones, yeast extract, sodium chloride, glucose, sodium sulfite, hemin, vitamin K, and laked rabbit blood. Used for the growth of heterotrophic microorganisms that require blood.
created by: Carrine Blank
IAO_0000119: From: Atlas RM, Handbook of Microbiological Media, 3rd edition, pg. 1472 Composition per liter: Agar 15.0 g Pancreatic digest of casein 10.0 g Peptic digest of animal tissue 10.0 g NaCl 5.0 g Yeast extract 2.0 g Glucose 1.0 g NaHSO3 0.1 g Rabbit blood, laked 50.0 mL Hemin solution 1.0 mL Vitamin K1 solution 1.0 mL pH 7.0 +/- 0.2 at 25˚C Hemin solution: Composition per 100.0 mL: Hemin 0.5 g NaOH (1N solution) 10.0 mL Preparation of Hemin Solution: Add hemin to 10.0 mL of NaOH solution. Mix thoroughly. Vitamin K1 solution: Composition per 20.0 mL: Vitamin K1 (phytomenadione) 0.2 g Ethanol (95% solution) 20.0 mL Preparation of Vitamin K1 Solution: Add vitamin K1 to 20.0 mL of ethanol. Mix thoroughly. Preparation of Medium: Add components, except vitamin K1 solution and laked rabbit blood, to distilled/deionized water and bring volume to 849.0 mL. Mix thoroughly. Gently heat and bring to boiling. Autoclave for 15 min at 15 psi pressure-121˚C. Cool to 45-55˚C. Aseptically add 1.0 mL of sterile vitamin K1 solution and 50.0 mL of sterile laked rabbit blood. Laked blood is prepared by freezing whole blood overnight and thawing to room temperature. Mix thoroughly. Pour into steril Petri dishes or distribute into sterile tubes. Use: For the cultivation and enhancement of pigment production of a variety of anaerobic bacteria.

R2A medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50144
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: casamino acids
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0002561
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: An organic-rich, liquid microbiological culture medium containing yeast extract, proteose peptone, casamino acids, glucose, starch, and pyruvate. Used for the growth of heterotrophic bacteria from potable (fresh) water.
has exact synonym: Reasoner's 2A
IAO_0000119: From: Wikipedia: R2a agar R2A agar (Reasoner´s 2A agar) is a culture medium developed to study bacteria which normally inhabit potable water. These bacteria tend to be slow-growing species and would quickly be suppressed by faster-growing species on a richer culture medium. Since its development in 1979, it has been found to allow the culturing of many other bacteria that will not readily grow on fuller, complex organic media. Typical Composition (g/l) Proteose peptone, 0.5 Casamino acids, 0.5 Yeast extract, 0.5 Dextrose, 0.5 Soluble starch, 0.5 Dipotassium phosphate, 0.3 Magnesium sulfate 7H2O, 0.05 Sodium pyruvate, 0.3 Agar, 15 Final pH 7 ± 0.2
has exact synonym: R2A broth
created by: Carrine Blank

R3A medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50144
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: casamino acids
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0002561
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
IAO_0000119: From: Reasoner DJ & Geldreich EE. 1985. A new medium for the enumeration and subculture of bacteria from potable water. AEM 49(1):1-7. Composiotn of R3A Experimental Media (From Table 1): Yeast extract, 1.0 g/L Difco Proteose Peptone No. 3, 1.0 g/L Casamino Acids, 1.0 g/L Glucose, 1.0 g/L Soluble starch, 1.0 g/L Sodium pyruvate, 0.5 g/L K2HPO4, 0.6 g/L MgSO4x7H2O, 0.1 g/L Agar, 15.0 g/L Final pH 7.2; adjust with crystalline K2HPO4 or KH2PO4 before adding agar. Add agar, heat medium to boiling to dissolve agar, and autoclave for 15 min at 121°C and 15 lb/in2.
definition: An organic-rich, liquid microbiological culture medium containing yeast extract, proteose peptone, casamino acids, glucose, starch, and pyruvate. Concentration of organic and inorganic constituents are twice that in R2A medium. Used for the growth of heterotrophic bacteria from potable (fresh) water.

R2A agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_50144
  intersection of: Restriction
    on property: has ingredient
    some values from: proteose peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: casamino acids
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0002561
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: An organic-rich, solid microbiological culture medium containing yeast extract, proteose peptone, casamino acids, glucose, starch, and pyruvate. Used for the growth of heterotrophic bacteria from potable (fresh) water.
created by: Carrine Blank
has exact synonym: R2A plates
IAO_0000119: From: Wikipedia: R2a agar R2A agar (Reasoner´s 2A agar) is a culture medium developed to study bacteria which normally inhabit potable water. These bacteria tend to be slow-growing species and would quickly be suppressed by faster-growing species on a richer culture medium. Since its development in 1979, it has been found to allow the culturing of many other bacteria that will not readily grow on fuller, complex organic media. Typical Composition (g/l) Proteose peptone, 0.5 Casamino acids, 0.5 Yeast extract, 0.5 Dextrose, 0.5 Soluble starch, 0.5 Dipotassium phosphate, 0.3 Magnesium sulfate 7H2O, 0.05 Sodium pyruvate, 0.3 Agar, 15 Final pH 7 ± 0.2

YPD broth
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001404
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: GYEA
definition: An organic-rich, liquid microbiological culture medium containing yeast extract, peptone, and dextrose (D-glucose). Used for the cultivation of yeasts.
has exact synonym: PYG medium
has exact synonym: peptone yeast glucose broth
has exact synonym: peptone/yeast-extract/glucose broth
IAO_0000119: From: Yeast Extract-Peptone-Dextrose Broth (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use YPD Agar and YPD Broth are used for maintaining and propagating yeasts in molecular microbiology procedures. Principles of the Procedure YPD Agar and YPD Broth contain peptone as a source of carbon, nitrogen, vitamins and minerals. Yeast extract supplies B-complex vitamins which stimulate bacterial growth. Dextrose is the carbohydrate source. YPD Agar contains agar as the solidifying agent. Formulae Difco™ YPD Agar Approximate Formula* Per Liter Yeast Extract.............................................................. 10.0 g Peptone..................................................................... 20.0 g Dextrose.................................................................... 20.0 g Agar.......................................................................... 15.0 g Difco™ YPD Broth Consists of the same ingredients without the agar. *Adjusted and/or supplemented as required to meet performance criteria. pH 6.5 ± 0.2
created by: Carrine Blank
has exact synonym: peptone-yeast extract-glucose
has exact synonym: Glucose-yeast extract agar
comment: pH is 6.5
has exact synonym: PYG broth

YPD agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: PYG plates
created by: Carrine Blank
definition: An organic-rich, solid microbiological culture medium containing yeast extract, peptone, and dextrose (D-glucose). Used for the cultivation of yeasts.
comment: pH is 6.5
has exact synonym: PYG agar
IAO_0000119: From: Yeast Extract-Peptone-Dextrose Broth (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use YPD Agar and YPD Broth are used for maintaining and propagating yeasts in molecular microbiology procedures. Principles of the Procedure YPD Agar and YPD Broth contain peptone as a source of carbon, nitrogen, vitamins and minerals. Yeast extract supplies B-complex vitamins which stimulate bacterial growth. Dextrose is the carbohydrate source. YPD Agar contains agar as the solidifying agent. Formulae Difco™ YPD Agar Approximate Formula* Per Liter Yeast Extract.............................................................. 10.0 g Peptone..................................................................... 20.0 g Dextrose.................................................................... 20.0 g Agar.......................................................................... 15.0 g Difco™ YPD Broth Consists of the same ingredients without the agar. *Adjusted and/or supplemented as required to meet performance criteria. pH 6.5 ± 0.2
has exact synonym: peptone-yeast extract-glucose agar

YPD-Tween medium
type: Class
equivalent class: Class
  intersection of: YPD broth
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53426
created by: Carrine Blank
definition: An organic-rich, liquid microbiological culture medium containing yeast extract, peptone, and glucose. Supplemented with Tween 80 (0.02%, aka polysorbate 80). Used for the cultivation of Bacteroides spp.
has exact synonym: PYG-Tween
has exact synonym: Peptone-yeast extract-tween basal medium
IAO_0000119: From: Cato EP, Holdeman LV, & Moore WEC. 1979. Proposal of neotype strains for seven non-saccharolytic Bacteroides species. IJSB 29(4):427-434. Growth was stimulated by the addition of ca. 0.02% Tween 80 to the media.

PYE medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: Peptone-yeast extract broth
has exact synonym: PY
created by: Carrine Blank
has exact synonym: PYE broth
IAO_0000119: From: Kampfer P, Busse H-J, Longaric I, Rossello-Mora R, Galatis H, & Lodders N. 2012. Pseudarcicella hirudinis gen. nov., sp. nov., isolated from the skin of the medical leech Hirudo medicinalis. IJSEM 62:2247-2251. 0.3% (w/v) peptone from casein 0.3% (w/v) yeast extract pH 7.2 at 28˚C
definition: An organic-rich, liquid microbiological culture medium containing casitone and yeast extract. Used for the growth of Pseudarcicella sp.

peptone water medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: peptone-water medium
created by: Carrine Blank
IAO_0000119: From: Peptone Water (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Peptone Water is used for cultivating nonfastidious organisms, for studying carbohydrate fermentation patterns and for performing the indole test. Principles of the Procedure Peptone Water contains peptone as a source of carbon, nitrogen, vitamins and minerals. Sodium chloride maintains the osmotic balance of the medium. Formula Difco™ Peptone Water Approximate Formula* Per Liter Peptone..................................................................... 10.0 g Sodium Chloride.......................................................... 5.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 7.2 ± 0.2
definition: An organic-rich, liquid microbiological culture medium containing peptone and sodium chloride.
has broad synonym: peptone water

plate count agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17634
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0000606
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: PCA
definition: An organic-rich, solid microbiological culture medium containing pancreatic digest of casein, yeast extract, and dextrose. Used for the enumeration of microorganisms that grow in dairy products.
has exact synonym: Standard methods agar
has exact synonym: Tryptone Glucose Yeast Extract Agar
has exact synonym: PCA agar
has exact synonym: Tryptone glucose yeast agar
created by: Carrine Blank
IAO_0000119: From: Plate Count Agar/Standard Methods Agar (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Plate Count Agar and Standard Methods Agar (Plate Count Agar; Tryptone Glucose Yeast Agar) are used for obtaining microbial plate counts from milk and dairy products, foods, water and other materials of sanitary importance. Principles of the Procedure Enzymatic digest of casein provides the amino acids and other complex nitrogenous substances necessary to support bacterial growth. Yeast extract primarily supplies the B-complex vitamins, and dextrose is an energy source. TTC is reduced to the insoluble formazan inside the bacterial cell producing red-colored colonies. Formula Difco™ Plate Count Agar or BBL™ Standard Methods Agar Approximate Formula* Per Liter Pancreatic Digest of Casein.......................................... 5.0 g Yeast Extract................................................................ 2.5 g Dextrose...................................................................... 1.0 g Agar.......................................................................... 15.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 7.0 ± 0.2
has exact synonym: TGY agar
has exact synonym: pca medium

Pseudomonas isolation agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_164200
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32036
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 6636
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: PIA
definition: An organic-rich, solid microbiological culture medium containing peptone, potassium sulfate, magnesium chloride, and Irgasan (aka triclosan; a broad spectrum antibiotic). Is a selective medium used for the isoaltion and growth of Pseudomonas.
IAO_0000119: From: Pseudomonas Isolation Agar (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Pseudomonas Isolation Agar is used with added glycerol in isolating Pseudomonas and differentiating Pseudomonas aeruginosa from other pseudomonads based on pigment formation. Principles of the Procedure Peptone provides the carbon and nitrogen necessary for bacterial growth. Magnesium chloride and potassium sulfate promote production of pyocyanin. Irgasan, an antimicrobial agent, selectively inhibits gram-positive and gram-negative bacteria other than Pseudomonas spp. Agar is the solidifying agent. Glycerol serves as an energy source and also helps to promote pyocyanin production. Formula Difco™ Pseudomonas Isolation Agar Approximate Formula* Per Liter Peptone..................................................................... 20.0 g Magnesium Chloride.................................................... 1.4 g Potassium Sulfate....................................................... 10.0 g Irgasan™..................................................................... 25.0 mg Agar.......................................................................... 13.6 g *Adjusted and/or supplemented as required to meet performance criteria. pH 7.0 ± 0.2
created by: Carrine Blank

OF basal agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86155
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
has exact synonym: O/F medium
has exact synonym: Leifson's O/F medium
has exact synonym: Hugh and Leifson's OF basal medium
has related synonym: oxidation fermentation medium
has exact synonym: Leifson's O-F medium
has exact synonym: Hugh and Leifson's
created by: Carrine Blank
has exact synonym: OF basal medium
definition: An organic-rich, liquid microbiological culture medium containing peptone, glucose, sodium chloride, and a pH indicator (bromthymol blue). Used to test for the ability of a microorganism to metabolize specific carbohydrates, which are added to the basal medium.
IAO_0000119: From: http://www.microbelibrary.org/component/resource/laboratory-test/3151-oxidative-fermentative-test-protocol RECIPE Hugh and Leifson’s OF basal medium (6, 8) Peptone (tryptone) 2.0 g Sodium chloride 5.0 g Glucose (or other carbohydrate)a 10.0 g Bromthymol blue 0.03 g Agar 3.0 g Dipotassium phosphate 0.30 g Bring to 1 liter with distilled water. The pH should be adjusted to 7.1 prior to autoclaving (7). After the medium is autoclaved at 121°C for 15 minutes, a filter sterilized solution of 10% solution of carbohydrate (6, 8) is aseptically added to the medium to a final concentration of 1%. The sterile medium containing the carbohydrate is aliquoted aseptically into sterile test tubes and cooled unslanted as stabs (5). Some procedures call for the addition of 10 g/liter of carbohydrate to the medium prior to sterilization. The medium is then dissolved by heating to a boil on a hot plate or by steaming for 20 minutes prior to aliquoting into test tubes. The tubed medium is then steamed for 20 minutes in place of autoclaving to prevent breaking down of the carbohydrate (7). OF basal medium is commercially available in a premixed form from biological supply companies. The carbohydrate source is not included and must be added as stated above.

OF agar with MCS
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32588
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86155
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86345
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001292
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Marine Cations Supplement 1558 (From: Farmer, J. J., III & Hickman-Brenner, F. W. (2006). The genera Vibrio and Photobacterium. In The Prokaryotes: a Handbook on the Biology of Bacteria, 3rd edn, vol. 6, pp. 508–563. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer., pages 532 and 535). This medium is useful for increasing the salt content of bacteriological media to enhance the growth of marine bacteria. It contains Na+, K+, Mg++, and Ca++ at 10 times the in-use concentration. It is our formulation which was modified from the “electrolyte supplement” of Furniss et al. (1978), and it is added in the ratio of one volume of supplement to nine volumes of medium. Sodium chloride (NaCl) 150 g Potassium chloride (KCl) 3.7 g Magnesium chloride (MgCl2 · 6H2O) 51 g Calcium chloride (CaCl2 · 2H20) 7.4 g Water 912 ml Dissolve the ingredients in the order listed. All should dissolve readily, and a crystal-clear, colorless solution should result. The volume of the solution will expand to 1 liter after the salts dissolve. Dispense and autoclave at 121°C for 15 minutes. It should remain crystal clear after autoclaving, but a slight amount of fine precipitate may form and settle to the bottom of the container. To use this supplement in other media: aseptically add one volume of marine cations, supplement 1558 to nine volumes of the sterile medium, and mix thoroughly.
definition: An organic-rich, solid microbiological culture medium containing peptone, glucose, sodium chloride, and a pH indicator (bromthymol blue). Supplemented with MCS (marine cations supplement), which includes sodium chloride, potassium chloride, magnesium chloride, and calcium chloride. Used to test for the ability of a marine microorganism to metabolize specific carbohydrates, which are added to the basal medium.
created by: Carrine Blank
has exact synonym: O/F medium (with MCS)
IAO_0000119: Lucena T, Pascual J, Giordano A, Gambacorta A, Garay E, Arahal DR, Macian MC, & Pujalte MJ. 2010. Euzebyella saccharophila gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae. IJSEM 60:2871-2876. MCS = marine cations supplement

nutrient agar 1.5%
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_26710
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: beef extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001383
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
IAO_0000119: From: Nutrient Agar 1.5 % (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Nutrient Agar 1.5% is used for cultivating a variety of microorganisms and with the addition of blood or other enrichment can be used for cultivating fastidious microorganisms. Principles of the Procedure Beef extract and peptone provide the nitrogen, vitamins, amino acids and carbon sources in Nutrient Agar 1.5%. Sodium chloride maintains the osmotic balance so that red blood cells will not rupture when blood is added as supplement.1 Agar is the solidifying agent. Formula Difco™ Nutrient Agar 1.5% Approximate Formula* Per Liter Beef Extract.................................................................. 3.0 g Peptone....................................................................... 5.0 g Sodium Chloride.......................................................... 8.0 g Agar.......................................................................... 15.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 7.3 ± 0.2
created by: Carrine Blank
definition: An organic-rich, solid microbiological culture medium containing beef extract, peptone and sodium chloride (8g/L). Used for the cultivation of general heterotrophic microorganisms.

MRS agar
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_131527
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI 2509
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_32138
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_53426
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_63037
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86358
  intersection of: Restriction
    on property: has ingredient
    some values from: peptone
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has ingredient
    some values from: MICRO_0001226
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001291
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001404
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
definition: A slightly-acidic, organic-rich, solid microbiological culture medium containing peptones, egg extract, yeast extract, glucose, Tween 80, and minerals salts. Used for the cultivation of Lactobacilli.
created by: Carrine Blank
has exact synonym: de Man-Rogosa-Sharpe medium
IAO_0000119: From: Wikipedia:MRS_agar Often abbreviated to MRS, this type of bacterial growth medium is so-named by its inventors: de Man, Rogosa and Sharpe. Developed in 1960, this medium was designed to favour the luxuriant growth of Lactobacilli for lab study. It contains sodium acetate, which suppresses the growth of many competing bacteria (although some other Lactobacillales, like Leuconostoc and Pediococcus, may grow). This medium has a clear brown colour.[1] MRS agar typically contains(w/v):[2] 1.0 % peptone 0.8 % egg extract 0.4 % yeast extract 2.0 % glucose 0.5 % sodium acetate trihydrate 0.1 % polysorbate 80 (also known as Tween 80) 0.2 % dipotassium hydrogen phosphate 0.2 % triammonium citrate 0.02 % magnesium sulfate heptahydrate 0.005 % manganese sulfate tetrahydrate 1.0 % agar pH adjusted to 6.2 at 25°C

MM1 medium
type: Class
equivalent class: Class
  intersection of: microbiological culture medium
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_17234
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_31795
  intersection of: Restriction
    on property: has ingredient
    some values from: CHEBI_86158
  intersection of: Restriction
    on property: has ingredient
    some values from: yeast extract
  intersection of: Restriction
    on property: has salinity
    some values from: MICRO_0001290
  intersection of: Restriction
    on property: has pH
    some values from: MICRO_0001404
  intersection of: Restriction
    on property: has redox
    some values from: MICRO_0001388
created by: Carrine Blank
definition: A dilute organic carbon-containing, solid microbiological culture medium with glucose, yeast extract, and divalent mineral-salts. Used for the cultivation of Mucilagibacter sp.
IAO_0000232: The pH of the medium is not specified, and the medium itself is unbuffered. The optimal pH of growth for the organism in the study, however, was pH 6.0-6.5.
IAO_0000119: From: Pankratov TA, Tindall BJ, Liesack W, & Dedysh SN. 2007. Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog. IJSEM 57:2349-2354. All tests were carried out using medium MM1 containing (per liter distilled water) 0.5 g glucose, 0.04 g MgSO4.7H2O, 0.02 g CaCl2.2H2O and 0.1 g yeast extract.

filtered tomato juice
type: Class
equivalent class: Class
  intersection of: undefined organic chemical mixture
  intersection of: Restriction
    on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
    some values from: Class
      intersection of: NCBITaxon 4081
      intersection of: Restriction
        on property: Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y.
        some values from: PO_0009001
definition: An undefined organic chemical mixture derived from the juice of a tomato (the fruit of Solanum lycopersicum), formed through the process of maceration (homogenization) followed by filtration.
created by: Carrine Blank

Class
intersection of: Restriction
  on property: IAO_0000039
  has value: MICRO_0000428
intersection of: Restriction
  on property: has cell width
  qualified cardinality: 2
  on data range: int

Restriction
on property: has cell width
qualified cardinality: 2
on data range: int

Class
intersection of: Restriction
  on property: IAO_0000039
  has value: MICRO_0000428
intersection of: Restriction
  on property: has cell width
  min qualified cardinality: 2
  on data range: int

Restriction
on property: has cell width
min qualified cardinality: 2
on data range: int

Class
intersection of: Restriction
  on property: IAO_0000039
  has value: MICRO_0000428
intersection of: Restriction
  on property: has cell width
  qualified cardinality: 1
  on data range: int

Restriction
on property: has cell width
qualified cardinality: 1
on data range: int

Class
intersection of: Restriction
  on property: IAO_0000039
  has value: MICRO_0000428
intersection of: Restriction
  on property: has cell width
  qualified cardinality: 1
  on data range: int

Restriction
on property: has cell width
qualified cardinality: 1
on data range: int