DataPLANT Biology Ontology
type: Ontology
version IRI: dpbo.owl
creator: https://orcid.org/0000-0001-9021-3197
creator: https://orcid.org/0000-0003-1476-2121
default-namespace: DPBO
has_obo_format_version: 1.2
saved-by: muehlhaus
treat-xrefs-as-equivalent: MIAPPE
treat-xrefs-as-equivalent: NCBITaxon
treat-xrefs-as-equivalent: NCIT
treat-xrefs-as-equivalent: NFDI4PSO
comment: coverage: Missing Terms for the DataPLANT end-point repository templates
comment: creator: Dominik Brilhaus <dominik.brilhaus<-at->hhu.de>
comment: creator: Hajira Jabeen <hajira.jabeen<-at->uni-koeln.de>
comment: curator: Kathryn Dumschott <k.dumschott@fz-juelich.de>
comment: curator: Stella Eggels <s.eggels@fz-juelich.de>

definition
type: AnnotationProperty

created by
type: AnnotationProperty

creation date
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

treat-xrefs-as-equivalent
type: AnnotationProperty

imaging
type: Class
definition: Imaging is a process that produces an image of something.
has_obo_namespace: DPBO
id: AFP:0003774

measurement time
type: Class
definition: The date/time of the measurement.
has_obo_namespace: DPBO
id: AFR:0000952

Axiom
annotated source: measurement time
annotated property: definition
annotated target: The date/time of the measurement.
database_cross_reference: Allotrope

temperature setting
type: Class
definition: A temperature setting is a setting that specifies some temperature configuration of a temperature controlling or monitoring device, that controls or monitors the target temperature at the site of some system component.
has_obo_namespace: DPBO
id: AFR:0001255

Axiom
annotated source: temperature setting
annotated property: definition
annotated target: A temperature setting is a setting that specifies some temperature configuration of a temperature controlling or monitoring device, that controls or monitors the target temperature at the site of some system component.
database_cross_reference: Allotrope

injection volume setting
type: Class
definition: The injection volume setting is an injection setting that specifies the volume of the fluid to be injected.
has_obo_namespace: DPBO
id: AFR:0001577

sample temperature
type: Class
definition: A sample temperature result is a quality quantification facet that quantifies the temperature of the sample.
has_obo_namespace: DPBO
id: AFR:0002149

cycle count
type: Class
definition: A cycle count is a count of the number of iterations of a repeated process.
has_obo_namespace: DPBO
id: AFR:0002311

Axiom
annotated source: cycle count
annotated property: definition
annotated target: A cycle count is a count of the number of iterations of a repeated process.
database_cross_reference: Allotrope

irrigation process
type: Class
definition: A planned process in which water is artificially supplied to plant or soil to sustain plants.
has_obo_namespace: DPBO
id: AGRO:00000006

desuckering
type: Class
subclass of: thinning
definition: A pruning process in which one or more suckers are removed.
has_exact_synonym: desuckering process
has_obo_namespace: DPBO
id: AGRO:00000007
comment: Which suckers are removed depends on the criteria set by the agent of the desuckering process.

thinning
type: Class
subclass of: pruning process
definition: A planned process in which selected parts of the plant are removed. The practice entails targeted removal of diseased, damaged, dead, non-productive, structurally unsound, or otherwise unwanted tissue from plants. This is done in order to shape the plant or tree, improve plant or tree health, reduce the risk from falling branches, prepare nursery specimens for transplanting, and increase the yield or quality of harvested products.
creator: https://orcid.org/0000-0001-6284-4821
has_broad_synonym: pruning
has_exact_synonym: thinning process
has_obo_namespace: DPBO
id: AGRO:00000027

Axiom
annotated source: thinning
annotated property: definition
annotated target: A planned process in which selected parts of the plant are removed. The practice entails targeted removal of diseased, damaged, dead, non-productive, structurally unsound, or otherwise unwanted tissue from plants. This is done in order to shape the plant or tree, improve plant or tree health, reduce the risk from falling branches, prepare nursery specimens for transplanting, and increase the yield or quality of harvested products.
database_cross_reference: http://aims.fao.org/aos/agrovoc/c_6274
database_cross_reference: https://en.wikipedia.org/wiki/Pruning#Types_of_pruning

experimental site
type: Class
definition: Location where the experiment is implemented.
has_obo_namespace: DPBO
id: AGRO:00000360

farmer field
type: Class
subclass of: experimental site
subclass of: Growth facility
definition: Experimental site in which the experiment is implemented on the field of a farmer.
has_obo_namespace: DPBO
id: AGRO:00000361

research station field
type: Class
subclass of: experimental site
subclass of: Growth facility
definition: Experimental site in which the experiment is done in a the field of a research station.
has_exact_synonym: experimental station field
has_obo_namespace: DPBO
id: AGRO:00000362

greenhouse
type: Class
subclass of: experimental site
subclass of: Growth facility
definition: An experimental site in which the experiment is performed in a structure with walls and roof made chiefly of transparent material, such as glass, with the possibility to regulate climatic conditions.
has_broad_synonym: hothouse
has_broad_synonym: screenhouse
has_exact_synonym: glasshouse
has_obo_namespace: DPBO
id: AGRO:00000363

Axiom
annotated source: greenhouse
annotated property: definition
annotated target: An experimental site in which the experiment is performed in a structure with walls and roof made chiefly of transparent material, such as glass, with the possibility to regulate climatic conditions.
database_cross_reference: https://en.wikipedia.org/wiki/Greenhouse

governmental forest
type: Class
subclass of: experimental site
subclass of: Growth facility
definition: Experimental site where the experiment is done in a forest owned by a government.
has_obo_namespace: DPBO
id: AGRO:00000364

private forest
type: Class
subclass of: experimental site
subclass of: Growth facility
definition: Experimental site where the experiment is done in a private forest.
has_obo_namespace: DPBO
id: AGRO:00000365

farmer
type: Class
subclass of: person role within the experiment
definition: A person engaged in agriculture, raising living organisms for food or raw materials.
has_obo_namespace: DPBO
id: AGRO:00000372

researcher
type: Class
subclass of: person role within the experiment
definition: A person who conducts research.
has_exact_synonym: scientist
has_obo_namespace: DPBO
id: AGRO:00000373

student
type: Class
subclass of: person role within the experiment
definition: A person that is enrolled or attends classes at a school, college, or university.
has_obo_namespace: DPBO
has_related_synonym: intern
id: AGRO:00000374

research station employee
type: Class
subclass of: person role within the experiment
definition: A person that works in a research station.
has_obo_namespace: DPBO
id: AGRO:00000375

extension agent
type: Class
subclass of: person role within the experiment
definition: A person that is employed by the government to assist people in rural areas with methods of farming and home economics.
has_obo_namespace: DPBO
id: AGRO:00000376

faculty member
type: Class
subclass of: person role within the experiment
definition: A person that is an educator who works at a college or university.
has_obo_namespace: DPBO
id: AGRO:00000377

person role within the experiment
type: Class
definition: Roled performed by a person during an experiment.
has_obo_namespace: DPBO
id: AGRO:00000378

data collector
type: Class
subclass of: person role within the experiment
definition: A person that has a role of collecting data related to the experiment.
has_obo_namespace: DPBO
id: AGRO:00000379

principal investigator
type: Class
subclass of: person role within the experiment
definition: A person that is the holder of an independent grant and the lead researcher for the grant project.
has_obo_namespace: DPBO
id: AGRO:00000380

experiment manager
type: Class
subclass of: person role within the experiment
definition: A person that has a role of managing the experiment.
has_obo_namespace: DPBO
id: AGRO:00000381

field laborer
type: Class
subclass of: person role within the experiment
definition: A person that has a role of performing the operations required to run the experiment in the field.
has_obo_namespace: DPBO
id: AGRO:00000382

pruning process
type: Class
subclass of: agricultural process
definition: Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots.
creator: http://orcid.org/0000-0001-6284-4821
has_exact_synonym: pruning
has_exact_synonym: pruning method
has_obo_namespace: DPBO
id: AGRO:00000566

Axiom
annotated source: pruning process
annotated property: definition
annotated target: Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots.
database_cross_reference: https://en.wikipedia.org/wiki/Pruning

GPS coordinates
type: Class
definition: A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters
creator: http://orcid.org/0000-0001-6284-4821
has_broad_synonym: geographic coordinate system
has_exact_synonym: GPS coordinates measurement datum
has_exact_synonym: geo-location
has_exact_synonym: geolocation
has_obo_namespace: DPBO
id: AGRO:00000572

Axiom
annotated source: GPS coordinates
annotated property: definition
annotated target: A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters
database_cross_reference: https://whatis.techtarget.com/definition/GPS-coordinates

field owner
type: Class
subclass of: person role within the experiment
definition: A person that own an agricultural field.
has_obo_namespace: DPBO
id: AGRO:00000659

agricultural process
type: Class
definition: A planned process which occurs in an agricultural field.
creator: http://orcid.org/0000-0002-8461-9745
has_obo_namespace: DPBO
id: AGRO:00002071

DNA
type: Class
subclass of: bio entity
definition: DNA or deoxyribonucleic acid is the genetic material in all the living things, and some viruses. It is a polymer of nucleotides, with a backbone made of deoxyribose sugar and phosphate groups joined together by ester bonds.
has_obo_namespace: DPBO
id: BAO:0000269

genomic DNA
type: Class
subclass of: bio entity
definition: DNA that is linear and not circular. Examples of linear DNA include synthetic oligonucleotide, restriction endonuclease digestion product, polymerase chain reaction product, mechanically sheared genomic DNA, etc.
has_obo_namespace: DPBO
id: BAO:0000316

96 well plate
type: Class
definition: This microplate contains 96 wells. It is suitable for a low throughput assay.
has_obo_namespace: DPBO
id: BAO:0000513

instrumentation manufacturer
type: Class
definition: The role of a company as a creator of detection instrumentation.
has_obo_namespace: DPBO
id: BAO:0002628

6 well plate
type: Class
has_obo_namespace: DPBO
id: BAO:0010013

protein profiling assay
type: Class
definition: Protein profiling assays can be used to identify and quantify proteins together with their post-translational modifications
IAO_0000118: protein profiling
IAO_0000118: protein quantification assay
has_obo_namespace: DPBO
id: BAO:0010026

shotgun MS protein profiling assay
type: Class
subclass of: protein profiling assay
definition: An assay that is used to identify in a data-dependent mode proteins by combining the HPLC and MS methods. It is also known as liquid chromatography-coupled tandem mass spectrometry (LC-MS)
has_obo_namespace: DPBO
id: BAO:0010027

SWATH MS protein profiling assay
type: Class
subclass of: protein profiling assay
definition: Sequential window acquisition of all theoretical mass spectra (SWATH) MS is a mass spectrometrical method thatcouples data-independent acquisition is coupled with peptide spectral library match
has_obo_namespace: DPBO
id: BAO:0010028

P100 protein profiling assay
type: Class
subclass of: protein profiling assay
definition: A targeted phosphoproteomic assay that uses a data-driven approach to identify and quantify a set of 96 phosphopeptide probes
has_obo_namespace: DPBO
id: BAO:0010029

RPPA protein profiling assay
type: Class
subclass of: protein profiling assay
definition: Reverse phase protein array (RPPA) is a an assay that measures multiple protein expression levels in a large number of biological samples simultaneously using high quality antibodies
has_obo_namespace: DPBO
id: BAO:0010030

Microwestern
type: Class
subclass of: protein profiling assay
has_obo_namespace: DPBO
id: BAO:0010049

ELISA protein state assay
type: Class
subclass of: protein profiling assay
has_obo_namespace: DPBO
id: BAO:0010052

Tandem Mass Tag (TMT) MS Protein Quantification
type: Class
subclass of: protein profiling assay
has_obo_namespace: DPBO
id: BAO:0010070

Liquid Chromatography/Mass Spectroscopy (LC/MS) protein quantification
type: Class
subclass of: protein profiling assay
has_obo_namespace: DPBO
id: BAO:0010071

stationary phase culture
type: Class
subclass of: growth phase culture
definition: A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die.
has_obo_namespace: BrendaTissueOBO
id: BTO:0001899

Axiom
annotated source: stationary phase culture
annotated property: definition
annotated target: A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die.
database_cross_reference: Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Stationary+phase

growth phase culture
type: Class
definition: The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time.
has_obo_namespace: BrendaTissueOBO
id: BTO:0001900

Axiom
annotated source: growth phase culture
annotated property: definition
annotated target: The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time.
database_cross_reference: Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Growth+phase

death phase culture
type: Class
subclass of: growth phase culture
definition: A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases.
has_obo_namespace: BrendaTissueOBO
id: BTO:0001901

Axiom
annotated source: death phase culture
annotated property: definition
annotated target: A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases.
database_cross_reference: Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Death+phase

lag phase culture
type: Class
subclass of: growth phase culture
definition: The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth.
has_obo_namespace: BrendaTissueOBO
id: BTO:0001902

Axiom
annotated source: lag phase culture
annotated property: definition
annotated target: The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth.
database_cross_reference: Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Lag+phase

logarithmic phase culture
type: Class
subclass of: growth phase culture
definition: A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes.
has_obo_namespace: BrendaTissueOBO
has_related_synonym: exponential growth phase culture
has_related_synonym: log phase culture
id: BTO:0001903

Axiom
annotated source: logarithmic phase culture
annotated property: definition
annotated target: A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes.
database_cross_reference: Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Logarithmic+phase

agar
type: Class
subclass of: rooting medium solidifier
definition: A complex mixture of polysaccharides extracted from species of red algae. Its two main components are agarose and agaropectin. Agarose is the component responsible for the high-strength gelling properties of agar, while agaropectin provides the viscous properties.
has_obo_namespace: DPBO
id: CHEBI:2509

protein
type: Class
subclass of: bio entity
definition: biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
has_obo_namespace: DPBO
id: CHEBI:36080

mobile phase
type: Class
definition: A fluid that percolates through or along the stationary bed in chromatography.
has_obo_namespace: DPBO
id: CHMO:0000995

derivatisation
type: Class
subclass of: material processing
definition: The transformation of a chemical compound (the 'educt') into another similar compound (the 'derivative') by altering one or more of its functional groups. Derivatisation is generally perfomed to alter reactivity or change a physical property such as solubility, boiling point, melting point, thermal stability etc.
has_exact_synonym: derivatization
has_obo_namespace: DPBO
id: CHMO:0001485

Axiom
annotated source: derivatisation
annotated property: definition
annotated target: The transformation of a chemical compound (the 'educt') into another similar compound (the 'derivative') by altering one or more of its functional groups. Derivatisation is generally perfomed to alter reactivity or change a physical property such as solubility, boiling point, melting point, thermal stability etc.
database_cross_reference: https://orcid.org/0000-0002-0640-0422

sample drying
type: Class
subclass of: material processing
definition: The process of removing a solvent from a substance.
has_obo_namespace: DPBO
has_related_synonym: drying
id: CHMO:0001549

Axiom
annotated source: sample drying
annotated property: definition
annotated target: The process of removing a solvent from a substance.
database_cross_reference: https://orcid.org/0000-0002-0640-0422

Axiom
annotated source: sample drying
annotated property: has_related_synonym
annotated target: drying
has_synonym_type: non-mining synonym

vacuum drying
type: Class
subclass of: sample drying
definition: The removal of water from a sample by placing it under reduced pressure. This allows water to evaporate from (heat-sensitive) samples at a lower temperature.
has_obo_namespace: DPBO
id: CHMO:0001557

Axiom
annotated source: vacuum drying
annotated property: definition
annotated target: The removal of water from a sample by placing it under reduced pressure. This allows water to evaporate from (heat-sensitive) samples at a lower temperature.
database_cross_reference: https://orcid.org/0000-0002-0640-0422

extraction
type: Class
definition: The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it.
has_obo_namespace: DPBO
id: CHMO:0001577

liquid-solid extraction
type: Class
definition: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (e.g. silica particles).
has_exact_synonym: liquid-solid extraction
has_exact_synonym: solid phase extraction
has_exact_synonym: solid-phase extraction
has_exact_synonym: sorbent extraction
has_exact_synonym: sorptive extraction
has_obo_namespace: DPBO
has_related_synonym: LSE
has_related_synonym: SPE
id: CHMO:0001583

Axiom
annotated source: liquid-solid extraction
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (e.g. silica particles).
database_cross_reference: ISBN:0-13-147835-4

Axiom
annotated source: liquid-solid extraction
annotated property: has_related_synonym
annotated target: LSE
has_synonym_type: non-mining synonym

Axiom
annotated source: liquid-solid extraction
annotated property: has_related_synonym
annotated target: SPE
has_synonym_type: non-mining synonym

normal-phase solid-phase extraction
type: Class
subclass of: liquid-solid extraction
definition: The process of transferring a substance from a liquid to a solid phase by passing the (polar) liquid sample through a (non-polar) stationary phase.
has_exact_synonym: normal phase SPE
has_exact_synonym: normal phase solid-phase extraction
has_exact_synonym: normal-phase SPE
has_obo_namespace: DPBO
id: CHMO:0001584

Axiom
annotated source: normal-phase solid-phase extraction
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by passing the (polar) liquid sample through a (non-polar) stationary phase.
database_cross_reference: ISBN:0-13-147835-4

reversed-phase solid-phase extraction
type: Class
subclass of: liquid-solid extraction
definition: The process of transferring a substance from a liquid to a solid phase by passing the (non-polar) liquid sample through a (polar) stationary phase.
has_exact_synonym: reverse phase SPE
has_exact_synonym: reverse phase solid-phase extraction
has_exact_synonym: reverse-phase SPE
has_exact_synonym: reverse-phase solid-phase extraction
has_exact_synonym: reversed phase SPE
has_exact_synonym: reversed-phase SPE
has_obo_namespace: DPBO
id: CHMO:0001585

Axiom
annotated source: reversed-phase solid-phase extraction
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by passing the (non-polar) liquid sample through a (polar) stationary phase.
database_cross_reference: ISBN:0-13-147835-4

solid-phase micro-extraction
type: Class
subclass of: liquid-solid extraction
definition: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter).
has_exact_synonym: SPME
has_exact_synonym: solid phase microextraction
has_exact_synonym: solid-phase microextraction
has_obo_namespace: DPBO
id: CHMO:0001586

Axiom
annotated source: solid-phase micro-extraction
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter).
database_cross_reference: ISBN:0-13-147835-4

capillary micro-extraction
type: Class
subclass of: solid-phase micro-extraction
definition: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary.
has_exact_synonym: CME
has_exact_synonym: capillary microextraction
has_obo_namespace: DPBO
id: CHMO:0001587

Axiom
annotated source: capillary micro-extraction
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary.
database_cross_reference: ISBN:0444505113

sol–gel capillary micro-extraction
type: Class
subclass of: capillary micro-extraction
definition: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small sol–gel-coated fused-silica capillary.
has_exact_synonym: sgCME
has_exact_synonym: sol-gel CME
has_exact_synonym: sol-gel capillary micro-extraction
has_exact_synonym: sol-gel capillary microextraction
has_exact_synonym: solgel CME
has_exact_synonym: solgel capillary microextraction
has_obo_namespace: DPBO
id: CHMO:0001588

Axiom
annotated source: sol–gel capillary micro-extraction
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small sol–gel-coated fused-silica capillary.
database_cross_reference: https://doi.org/10.1021/ac0109523

headspace solid-phase micro-extraction
type: Class
subclass of: solid-phase micro-extraction
definition: The process of transferring a substance from a liquid to a solid phase by exposing a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter) to the headspace above the liquid sample.
has_exact_synonym: HSPME
has_exact_synonym: HSSE
has_exact_synonym: hSPME
has_exact_synonym: headspace solid-phase micro-extraction
has_exact_synonym: headspace solid-phase microextraction
has_exact_synonym: headspace sorptive extraction
has_obo_namespace: DPBO
id: CHMO:0001589

Axiom
annotated source: headspace solid-phase micro-extraction
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by exposing a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter) to the headspace above the liquid sample.
database_cross_reference: https://orcid.org/0000-0002-0640-0422

micro-extraction in a packed syringe
type: Class
subclass of: solid-phase micro-extraction
definition: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (1 mg) packed into a microlitre syringe.
has_exact_synonym: MEPS
has_exact_synonym: micro extraction by packed sorbent
has_exact_synonym: micro-extraction in packed syringe
has_exact_synonym: microextraction in a packed syringe
has_exact_synonym: microextraction in packed syringe
has_exact_synonym: packed syringe micro-extraction
has_exact_synonym: packed syringe microextraction
has_exact_synonym: packed-syringe micro-extraction
has_exact_synonym: packed-syringe microextraction
has_obo_namespace: DPBO
id: CHMO:0001590

Axiom
annotated source: micro-extraction in a packed syringe
annotated property: definition
annotated target: The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (1 mg) packed into a microlitre syringe.
database_cross_reference: https://doi.org/10.1002/jms.73

solvent extraction
type: Class
subclass of: extraction
definition: The process of transferring a substance from any matrix to an appropriate liquid phase.
has_obo_namespace: DPBO
id: CHMO:0001598

Axiom
annotated source: solvent extraction
annotated property: definition
annotated target: The process of transferring a substance from any matrix to an appropriate liquid phase.
database_cross_reference: OrangeBook:9.4.1

grinding
type: Class
subclass of: material processing
definition: The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting.
has_exact_synonym: dry grinding
has_exact_synonym: milling
has_exact_synonym: solid-state grinding
has_exact_synonym: solvent-free grinding
has_obo_namespace: DPBO
id: CHMO:0001652

Axiom
annotated source: grinding
annotated property: definition
annotated target: The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting.
database_cross_reference: https://doi.org/10.1351/goldbook.M03928

methoxyamination derivatisation
type: Class
subclass of: derivatisation
subclass of: MS derivatization
definition: Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties.
has_exact_synonym: methoxyamination derivatization
has_obo_namespace: DPBO
id: CHMO:0002757
comment: this typically happens prior to GC-MS, but not LC-MS

Axiom
annotated source: methoxyamination derivatisation
annotated property: definition
annotated target: Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties.
database_cross_reference: https://doi.org/10.1039/9781847558107-00254
database_cross_reference: https://orcid.org/0000-0001-5985-7429

trimethylsilyl derivatisation
type: Class
subclass of: derivatisation
subclass of: MS derivatization
definition: Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups.
has_exact_synonym: TMS derivatisation
has_exact_synonym: trimethylsilyl derivatization
has_obo_namespace: DPBO
id: CHMO:0002758
comment: this typically happens prior to GC-MS, but not LC-MS

Axiom
annotated source: trimethylsilyl derivatisation
annotated property: definition
annotated target: Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups.
database_cross_reference: https://doi.org/10.1039/9781847558107-00254
database_cross_reference: https://orcid.org/0000-0001-5985-7429

dispersive solid phase extraction
type: Class
subclass of: liquid-solid extraction
has_exact_synonym: dispersive solid-phase extraction
has_obo_namespace: DPBO
id: CHMO:0002863

dispersive solid-phase microextraction
type: Class
subclass of: solid-phase micro-extraction
has_obo_namespace: DPBO
id: CHMO:0002887

growth plot design
type: Class
disjoint with: read alignment software
definition: A plan specification that states how treatments are allocated to the experimental units. It refers to the conceptual framework within which the experiment is conducted
has_obo_namespace: DPBO
has_related_synonym: Experimental Randomisation
id: DPBO:0000001

read alignment software
type: Class
definition: The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478
has_obo_namespace: DPBO
id: DPBO:0000002
comment: “We might need to add the relationship with the class referenced above”

read alignment software version
type: Class
definition: The version of the read alignment software (DPBO:0000002).
has_obo_namespace: DPBO
id: DPBO:0000003

read alignment software parameters
type: Class
definition: The parameters of the read alignment software (DPBO:0000002).
has_obo_namespace: DPBO
id: DPBO:0000004

humidity day
type: Class
definition: This term defines the relative humidity of the air at daytime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197)
has_obo_namespace: DPBO
id: DPBO:0000005
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"

humidity night
type: Class
definition: This term defines the relative humidity of the air at nighttime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197)
has_obo_namespace: DPBO
id: DPBO:0000006
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"

temperature day
type: Class
definition: This term defines the air temperature at daytime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001)
has_obo_namespace: DPBO
id: DPBO:0000007
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”

temperature night
type: Class
definition: This term defines the air temperature at nighttime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001)
has_obo_namespace: DPBO
id: DPBO:0000008
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”

sample collection method
type: Class
definition: Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ”
has_obo_namespace: DPBO
id: DPBO:0000009

metabolism quenching method
type: Class
definition: Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.”
has_obo_namespace: DPBO
id: DPBO:0000010
comment: “”

sample storage
type: Class
definition: The method used for sample storage. Should include the temperature of the sample. May include the medium (freezer or liquid nitrogen) and/or additional processing (freeze-drying) of the sample”
has_obo_namespace: DPBO
id: DPBO:0000011
comment: “”

bio entity
type: Class
definition: The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.”
has_obo_namespace: DPBO
id: DPBO:0000012
comment: “”

biosource amount
type: Class
definition: The amount (typically in milligram) of material from which a bio entity (DPBO:0000012) is extracted.”
has_obo_namespace: DPBO
id: DPBO:0000013
comment: “”

extraction kit
type: Class
definition: The name of the commercial kit used for extraction of a bio entity (DPBO:0000012). Should include the company name.”
has_obo_namespace: DPBO
id: DPBO:0000014
comment: “”

library layout
type: Class
definition: Determines the choice of DNA sequencing strategy, in which a single read is initiated from each end (paired-end) or one end (single-end) of DNA fragment”
has_obo_namespace: DPBO
id: DPBO:0000015
comment: “Adapted from http://purl.obolibrary.org/obo/NCIT_C150423"

library RNA amount
type: Class
definition: Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)”
has_obo_namespace: DPBO
id: DPBO:0000016
comment: “”

base-calling software
type: Class
definition: The name of the software used for base-calling.
has_obo_namespace: DPBO
id: DPBO:0000017
comment: term description for base-calling http://edamontology.org/operation_3185

base-calling software version
type: Class
definition: The version of the base-calling software (DPBO:0000017).”
has_obo_namespace: DPBO
id: DPBO:0000018
comment: “”

base-calling software parameters
type: Class
definition: The parameters of the base-calling software (DPBO:0000017).”
has_obo_namespace: DPBO
id: DPBO:0000019
comment: “”

library strand
type: Class
definition: Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (DPBO:0000015)”
has_obo_namespace: DPBO
id: DPBO:0000020
comment: “”

raw data file format
type: Class
definition: File format of the raw data file”
has_obo_namespace: DPBO
id: DPBO:0000021
comment: “This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915"

raw data file checksum
type: Class
definition: Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum
has_obo_namespace: DPBO
id: DPBO:0000022

data filtering software
type: Class
definition: Name of the software applied for data filtering
has_obo_namespace: DPBO
id: DPBO:0000023
comment: “For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)”

data filtering software version
type: Class
definition: The version of the data filtering software (DPBO:0000023).”
has_obo_namespace: DPBO
id: DPBO:0000024
comment: “”

data filtering software parameters
type: Class
definition: The parameters of the data filtering software (DPBO:0000023).”
has_obo_namespace: DPBO
id: DPBO:0000025
comment: “”

genome reference sequence
type: Class
definition: Name and version of the genome reference.”
database_cross_reference: MS:1002644
database_cross_reference: NCIT:C16438
has_obo_namespace: DPBO
id: DPBO:0000026
comment: “See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644”

processed data file format
type: Class
definition: File format of the processed data file”
has_obo_namespace: DPBO
id: DPBO:0000027
comment: “”

processed data file name
type: Class
definition: Name of the processed data file”
has_obo_namespace: DPBO
id: DPBO:0000028
comment: “”

processed data file checksum
type: Class
definition: Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum
has_obo_namespace: DPBO
id: DPBO:0000029

isolation and growth condition
type: Class
definition: Publication reference for isolation and growth condition specifications of the organism/material
has_obo_namespace: DPBO
id: DPBO:0000030
comment: for submission to ENA

number of chromosomes
type: Class
definition: The haploid chromosome count of a eukaryote
has_obo_namespace: DPBO
id: DPBO:0000031

estimated genome size
type: Class
definition: The estimated size of the genome prior to sequencing
has_obo_namespace: DPBO
id: DPBO:0000032
comment: adapted from MIXS:0000024

plant age
type: Class
definition: A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting).
has_obo_namespace: DPBO
id: DPBO:0000033
comment: “This is a specialization of age (http://www.ebi.ac.uk/efo/EFO_0000246)"

plant health state
type: Class
definition: Health status of the plant at the time of sample collection
has_obo_namespace: DPBO
id: DPBO:0000034

obsolete_Seurat
type: Class
subclass of: Obsolete Class
definition: Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
has_obo_namespace: DPBO
id: DPBO:0000035
deprecated: true

obsolete_library selection
type: Class
subclass of: Obsolete Class
definition: The method used to select for or against, enrich, or screen the material being sequenced.
database_cross_reference: GENEPIO:0001940
has_obo_namespace: DPBO
id: DPBO:0000036
comment: term is redundant, please use GENEPIO:0001940
deprecated: true

subspecific taxonomic rank
type: Class
definition: Determination of the taxonomic ranking that is below species level i.e. variety, cultivar, ecotype, inbred line
has_obo_namespace: DPBO
id: DPBO:0000037

rooting medium pH
type: Class
definition: pH measurement of the culture rooting medium
has_obo_namespace: DPBO
id: DPBO:0000038
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist

rooting medium macronutrients
type: Class
definition: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)
has_obo_namespace: DPBO
id: DPBO:0000039
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist

next generation sequencing instrument model
type: Class
definition: Model name or number of next generation sequencing instrument
database_cross_reference: EFO:0003739
has_obo_namespace: DPBO
id: DPBO:0000040

growth day length
type: Class
definition: The time (e.g. hours of light) of the light regime in a growth experiment (e.g. 12hr light /12hr dark, 12/12, short day, long day)
database_cross_reference: PECO:0007078
database_cross_reference: ZECO:0000147
has_exact_synonym: light duration
has_obo_namespace: DPBO
id: DPBO:0000041
comment: “Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078"

biological replicate identifier
type: Class
definition: Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2')
database_cross_reference: MS:1001809
has_obo_namespace: DPBO
id: DPBO:0000042

MS sample post-extraction
type: Class
definition: Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection)
has_obo_namespace: DPBO
id: DPBO:0000043

MS sample resuspension
type: Class
definition: Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile)
has_obo_namespace: DPBO
id: DPBO:0000044

MS sample type
type: Class
definition: Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control)
has_obo_namespace: DPBO
id: DPBO:0000045

chromatography instrument model
type: Class
definition: Company name, and instrument name or serial number of the chromatography instrument
has_obo_namespace: DPBO
id: DPBO:0000046

chromatography autosampler model
type: Class
definition: Company name, and name or serial number of the chromatography autosampler model
has_obo_namespace: DPBO
id: DPBO:0000047

chromatography column model
type: Class
definition: Company name, and name or serial number of the chromatography column
has_obo_namespace: DPBO
id: DPBO:0000048

chromatography guard column model
type: Class
definition: Company name, and name or serial number of the chromatography guard column
has_obo_namespace: DPBO
id: DPBO:0000049

extraction buffer
type: Class
definition: Chemical buffer, solvent or solution used to extract a component from a biological sample.
has_obo_namespace: DPBO
id: DPBO:0000050
comment: “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884). DB"

extraction buffer volume
type: Class
definition: Volume of the buffer (DPBO:0000050) used during extraction.
has_obo_namespace: DPBO
id: DPBO:0000051
comment: “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884)"

MS derivatization
type: Class
subclass of: material processing
definition: Derivatization for metabolomics mass spectrometry.
database_cross_reference: CHMO:0001485
has_obo_namespace: DPBO
id: DPBO:0000052

chromatography column type
type: Class
definition: Type of chromatography column (DPBO:0000048)
database_cross_reference: CHMO:0001000
has_obo_namespace: DPBO
id: DPBO:0000053

extraction method
type: Class
definition: Method or kit that was used to extract DNA or RNA
has_obo_namespace: DPBO
id: DPBO:0000054
comment: “More general than DPBO:0000014, because not everyone uses a kit for RNA/DNA extraction"

rooting medium micronutrients
type: Class
definition: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)
has_obo_namespace: DPBO
id: DPBO:0000055
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist

library DNA amount
type: Class
definition: Amount of DNA (microgram) used as starting material for library construction
has_obo_namespace: DPBO
id: DPBO:0000056
comment: “"

next generation sequencing platform
type: Class
definition: Name of the company that produces next generation sequencing instruments
database_cross_reference: GENEPIO:0000071
has_obo_namespace: DPBO
id: DPBO:0000057

rooting medium organic supplements
type: Class
definition: Organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L)
has_obo_namespace: DPBO
id: DPBO:0000058
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist

sequence assembly method
type: Class
definition: Strategy that was used to assemble reads into contigs
database_cross_reference: GENEPIO:0000090
has_obo_namespace: DPBO
id: DPBO:0000059
comment: “Just two options should be possible: de-novo assembly or mapping"

sequence assembly algorithm version
type: Class
definition: The version of the sequence assembly algorithm (OBI_0001522)
has_obo_namespace: DPBO
id: DPBO:0000060
comment: “"

genome status
type: Class
definition: Status of the genome sequence that is uploaded
has_obo_namespace: DPBO
id: DPBO:0000061
comment: “Just two options should be possible: full or partial"

RNA quality check
type: Class
definition: Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis.
has_obo_namespace: DPBO
id: DPBO:0000062

BioProject accession number
type: Class
definition: The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345.
database_cross_reference: NCIT:C175890
has_obo_namespace: DPBO
id: DPBO:0000063
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"

sample type
type: Class
definition: Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly
database_cross_reference: NCIT:C70713
has_obo_namespace: DPBO
id: DPBO:0000064
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"

rooting medium carbon source
type: Class
definition: Source of organic carbon in the culture rooting medium; e.g. sucrose
has_obo_namespace: DPBO
id: DPBO:0000065
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist

rooting medium growth regulators
type: Class
definition: Growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA
has_obo_namespace: DPBO
id: DPBO:0000066
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist

rooting medium solidifier
type: Class
definition: Specification of the solidifying agent in the culture rooting medium; e.g. agar
has_obo_namespace: DPBO
id: DPBO:0000067
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist

obsolete_cell line
type: Class
subclass of: Obsolete Class
definition: A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [ NCI On-line Medical Dictionary ]
database_cross_reference: NCIT:C16403
has_obo_namespace: DPBO
id: DPBO:0000068
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]"
deprecated: true

obsolete_cell type
type: Class
subclass of: Obsolete Class
definition: The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. [Definition Source: NCI]
has_obo_namespace: DPBO
id: DPBO:0000069
comment: term is redundant, please use NCIT:C12508
deprecated: true

5' partial CDS
type: Class
definition: Incomplete CDS (coding sequence) with the start codon upstream of the submitted sequence.
has_obo_namespace: DPBO
id: DPBO:0000070
comment: adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences.

3' partial CDS
type: Class
definition: Incomplete CDS (coding sequence) with the stop codon downstream of the submitted sequence.
has_obo_namespace: DPBO
id: DPBO:0000071
comment: adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences.

plant disease stage
type: Class
definition: Stage of plant disease at the time of sampling.
has_obo_namespace: DPBO
id: DPBO:0000072

phenotype
type: Class
definition: Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601
database_cross_reference: NCIT:C16977
has_obo_namespace: DPBO
id: DPBO:0000073
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"

geographic area
type: Class
definition: Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg 'Canada: Vancouver' or 'Germany: halfway down Zugspitze, Alps'
database_cross_reference: NCIT:C16632
has_obo_namespace: DPBO
id: DPBO:0000074
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"

5' partial promoter
type: Class
definition: Incomplete promoter with its 5' end upstream of the submitted sequence.
has_obo_namespace: DPBO
id: DPBO:0000075
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.

3' partial promoter
type: Class
definition: Incomplete promoter with its 3' end downstream of the submitted sequence.
has_obo_namespace: DPBO
id: DPBO:0000076
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.

metabolite assignment file
type: Class
definition: metabolite assignment file (MAF) as required by MetaboLights to describe metabolites analyzed during a metabolomics assay. Details see: https://www.ebi.ac.uk/metabolights/guides/MAF/Title
has_obo_namespace: DPBO
id: DPBO:0000077
comment: “[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title"

BioSample accession number
type: Class
definition: BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]!
database_cross_reference: NCIT:C175889
has_obo_namespace: DPBO
id: DPBO:0000078
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"

promoter 5' end coordinate
type: Class
definition: Coordinate of the 5' end of the promoter within the submitted sequence.
has_obo_namespace: DPBO
id: DPBO:0000079
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.

promoter 3' end coordinate
type: Class
definition: Coordinate of the 3' end of the promoter within the submitted sequence.
has_obo_namespace: DPBO
id: DPBO:0000080
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.

chromatography gradient
type: Class
definition: Settings of the gradient used during (e.g. liquid, gas or ion) chromatography
has_obo_namespace: DPBO
id: DPBO:0000081

rRNA depletion
type: Class
definition: Method used for rRNA depletion during construction of the sequencing library.
has_obo_namespace: DPBO
id: DPBO:0000082
comment: "see also http://purl.obolibrary.org/obo/NCIT_C18685"

relative centrifugal force
type: Class
equivalent class: g-force
subclass of: acceleration unit
definition: Relative centrifugal force (RCF) is the amount of force applied to a sample when using a centrifuge. It is dependant on the speed of the centrifuge rotation as well as the distance of the sample from the center of rotation.
has_exact_synonym: RCF
has_obo_namespace: DPBO
id: DPBO:0000083

g-force
type: Class
subclass of: acceleration unit
definition: G-force is the force acting on an object as a result of acceleration or gravity.
has_obo_namespace: DPBO
id: DPBO:0000084

standard gravity
type: Class
subclass of: acceleration unit
definition: The standard acceleration of an object in free fall at or near sea level equivalent to 9.807 m/s2.
has_exact_synonym: g0
has_exact_synonym: standard acceleration due to gravity
has_exact_synonym: standard acceleration of free fall
has_obo_namespace: DPBO
id: DPBO:0000085

single-end
type: Class
subclass of: library layout
definition: A library layout which describes that only one end of the library fragment is sequenced
ER target: GEO_RNASEQ
ER target term: RAW FILES_single or paired-end
has_obo_namespace: DPBO
id: DPBO:0000086
comment: "Adapted from http://purl.obolibrary.org/obo/FBcv_0003220"

library ID
type: Class
definition: Short unique identifier for the sequencing library
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:0000087
comment: "Required for upload of next-generation sequencing data to SRA."

growth chamber
type: Class
subclass of: Growth facility
definition: A climatic chamber used for growing plants under controlled environmental conditions.
has_obo_namespace: DPBO
id: DPBO:0000088

SingleCellExperiment
type: Class
subclass of: R package
definition: Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.
has_obo_namespace: DPBO
id: DPBO:0000089

tidyverse
type: Class
subclass of: R package
definition: The core tidyverse includes the packages that you’re likely to use in everyday data analyses. As of tidyverse 1.3.0, the following packages are included in the core tidyverse: ggplot2, dplyr, tidyr, readr, purrr, tibble, stringr, forcats.
has_obo_namespace: DPBO
id: DPBO:0000090

Matrix
type: Class
subclass of: R package
definition: A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.
has_obo_namespace: DPBO
id: DPBO:0000091

scales
type: Class
subclass of: R package
definition: Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.
has_obo_namespace: DPBO
id: DPBO:0000092

cowplot
type: Class
subclass of: R package
definition: Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.
has_obo_namespace: DPBO
id: DPBO:0000093

RCurl
type: Class
subclass of: R package
definition: A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
has_obo_namespace: DPBO
id: DPBO:0000094

R package
type: Class
definition: Packages are collections of R functions, data, and compiled code in a well-defined format, created to add specific functionality.
has_obo_namespace: DPBO
id: DPBO:0000095

package version
type: Class
definition: The version of the software package or library that was used in the analysis.
has_obo_namespace: DPBO
id: DPBO:0000096

prm-PASEF
type: Class
definition: Targeted proteomics method that combines parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF).
has_obo_namespace: DPBO
id: DPBO:0000097
comment: Bruker Corporation term. Definition from https://www.bruker.com/

dda-PASEF
type: Class
definition: Data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF) technology for proteomics analysis.
has_obo_namespace: DPBO
id: DPBO:0000098
comment: Bruker Corporation term. Definition from https://www.bruker.com/

antibiotic concentration
type: Class
definition: Concentration of an antibiotic that was added to a growth medium.
has_obo_namespace: DPBO
id: DPBO:0000099

growth time
type: Class
definition: Duration of a bacterial cultivation.
has_obo_namespace: DPBO
id: DPBO:0000100

start OD600
type: Class
definition: The OD600 that was used to inoculate a bacterial culture.
has_obo_namespace: DPBO
id: DPBO:0000101

harvesting method
type: Class
definition: Method that was used to harvest bacterial cells.
has_obo_namespace: DPBO
id: DPBO:0000102

dissolved oxygen (DO)
type: Class
definition: Constant percentage of dissolved oxygen in a culture medium.
has_obo_namespace: DPBO
id: DPBO:0000103

oxygen limitation experiment
type: Class
subclass of: experimental process
definition: An experiment that is used to grow bacterial cells under oxygen limitation conditions.
has_obo_namespace: DPBO
id: DPBO:0000104

oxygen concentration
type: Class
definition: Percent of oxygen that is added to a culture medium via gassing.
has_obo_namespace: DPBO
id: DPBO:0000105

nitrogen concentration
type: Class
definition: Percent of nitrogen that is added to a culture medium via gassing.
has_obo_namespace: DPBO
id: DPBO:0000106

oxygen excess experiment
type: Class
subclass of: experimental process
definition: An experiment that is used to grow bacterial cells under oxygen excess conditions.
has_obo_namespace: DPBO
id: DPBO:0000107

transcriptional binding site identification
type: Class
definition: A measurement that is used to identify transcriptional binding sites in a genome.
has_obo_namespace: DPBO
id: DPBO:0000108

leaf gas exchange
type: Class
definition: Exchange of carbon dioxide, oxygen and water vapor between the plant leaf and the ambient air through stomata.
created by: Stella Eggels
has_obo_namespace: DPBO
id: DPBO:0000109

infrared gas analyzer
type: Class
definition: Analyzer that measures the concentration of gases in air based on their absorption of infrared radiation.
created by: Stella Eggels
has_obo_namespace: DPBO
id: DPBO:0000110

Explication
type: Class
definition: A word, term or short statement that clarifies the cause, context and/or consequence of another entity.
has_obo_namespace: DPBO
id: DPBO:0000111

Tissue
type: Class
definition: Multicellular structure comprising similar cells with some specific function.
has_obo_namespace: DPBO
id: DPBO:0000112
comment: adapted from FBcv:0003046

Sampling depth
type: Class
definition: The vertical distance below local surface at which the sample was taken. For sediment or soil samples depth is measured from sediment or soil surface, respectively.
has_obo_namespace: DPBO
id: DPBO:0000113
comment: adapted from MIXS:0000018

Number of injections
type: Class
definition: Number of injections of a sample into a mass spectrometer or chromatograph.
has_obo_namespace: DPBO
id: DPBO:0000114

inbred line
type: Class
subclass of: subspecific taxonomic rank
definition: Nearly identical and homozygous genotypes, resulting from repeated selfing over several generations.
has_obo_namespace: DPBO
id: DPBO:0000115

Infinite M200 plate reader (Tecan)
type: Class
subclass of: microplate reader
database_cross_reference: BAO:0150076
has_obo_namespace: DPBO
id: DPBO:0000116

buffer volume
type: Class
definition: Volume of the buffer in which the sample is diluted.
has_obo_namespace: DPBO
id: DPBO:0000117
comment: Suggested by Lukas Weil | 0000-0003-1945-6342

mortar and pestle
type: Class
subclass of: grinding device
definition: Combination of two tools used for grinding or shearing substances to a fine paste or powder.
has_obo_namespace: DPBO
id: DPBO:0000118
comment: Suggested by Lukas Weil | 0000-0003-1945-6342

grinding device
type: Class
definition: Device used for the mechanical reduction of the particle size of a solid sample.
has_obo_namespace: DPBO
id: DPBO:0000119
comment: definition adapted from CHMO:0001652

sugar measurement
type: Class
subclass of: carbohydrate measurement
definition: The quantification of some sugar.
has_obo_namespace: DPBO
id: DPBO:0000120
comment: Suggested by Lukas Weil | 0000-0003-1945-6342

TAP medium
type: Class
subclass of: culture medium
definition: Tris-Acetate-Phosphate medium for the growth of Chlamydomonas.
has_obo_namespace: DPBO
id: DPBO:0000121
comment: Medium composition can be found at doi.org/10.1101/pdb.rec560

environment (feature)
type: Class
definition: Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake.
database_cross_reference: ENVO:01000813
has_obo_namespace: DPBO
id: DPBO:00002008
comment: EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []

alias
type: Class
definition: Unique identificator for a study. This is used to link experiments to the study.
has_obo_namespace: DPBO
id: DPBO:0002000

study abstract
type: Class
definition: Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.
has_obo_namespace: DPBO
id: DPBO:0002001

title
type: Class
definition: Title of the study as would be used in a publication.
has_obo_namespace: DPBO
id: DPBO:0002002

project name
type: Class
definition: Name of the project within which the experiment was organized.
has_obo_namespace: DPBO
id: DPBO:0002005

sequencing method
type: Class
definition: Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid.
has_obo_namespace: DPBO
id: DPBO:0002006

investigation type
type: Class
definition: Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium
has_obo_namespace: DPBO
id: DPBO:0002007

environment (material)
type: Class
definition: The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water.
database_cross_reference: ENVO:00010483
has_obo_namespace: DPBO
id: DPBO:0002009
comment: EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []

plant-associated environmental package
type: Class
definition: MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
has_obo_namespace: DPBO
id: DPBO:0002010

ENA
type: Class
subclass of: endpoint repository
definition: The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data.
creator: http://orcid.org/0000-0001-9021-3197
date: 2022-02-02T08:33:08Z
created by: Dominik Brilhaus
database_cross_reference: ENSGLOSSARY:0000217
has_obo_namespace: DPBO
id: DPBO:0010000
comment: https://www.ebi.ac.uk/ena/

BioSample
type: Class
subclass of: endpoint repository
definition: The BioSample database contains descriptions of biological source materials used in experimental assays.
creator: http://orcid.org/0000-0001-9021-3197
date: 2022-02-02T08:33:08Z
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010002
comment: https://www.ncbi.nlm.nih.gov/biosample/

BioProject
type: Class
subclass of: endpoint repository
definition: A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
creator: http://orcid.org/0000-0001-9021-3197
date: 2022-02-02T08:58:37Z
created by: Dominik Brilhaus
database_cross_reference: GENEPIO:0001836
has_obo_namespace: DPBO
id: DPBO:0010004
comment: https://www.ncbi.nlm.nih.gov/bioproject/

GenBank
type: Class
subclass of: endpoint repository
definition: GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.
creator: http://orcid.org/0000-0001-9021-3197
date: 2022-02-02T08:59:49Z
created by: Dominik Brilhaus
database_cross_reference: NCIT:C43818
has_obo_namespace: DPBO
id: DPBO:0010005
comment: https://www.ncbi.nlm.nih.gov/genbank/

SRA
type: Class
subclass of: endpoint repository
definition: Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis.
creator: http://orcid.org/0000-0001-9021-3197
date: 2022-02-02T09:02:27Z
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010006
comment: https://www.ncbi.nlm.nih.gov/sra/

PGP
type: Class
subclass of: endpoint repository
definition: Plant Genomics & Phenomics Research Data Repository
creator: http://orcid.org/0000-0001-9021-3197
date: 2022-02-02T09:03:35Z
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010007
comment: https://edal-pgp.ipk-gatersleben.de

BIA
type: Class
subclass of: endpoint repository
definition: The BioImage Archive (BIA) stores and distributes biological images that are useful to life sciences researchers. It also provides data archiving services to the broader bioimaging database community including added-value bioimaging data resources such as EMPIAR, Cell-IDR and Tissue-IDR.
creator: http://orcid.org/0000-0001-9021-3197
date: 2022-02-02T09:04:46Z
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010008
comment: https://www.ebi.ac.uk/bioimage-archive/

biosource material state
type: Class
definition: The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay.
creator: http://orcid.org/0000-0001-9021-3197
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010009
comment: "Relates to DPBO:0000013"

fresh material
type: Class
subclass of: biosource material state
definition: Fresh (non-dry) biosource material
creator: http://orcid.org/0000-0001-9021-3197
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010010
comment: "Relates to https://cropontology.org/rdf/CO_347:0000193

dry material
type: Class
subclass of: biosource material state
definition: Dry biosource material
creator: http://orcid.org/0000-0001-9021-3197
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010011
comment: "Relates to https://cropontology.org/rdf/CO_347:0000196

internal standard
type: Class
definition: Internal standard added in known amount to an analytical sample
creator: http://orcid.org/0000-0001-9021-3197
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010012
comment: "Similar to http://purl.obolibrary.org/obo/MSIO_0000005

sample volume
type: Class
definition: Volume taken from the sample to be assayed (measured).
creator: http://orcid.org/0000-0001-9021-3197
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010013

chromatography injection volume
type: Class
definition: Volume of the sample injected during chromatography
creator: http://orcid.org/0000-0001-9021-3197
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010014
comment: "Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577

chromatography injection mode
type: Class
definition: This is to specify split / splitless runs during e.g. gas-chromatography.
creator: http://orcid.org/0000-0001-9021-3197
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:0010015
comment: "Compare to http://purl.obolibrary.org/obo/OBI_0000525

obsolete_RNA-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of RNA-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000003
comment: To be transformed to an instance. DB
deprecated: true

miRNA-seq
type: Class
subclass of: library strategy
definition: A library strategy that can identify and quantify the microRNA sequences present in a biological sample.
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000004
comment: "Adapted from http://purl.obolibrary.org/obo/NCIT_C156057"

ncRNA-seq
type: Class
subclass of: library strategy
definition: A next-generation sequencing library strategy that can determine the small and large non-protein coding RNA transcripts in a sample.
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000005
comment: "Adapted from http://purl.obolibrary.org/obo/NCIT_C172858"

RNA-seq (size fractionation)
type: Class
subclass of: library strategy
definition: A library strategy with an additional size fractionation step after RNA-seq library preparation
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000006

RNA-seq (CAGE)
type: Class
subclass of: library strategy
definition: A library strategy that is used to sequence the 5' capped transcripts, using CAGE to biotinylate and isolate the 7-methylguanosine cap.
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000007
comment: "Adapted from http://purl.obolibrary.org/obo/FBcv_0003051"

RNA-seq (RACE)
type: Class
subclass of: library strategy
definition: Rapid Amplification of cDNA Ends (RACE) is a library strategy for RNA-seq that is used to obtain the full length sequence of an RNA transcript found within a cell. RACE produces a cDNA copy of the RNA through reverse transcription which is amplified and sequenced.
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000008
comment: "Adapted from http://www.ebi.ac.uk/efo/EFO_0004182."

obsolete_ssRNA-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of ssRNA-seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000009
comment: To be transformed to an instance. DB
deprecated: true

obsolete_ChIP-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of ChIP-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000010
comment: To be transformed to an instance. DB
deprecated: true

obsolete_MNase-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of MNase-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000011
comment: To be transformed to an instance. DB
deprecated: true

obsolete_MBD-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of MBD-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000012
comment: To be transformed to an instance. DB
deprecated: true

obsolete_MRE-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of MRE-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000013
comment: To be transformed to an instance. DB
deprecated: true

obsolete_Bisulfite-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of Bisulfite-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000014
comment: Replaced by EFO term Bisulfite-seq (id:0003753)
deprecated: true

Bisulfite-seq (reduced representation)
type: Class
subclass of: library strategy
definition: A library strategy that uses one or more restriction enzymes on a genomic DNA sample prior to sequencing to produce sequence-specific fragmentation
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_exact_synonym: RRBS-Seq
has_exact_synonym: reduced-representation bisulfite sequencing
has_obo_namespace: DPBO
id: DPBO:1000015
comment: To be transformed to an instance. DB

obsolete_MeDIP-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of MeDIP-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000016
comment: To be transformed to an instance. DB
deprecated: true

DNase hypersensitivity
type: Class
subclass of: library strategy
definition: A library strategy that is used to characterize the DNase hypersensitivity of a genome by treatment with DNase before library preparation.
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000017
comment: "Adapted from FBcv:0003058."

Tn-seq
type: Class
subclass of: library strategy
definition: A library strategy that is used to sequence transposons.
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000018
comment: "Adapted from http://www.ebi.ac.uk/efo/EFO_0008973."

obsolete_FAIRE-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of FAIRE-seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000019
comment: To be transformed to an instance. DB
deprecated: true

SELEX
type: Class
subclass of: library strategy
definition: A library strategy for high-througput sequencing that is based on Systematic evolution of ligands by exponential enrichment.
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000020
comment: "Adapted from http://www.ebi.ac.uk/efo/EFO_0008918."

obsolete_RIP-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of RIP-Seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000021
comment: To be transformed to an instance. DB
deprecated: true

obsolete_ATAC-seq
type: Class
subclass of: Obsolete Class
definition: placeholder def of ATAC-seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000022
comment: To be transformed to an instance. DB
deprecated: true

obsolete_ChIA-PET
type: Class
subclass of: Obsolete Class
definition: placeholder def of ChIA-PET
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000023
comment: To be transformed to an instance. DB
deprecated: true

obsolete_Hi-C
type: Class
subclass of: Obsolete Class
definition: placeholder def of Hi-C
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000024
comment: To be transformed to an instance. DB
deprecated: true

OTHER: specify
type: Class
subclass of: library strategy
definition: Any other possible library strategy that can be used for RNA-seq
ER target: GEO_RNASEQ
ER target term: PROTOCOLS_library strategy
has_obo_namespace: DPBO
id: DPBO:1000025
comment: "This is a term that is used to enter a library strategy as free text in the checklist of GEO for the upload of RNA-seq data."

obsolete_fastq
type: Class
subclass of: Obsolete Class
definition: placeholder def of fastq
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000026
comment: To be transformed to an instance. DB
deprecated: true

bam
type: Class
subclass of: raw data file format
definition: Binary format for storing of sequencing data
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000027
comment: Adapted from http://purl.obolibrary.org/obo/NGBO_6000021.

Illumina_native_qseq
type: Class
subclass of: raw data file format
definition: Illumina´s native QSEQ format
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000028

Illumina_native
type: Class
subclass of: raw data file format
definition: Illumina´s native sequencing format
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000029

SOLiD_native_csfasta
type: Class
subclass of: raw data file format
definition: SOLID´s native csfasta sequencing format
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000030

SOLiD_native_qual
type: Class
subclass of: raw data file format
definition: SOLI´s native quality sequencing format
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000031

sff
type: Class
subclass of: raw data file format
definition: Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000032
comment: http://edamontology.org/format_3284

454_native_seq
type: Class
subclass of: raw data file format
definition: 454 pyrosequencing native sequencing file format
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000033

454_native_qual
type: Class
subclass of: raw data file format
definition: 454 pyrosequencing native quality sequencing file format
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000034

Helicos_native
type: Class
subclass of: raw data file format
definition: Helicos native file format
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000035

srf
type: Class
subclass of: raw data file format
definition: Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000036
comment: http://edamontology.org/format_3017

PacBio_HDF5
type: Class
subclass of: raw data file format
definition: PacBio hierarchical, filesystem-like data format that can store metadata in the form of user-defined, named attributes, which are attached to groups and datasets, and representations of images and tables built up using datasets, groups and attributes.
ER target: GEO_RNASEQ
ER target term: RAW FILES_file type
has_obo_namespace: DPBO
id: DPBO:1000037
comment: Adapted from http://purl.obolibrary.org/obo/NCIT_C184763

obsolete_Illumina Genome Analyzer IIx
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000038
comment: term is redundant, use EFO:0004202 or OBI:0002000 instead
deprecated: true

obsolete_Illumina HiSeq 1000
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000039
comment: term is redundant, use EFO:0004204 or OBI:0002022 instead
deprecated: true

obsolete_Illumina HiSeq 1500
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000040
comment: term is redundant, use GENEPIO:0100115, OBI:0003386 or EFO:0011027
deprecated: true

obsolete_Illumina HiSeq 2000
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000041
comment: Term is redundant, please use OBI:0002001 or EFO:0004203
deprecated: true

obsolete_Illumina HiSeq 2500
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000042
comment: Term is redundant, please use OBI:0002002 or EFO:0008565
deprecated: true

obsolete_Illumina HiSeq 3000
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000043
comment: Term is redundant, please use OBI:0002048 or EFO:0008564
deprecated: true

obsolete_Illumina HiSeq 4000
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000044
comment: Term is redundant, please use OBI:0002049 or EFO:0008563
deprecated: true

obsolete_Illumina NextSeq 500
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000045
comment: Term is redundant, please use EFO:0009173
deprecated: true

obsolete_Illumina NextSeq 550
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000046
comment: Term is redundant, please use GENEPIO:0100128 or EFO:0008566
deprecated: true

obsolete_Illumina HiSeq X Ten
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000047
comment: Term is redundant, please use GENEPIO:0100113 or OBI:0002129
deprecated: true

obsolete_Illumina HiSeq X Five
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000048
comment: Term is redundant, please use GENEPIO:0100112
deprecated: true

obsolete_Illumina NovaSeq 6000
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000049
comment: Term is redundant, please use GENEPIO:0100123, OBI:0002630 or EFO:0008637
deprecated: true

obsolete_Illumina MiSeq
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000050
comment: Redundant term, please use EFO:0004205 instead
deprecated: true

obsolete_Illumina HiScanSQ
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000051
comment: Redundant term, please use GENEPIO:0100109 instead
deprecated: true

obsolete_Illumina MiniSeq
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000052
comment: Term is redundant, please use GENEPIO:0100124, OBI:0003114 or EFO:0008636 instead.
deprecated: true

obsolete_Illumina iSeq 100
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000053
comment: Term is redundant, please use GENEPIO:0100121 or EFO:0008635 instead
deprecated: true

obsolete_BGISEQ-500
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000054
comment: Term is redundant, please use NCIT:C146812 or GENEPIO:0100145 instead
deprecated: true

obsolete_DNBSEQ-G400
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000055
comment: Term is redundant, please use GENEPIO:0100148
deprecated: true

obsolete_DNBSEQ-T7
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000056
comment: Term is redundant, please use GENEPIO:0100147
deprecated: true

obsolete_DNBSEQ-G50
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000057
comment: Term is redundant, please use GENEPIO:0100150
deprecated: true

obsolete_Ion Torrent PGM
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000058
comment: Term is redundant, please use GENEPIO:0100136
deprecated: true

obsolete_Ion Torrent Proton
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000059
comment: Term is redundant, please use GENEPIO:0100137
deprecated: true

obsolete_Ion Torrent S5
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000060
comment: Term is redundant, please use GENEPIO:0100139
deprecated: true

obsolete_Ion Torrent S5 XL
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000061
comment: Term is redundant, please use GENEPIO:0100138
deprecated: true

obsolete_PacBio RS
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000062
comment: Term is redundant, please use GENEPIO:0100131
deprecated: true

obsolete_PacBio RS II
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000063
comment: Term is redundant, please use OBI:0002012 or EFO:0008631
deprecated: true

obsolete_Sequel
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000064
comment: Term is redundant, please use GENEPIO:0100133 or OBI:0002632
deprecated: true

obsolete_Sequel II
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000065
comment: Term is redundant, please use GENEPIO:0100134 or OBI:0002633
deprecated: true

obsolete_AB SOLiD System 2.0
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000066
comment: Term is redundant, please use GENEPIO:0001932 or EFO:0004442
deprecated: true

obsolete_AB SOLiD System 3.0
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000067
comment: Term is redundant, please use EFO:0004439 or GENEPIO:0001933
deprecated: true

obsolete_AB SOLiD 3 Plus System
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000068
comment: Term is redundant, please use OBI:0002007.
deprecated: true

obsolete_AB SOLiD 4 System
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000069
comment: Term is redundant, please use EFO:0004438
deprecated: true

obsolete_AB SOLiD 4hq System
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000070
comment: Term is redundant, please use GENEPIO:0001928 or EFO:0004441
deprecated: true

obsolete_AB SOLiD PI System
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000071
comment: Term is redundant, please use EFO:0004437 or GENEPIO:0001931
deprecated: true

AB 5500 Genetic Analyzer
type: Class
subclass of: next generation sequencing instrument model
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000072

AB 5500xl Genetic Analyzer
type: Class
subclass of: next generation sequencing instrument model
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000073

AB 5500xl-W Genetic Analysis System
type: Class
subclass of: next generation sequencing instrument model
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000074

obsolete_454 GS
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000075
comment: Term is redundant, please use EFO:0004431
deprecated: true

obsolete_454 GS 20
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000076
comment: Term is redundant, please use EFO:0004206
deprecated: true

obsolete_454 GS FLX
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000077
comment: Term is redundant, please use EFO:0004432 or OBI:0000702
deprecated: true

454 GS FLX+
type: Class
subclass of: next generation sequencing instrument model
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000078

obsolete_454 GS Junior
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000079
comment: Term is redundant, please use EFO:0004434 or GENEPIO:0001938
deprecated: true

obsolete_454 GS FLX Titanium
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000080
comment: Term is redundant, please use EFO:0004433 or GENEPIO:0001936
deprecated: true

obsolete_Complete Genomics
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000081
comment: Term is redundant, please use NCIT:C146815 or GENEPIO:0001924
deprecated: true

obsolete_Helicos HeliScope
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000082
comment: Term is redundant, please use OBI:0000717
deprecated: true

obsolete_GridION
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000083
comment: Term is redundant, please use GENEPIO:0100141
deprecated: true

obsolete_MinION
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000084
comment: Term is redundant, please use OBI:0002750, EFO:0008632 or GENEPIO:0100142
deprecated: true

obsolete_PromethION
type: Class
subclass of: Obsolete Class
ER target: GEO_RNASEQ
ER target term: RAW FILES_instrument model
has_obo_namespace: DPBO
id: DPBO:1000085
comment: Term is redundant, please use OBI:0002752 or GENEPIO:0100143
deprecated: true

obsolete_single
type: Class
subclass of: Obsolete Class
definition: placeholder def of single
ER target: GEO_RNASEQ
ER target term: RAW FILES_single or paired-end
has_obo_namespace: DPBO
id: DPBO:1000086
comment: Deprecated, please use DPBO:0000086 "single-end" instead
deprecated: true

paired-end
type: Class
subclass of: library layout
definition: A library layout which describes that both ends of the library fragment are sequenced
ER target: GEO_RNASEQ
ER target term: RAW FILES_single or paired-end
has_obo_namespace: DPBO
id: DPBO:1000087
comment: Adapted from http://purl.obolibrary.org/obo/FBcv_0003221

obsolete_total RNA
type: Class
subclass of: Obsolete Class
definition: placeholder def of total RNA
ER target: GEO_RNASEQ
ER target term: SAMPLES_molecule
has_obo_namespace: DPBO
id: DPBO:1000088
comment: term is redundant, please use EFO:0004964
deprecated: true

obsolete_polyA RNA
type: Class
subclass of: Obsolete Class
definition: placeholder def of polyA RNA
ER target: GEO_RNASEQ
ER target term: SAMPLES_molecule
has_obo_namespace: DPBO
id: DPBO:1000089
comment: Term is redundant, please use OBI_0000869

obsolete_cytoplasmic RNA
type: Class
subclass of: Obsolete Class
definition: placeholder def of cytoplasmic RNA
ER target: GEO_RNASEQ
ER target term: SAMPLES_molecule
has_obo_namespace: DPBO
id: DPBO:1000090
comment: Term is redundant, please use NCIT:C84512
deprecated: true

obsolete_nuclear RNA
type: Class
subclass of: Obsolete Class
definition: placeholder def of nuclear RNA
ER target: GEO_RNASEQ
ER target term: SAMPLES_molecule
has_obo_namespace: DPBO
id: DPBO:1000091
comment: Term is redundant. Please use EFO:0030052
deprecated: true

obsolete_genomic DNA
type: Class
subclass of: Obsolete Class
definition: placeholder def of genomic DNA
ER target: GEO_RNASEQ
ER target term: SAMPLES_molecule
has_obo_namespace: DPBO
id: DPBO:1000092
comment: Term is redundant, please use BAO:0000316
deprecated: true

obsolete_protein
type: Class
subclass of: Obsolete Class
definition: placeholder def of protein
ER target: GEO_RNASEQ
ER target term: SAMPLES_molecule
has_obo_namespace: DPBO
id: DPBO:1000093
comment: Term is redundant, please use CHEBI:36080
deprecated: true

other
type: Class
subclass of: bio entity
definition: Any other bio entity that can be characterized by high-throuput sequencing.
ER target: GEO_RNASEQ
ER target term: SAMPLES_molecule
has_obo_namespace: DPBO
id: DPBO:1000094

endpoint repository
type: Class
definition: Parent term to collect endpoint repositories (ER).
has_obo_namespace: DPBO
id: DPBO:1000095
comment: "For an overview of relevant repositories, check https://www.re3data.org or https://fairsharing.org"

GEO
type: Class
subclass of: endpoint repository
disjoint with: MetaboLights
definition: GEO (Gene Expression Omnibus) is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
has_obo_namespace: DPBO
id: DPBO:1000096
comment: https://www.ncbi.nlm.nih.gov/geo/

MetaboLights
type: Class
subclass of: endpoint repository
definition: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. MetaboLights is the recommended Metabolomics repository for a number of leading journals.
has_obo_namespace: DPBO
id: DPBO:1000097
comment: https://www.ebi.ac.uk/metabolights/

PRIDE
type: Class
subclass of: endpoint repository
definition: The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to ProteomeXchange via PRIDE and are handled by expert bio-curators. All PRIDE public datasets can also be searched in ProteomeCentral, the portal for all ProteomeXchange datasets.
has_obo_namespace: DPBO
id: DPBO:1000098
comment: https://www.ebi.ac.uk/pride/

GEO_RNAseq
type: Class
subclass of: GEO
disjoint with: GEO_microarray
definition: Parent term to collect terms required for RNASeq submission to GEO
has_obo_namespace: DPBO
id: DPBO:1000099

GEO_microarray
type: Class
subclass of: GEO
definition: Parent term to collect terms required for microarray submission to GEO
has_obo_namespace: DPBO
id: DPBO:1000100

obsolete_well
type: Class
subclass of: Obsolete Class
definition: A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well.
database_cross_reference: OME:Well
has_obo_namespace: DPBO
id: DPBO:1000101
comment: term is redundant, please use REPR:Well
deprecated: true

well Number
type: Class
definition: The number of a well in a well plate.
has_obo_namespace: DPBO
id: DPBO:1000102

siRNA identifier
type: Class
definition: The identifier of a siRNA from a reagent library.
has_obo_namespace: DPBO
id: DPBO:1000103

obsolete_compound name
type: Class
subclass of: Obsolete Class
definition: Unique name of a chemical compound.
database_cross_reference: EDAM:data_0990
has_obo_namespace: DPBO
id: DPBO:1000104
comment: term is redundant, please use data:0990
deprecated: true

obsolete_compound identifier
type: Class
subclass of: Obsolete Class
definition: Identifier of an entry from a database of chemicals.
has_obo_namespace: DPBO
id: DPBO:1000105
comment: term is redundant, please use data:1086
deprecated: true

compound class
type: Class
definition: The class a compound belongs to, defined by its biological function or the chemical property.
has_obo_namespace: DPBO
id: DPBO:1000106
comment: "Needed for imaging templates"

obsolete_gene identifier
type: Class
subclass of: Obsolete Class
definition: A unique gene name within a specific repository, database, or collection.
database_cross_reference: NCIT:C48664
has_obo_namespace: DPBO
id: DPBO:1000108
deprecated: true

sense sequence
type: Class
definition: The sequence of the sense strand.
has_obo_namespace: DPBO
id: DPBO:1000109
comment: "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html"

antisense sequence
type: Class
definition: The sequence of the antisense strand.
has_obo_namespace: DPBO
id: DPBO:1000110
comment: "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html"

obsolete_control type
type: Class
subclass of: Obsolete Class
definition: A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated.
database_cross_reference: NCIT:C49647
has_obo_namespace: DPBO
id: DPBO:1000111
comment: term is redundant, please use NCIT:C49647
deprecated: true

quality control
type: Class
definition: Result of quality control. This can be: pass/fail, or other information such as: no cells
has_obo_namespace: DPBO
id: DPBO:1000112
comment: "Definition according to IDR"

channel
type: Class
definition: The label used in a microscopy assay and what it targets, separated by a colon. Each pair of labels and visualized object is separated by a semi-colon. E.g. DAPI:nuclei;TRITC:HA_Flag tagged protein.
has_obo_namespace: DPBO
id: DPBO:1000113
comment: "Needed for imaging templates. Definition form IDR"

screen technology type
type: Class
definition: The type of a high content screening experiment like RNAi screen or antibody screen.
has_obo_namespace: DPBO
id: DPBO:1000114
comment: "Needed for imaging templates"

library version
type: Class
definition: Version of a reagent library used e.g. in high content screening.
has_obo_namespace: DPBO
id: DPBO:1000116
comment: "Needed for imaging templates"

obsolete_antibody
type: Class
subclass of: Obsolete Class
definition: A type of protein made by B lymphocytes in response to a foreign substance (antigen). Each antibody only binds to a specific antigen, helping to destroy the antigen directly or by assisting white blood cells to destroy the antigen.
database_cross_reference: NCIT:C16295
has_obo_namespace: DPBO
id: DPBO:1000117
comment: term is redundant, please use NCIT:C16295
deprecated: true

obsolete_cover slip
type: Class
subclass of: Obsolete Class
definition: A thin flat piece of transparent material that is placed over a specimen for viewing with a microscope.
database_cross_reference: NCIT:C126370
has_obo_namespace: DPBO
id: DPBO:1000118
comment: use NCIT:C126370
deprecated: true

image file path
type: Class
has_obo_namespace: DPBO
id: DPBO:1000120
comment: "Needed for imaging templates"

target compartment
type: Class
definition: Compartment of interest in the prepared sample
has_obo_namespace: DPBO
id: DPBO:1000121
comment: "Needed for imaging templates"

obsolete_imaging software name
type: Class
subclass of: Obsolete Class
definition: The name of the software program to capture and/or process imaging data.
database_cross_reference: NCIT:C175898
has_obo_namespace: DPBO
id: DPBO:1000122
comment: false
deprecated: true

imaging software version
type: Class
definition: The version of the software program to capture and/or process imaging data.
has_obo_namespace: DPBO
id: DPBO:1000123
comment: "Needed for imaging templates"

imaging software settings
type: Class
definition: The used settings in the software program to capture and/or process imaging data.
has_obo_namespace: DPBO
id: DPBO:1000124
comment: "Needed for imaging templates"

microscope filter
type: Class
definition: Channel the image was taken with.
has_obo_namespace: DPBO
id: DPBO:1000125
comment: "Needed for imaging templates"

dataset name
type: Class
database_cross_reference: dwc:datasetName
has_obo_namespace: DPBO
id: DPBO:1000126
comment: "Needed for imaging templates"

obsolete_assay name
type: Class
subclass of: Obsolete Class
definition: The name of the assay.
database_cross_reference: NCIT:C178857
has_obo_namespace: DPBO
id: DPBO:1000127
deprecated: true

image processing software
type: Class
definition: Software used for the processing of microscopy images like for adaption of contrast or stacking.
has_obo_namespace: DPBO
id: DPBO:1000128
comment: "Needed for imaging templates"

image data analysis software
type: Class
definition: Software used to analyze data extracted from microscopy images.
has_obo_namespace: DPBO
id: DPBO:1000129
comment: "Needed for imaging templates"

image processing software parameters
type: Class
definition: Applied settings of the software used for the processing of microscopy images
has_obo_namespace: DPBO
id: DPBO:1000130
comment: "Needed for imaging templates"

feature extraction software
type: Class
definition: Software used for the extraction of features from microscopy images.
has_obo_namespace: DPBO
id: DPBO:1000131
comment: "Needed for imaging templates"

feature extraction strategy
type: Class
definition: Description of the approach to extract features from microscopy images.
has_obo_namespace: DPBO
id: DPBO:1000133
comment: "Needed for imaging templates"

use of image
type: Class
definition: Whether a microscopy image is intended to be used illustrational or analytically by deriving values from it.
has_obo_namespace: DPBO
id: DPBO:1000135
comment: "Needed for imaging templates"

reagent design genome reference version
type: Class
definition: The gene annotation build the siRNAs for a high content screen library were mapped to.
has_obo_namespace: DPBO
id: DPBO:1000136
comment: "Needed for imaging templates"

control specification
type: Class
definition: additional information about the quality control in high content screening studies e.g. 'checks for transfection', 'gives strong phenotype'
has_obo_namespace: DPBO
id: DPBO:1000137
comment: "Needed for imaging templates. Definition from IDR."

quality control comments
type: Class
definition: additional information why a quality control passed or failed'
has_obo_namespace: DPBO
id: DPBO:1000138
comment: "Needed for imaging templates. Definition from IDR."

microscopy study type
type: Class
definition: Type of an imaging study.
has_obo_namespace: DPBO
id: DPBO:1000139
comment: "Needed for imaging templates"

magnification
type: Class
definition: The magnification of a microscopy image
has_obo_namespace: DPBO
id: DPBO:1000140
comment: "Needed for imaging templates"

image dimensionality
type: Class
definition: The sizes along the axis of the XYZCT dimensions in a microscopy image.
has_obo_namespace: DPBO
id: DPBO:1000141
comment: "Needed for imaging templates"

obsolete_objective
type: Class
subclass of: Obsolete Class
definition: The microscope's objective lens.
database_cross_reference: OME:Objective
has_obo_namespace: DPBO
id: DPBO:1000142
comment: use OME:objective
deprecated: true

microscopy sample preparation
type: Class
definition: How a sample was further prepared for microscopy.
database_cross_reference: MS:1000831
has_obo_namespace: DPBO
id: DPBO:1000143

material fixation
type: Class
definition: Plant material fixation on a microscopy slide.
has_obo_namespace: DPBO
id: DPBO:1000144
comment: "Needed for imaging templates"

prepared organism part
type: Class
definition: The part of an organism that has been prepared for an experiment
has_obo_namespace: DPBO
id: DPBO:1000145
comment: "Needed for imaging templates"

obsolete_strain
type: Class
subclass of: Obsolete Class
definition: A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
database_cross_reference: EFO:0005135
has_obo_namespace: DPBO
id: DPBO:1000146
comment: use EFO:0005135
deprecated: true

obsolete_container
type: Class
subclass of: Obsolete Class
definition: A device that can be used to restrict the location of material entities over time
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
database_cross_reference: OBI:0000967
has_obo_namespace: DPBO
id: DPBO:1000147
comment: term is redundant, please use OBI:0000967
deprecated: true

jar
type: Class
subclass of: container
definition: A wide-mouthed cylindrical container made of glass or pottery and typically having a lid
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000148

plate
type: Class
subclass of: container
definition: A flat dish, typically circular
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000149

obsolete_contamination
type: Class
subclass of: Obsolete Class
definition: The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. [database_cross_reference: https://en.wikipedia.org/wiki/Contamination][database_cross_reference: https://github.com/pato-ontology/pato/issues/420]
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
database_cross_reference: PATO:0015031
has_obo_namespace: DPBO
id: DPBO:1000150
deprecated: true

axenic
type: Class
subclass of: contamination
definition: Free from other living organisms
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000151

laboratory strain
type: Class
subclass of: strain
definition: Latest laboratory cultivated the strain. Who sent the strain to your laboratory
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000152

date
type: Class
definition: The day of the month or year as specified by a number. According to ISO 8601-1 [ISO 8601-1] please use the format YYYY-MM-DD.
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
database_cross_reference: dc:date
has_obo_namespace: DPBO
id: DPBO:1000153

obsolete_volume
type: Class
subclass of: Obsolete Class
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. [database_cross_reference: PATOC:GVG]
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
database_cross_reference: PATO:0000918
has_obo_namespace: DPBO
id: DPBO:1000154
comment: term is redundant, please use PATO:0000918
deprecated: true

culture medium volume
type: Class
subclass of: volume
definition: Volume of culture medium used to grow the organism
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000155

obsolete_light
type: Class
subclass of: Obsolete Class
definition: The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
database_cross_reference: EFO:0000568
has_obo_namespace: DPBO
id: DPBO:1000156
comment: term is redundant, please use EFO:0000568
deprecated: true

light quality
type: Class
subclass of: light
definition: The spectral distribution of light (blue, green, red, far red and other light spectrums emitted from a light source)
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000157
comment: "close to the term http://purl.obolibrary.org/obo/PECO_0007154"

obsolete_ratio
type: Class
subclass of: Obsolete Class
definition: A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b.
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000158
comment: term is redundant, please use UO:0010006
deprecated: true

Axiom
annotated source: obsolete_ratio
annotated property: definition
annotated target: A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b.
database_cross_reference: UOB:LKSR

260/280 ratio
type: Class
subclass of: ratio
definition: Nucleic acids have absorbance maxima at 260 nm. Historically, the ratio of this absorbance maximum to the absorbance at 280 nm has been used as a measure of purity in both DNA and RNA extractions. A 260/280 ratio of ~1.8 is generally accepted as pure for DNA; a ratio of ~2.0 is generally accepted as pure for RNA.
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000159
comment: "Thermofisher NanoDrop https://tools.thermofisher.com/content/sfs/brochures/T123-NanoDrop-Lite-Interpretation-of-Nucleic-Acid-260-280-Ratios.pdf"

260/230 ratio
type: Class
subclass of: ratio
definition: The 260/230 values for pure nucleic acid are often higher than the respective 260/280 values. Expected 260/230 values are commonly in the range of 2.0–2.2
created by: "Fabian Haas | ORCID:0000-0002-7711-5282"
has_obo_namespace: DPBO
id: DPBO:1000160
comment: "Thermofisher NanoDrop https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf"

protocol type
type: Class
definition: ISA-related term to identify the type of protocol (the set of procedures and rules that must be performed and when) used during the study or assay.
created by: Dominik Brilhaus
has_obo_namespace: DPBO
id: DPBO:1000161
comment: "This term is primarily used to group and hierarchically categorize types of experimental protocols for easier (interpretation of) user-input. For the initial categorization, 'type' is defined as the purpose of the experiment (i.e. extraction of a target material such as DNA) rather than the mechanism of the protocol (i.e. column-based extraction)."

obsolete_growth protocol
type: Class
subclass of: Obsolete Class
definition: A protocol that provides instructions for the growth of a biological sample. Describes the conditions, materials and procedure used to grow and/or maintain the sample.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
database_cross_reference: EFO:0003789
has_obo_namespace: DPBO
id: DPBO:1000162
comment: replaced term with EFO:0003789
deprecated: true

algae growth protocol
type: Class
subclass of: growth protocol
definition: A protocol that provides instructions for growing algae.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000163

plant growth protocol
type: Class
subclass of: growth protocol
definition: A protocol that provides instructions for growing a plant cultivar.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000164

microbe growth protocol
type: Class
subclass of: growth protocol
definition: A protocol that provides instructions for growing a microbial sample.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000165

bacteria growth protocol
type: Class
subclass of: microbe growth protocol
definition: A protocol that provides instructions for growing a bacterial sample.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000166

yeast growth protocol
type: Class
subclass of: microbe growth protocol
definition: A protocol that provides instructions for growing yeast.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000167

obsolete_treatment protocol
type: Class
subclass of: Obsolete Class
definition: A protocol that aims to treat sample or collection of samples, organism or group of organisms, for some experimental purpose.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
database_cross_reference: EFO:0003969
has_obo_namespace: DPBO
id: DPBO:1000168
comment: definition from http://www.ebi.ac.uk/efo/EFO_0003969. Term is redundant, please use EFO:0003969
deprecated: true

obsolete_sample collection protocol
type: Class
subclass of: Obsolete Class
definition: A protocol that provides instructions on how a biological sample for an experiment was collected.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
database_cross_reference: EFO:0005518
has_obo_namespace: DPBO
id: DPBO:1000169
comment: definition from http://www.ebi.ac.uk/efo/EFO_0005518. Term is redundant, please use EFO:0005518
deprecated: true

sample processing protocol
type: Class
subclass of: protocol type
definition: A protocol that details how a sample is processed or changed to prepare it for analysis.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000170

obsolete_extraction protocol
type: Class
subclass of: Obsolete Class
definition: A protocol used to obtain something of experimental interest from a sample via chemical, physical or mechanical means. Often tailored to match the starting material as well as the end goals (resulting material, quality level, etc.) of the procedure required by the following assay
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
database_cross_reference: EFO:0000490
has_obo_namespace: DPBO
id: DPBO:1000171
comment: definition taken heavily from http://www.ebi.ac.uk/efo/EFO_0000490. Term is redundant, please use EFO:0000490
deprecated: true

obsolete_DNA extraction protocol
type: Class
subclass of: Obsolete Class
definition: A protocol that describes how to remove and purify DNA from a sample. This requires physical and/or chemical methods in order to separate the DNA from cell membranes, proteins and other cellular components.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000172
comment: definition taken from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425773/. Term is redundant, please use EFO:0022384.
deprecated: true

obsolete_RNA extraction protocol
type: Class
subclass of: Obsolete Class
definition: A protocol that describes the steps for removing and purifying DNA from a biological sample
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
database_cross_reference: EFO:0010959
has_obo_namespace: DPBO
id: DPBO:1000173
comment: term is redundant, please use EFO:0010959
deprecated: true

obsolete_protein extraction protocol
type: Class
subclass of: Obsolete Class
definition: A protocol that describes how to isolate protein from a tissue, cell culture or other biological sample.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000174
comment: term is redundant, please use EFO:0022383
deprecated: true

metabolite extraction protocol
type: Class
subclass of: extraction protocol
definition: A protocol that describes the step by step process for removing metabolites from a biological sample.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000175

assay pre-processing protocol
type: Class
subclass of: protocol type
definition: A protocol that describes the steps to be taken to transform a sample before an assay can be performed
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-401
has_obo_namespace: DPBO
id: DPBO:1000176

assay protocol
type: Class
subclass of: protocol type
definition: A protocol that describes how to perform an assay.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-401
has_obo_namespace: DPBO
id: DPBO:1000177

data processing protocol
type: Class
subclass of: protocol type
definition: A protocol that describes the operations performed on data by a computer in order to retrieve, transform, or classify information.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-401
has_obo_namespace: DPBO
id: DPBO:1000178
comment: definition heavily based on http://purl.obolibrary.org/obo/NCIT_C47925

data filtering protocol
type: Class
subclass of: data processing protocol
definition: A protocol that describes the operations performed to filter or select a smaller part of the dataset to be used for or rejected from subsequent analysis steps
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-401
has_obo_namespace: DPBO
id: DPBO:1000179

data transformation protocol
type: Class
subclass of: data processing protocol
definition: A protocol that describes the operations performed to convert data from one format, structure, or value into another.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-401
has_obo_namespace: DPBO
id: DPBO:1000180

data extraction protocol
type: Class
subclass of: data processing protocol
definition: A protocol that describes the operations performed to take a specific data set out of a larger data set and present it in a useable format.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-401
has_obo_namespace: DPBO
id: DPBO:1000181

replicate group
type: Class
definition: An unique identifier for grouping experminental replicates - replication of an experiment to assess biological or technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, replicate groups must be the same for each replicate in the group (e.g. 'group 1' for each replicate in the group). This adds the possibility to aggregate the replicates without additional annotations.
created by: Kevin Schneider | ORCID: 0000-0002-2198-5262
has_obo_namespace: DPBO
id: DPBO:1000182

biological replicate group
type: Class
subclass of: replicate group
definition: An unique identifier for grouping biological replicates - replicates made from different individual biosamples to assess biological variation in an experiment. In contrast to other ways of annotating replicates in experimental design, biological replicate groups must be the same for each replicate in the group (e.g. 'b_1' for each biological replicate in the group). This adds the possibility to aggregate the biological replicates without additional annotations.
created by: Kevin Schneider | ORCID: 0000-0002-2198-5262
has_obo_namespace: DPBO
id: DPBO:1000183

technical replicate group
type: Class
subclass of: replicate group
definition: An unique identifier for grouping technical replicates - replicates made from different individual biosamples to assess technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, technical replicate groups must be the same for each replicate in the group (e.g. 't_1' for each technical replicate in the group). This adds the possibility to aggregate the technical replicates without additional annotations.
created by: Kevin Schneider | ORCID: 0000-0002-2198-526
has_obo_namespace: DPBO
id: DPBO:1000184

incubation time
type: Class
definition: The time that a sample should incubate (keep at a suitable temperature) during a experimental protocol to allow for a reaction or proces to occur.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-401
database_cross_reference: BAO:0002833
has_obo_namespace: DPBO
id: DPBO:1000185

Zeiss Axiovert
type: Class
subclass of: microscope
definition: Axiovert series, inverse microscope
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000186

Olympus SZX7 (Bino)
type: Class
subclass of: microscope
definition: binocular, stereo microscope
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000187

Zeiss AxioCam MRc5
type: Class
subclass of: digital camera
definition: camera
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000188

01
type: Class
subclass of: microscope filter
definition: white
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000189

01
type: Class
subclass of: microscope filter
definition: white
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000190

DIC
type: Class
subclass of: microscope filter
definition: differential interference contrast
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000191

09
type: Class
subclass of: microscope filter
definition: yellow
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000192

10
type: Class
subclass of: microscope filter
definition: green
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000193

15
type: Class
subclass of: microscope filter
definition: red
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000194

Zeiss ZEN 3.5 (blue edition)
type: Class
subclass of: Imaging Software Name
definition: software controlling imaging systems from ZEISS.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000195

Thermo Scientific Menzel slides, 76 x 26 mm, 1,0 mm
type: Class
subclass of: microscope slide
definition: microscope slide
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000196

VWR frosted edges, ground edges 90°, 76 x 26 mm, 0,8 - 1,0 mm
type: Class
subclass of: microscope slide
definition: microscope slide
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000197

Roth SuperFrost® white, cut edges, 76 x 26 mm, 1,0 mm
type: Class
subclass of: microscope slide
definition: microscope slide
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000198

Menzel, 24 x 50 mm, selected 0,17 +/- 0,01, strength 1,5
type: Class
subclass of: Cover Slip
definition: cover slip
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000199

Roth, 24 x 50 mm, strength 1
type: Class
subclass of: Cover Slip
definition: cover slip
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000200

VWR, 18 x 18 mm, 0,13 - 0,16 mm, strength 1,5
type: Class
subclass of: Cover Slip
definition: cover slip
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000201

0.8x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000202

1x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000203

1.25x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000204

1.6x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000205

2x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000206

2.5x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000207

3.2x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000208

4x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000209

5x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000210

5.6x
type: Class
subclass of: magnification
definition: magnification of Olympus SZX7 (Bino)
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000211

Plan-Neofluar 5x/0.15
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axioplan 2
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000212

Plan-Neofluar 10x/0.3
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axioplan 2
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000213

Plan-Neofluar 20x/0.50 Ph2
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axioplan 2
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000214

Plan-Neofluar 40x/0.75
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axioplan 2
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000215

Plan-Neofluar 63x/1.25 Oil
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axioplan 2
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000216

Plan-Neofluar 100x/1.30 Oil
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axioplan 2
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000217

Achroplan 5x/012
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axiovert
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000218

Achroplan 10x/0.25 Ph1
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axiovert
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000219

Achroplan 20x/0.40
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axiovert
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000220

Achroplan 40x/0.60 korr Ph2
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axiovert
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000221

Achroplan 63x/0.75 korr Ph2
type: Class
subclass of: Objective Lens
definition: objective lens of Zeiss Axiovert
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000222

Knop medium
type: Class
subclass of: culture medium
definition: A solution designed for the growth of plant cell, tissue and organ culture.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
has_related_synonym: Knop ME
has_related_synonym: Knop solution
id: DPBO:1000223

phenotyping
type: Class
definition: The activity or process of determining, analyzing, or predicting all or part of an organism's phenotype.
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000224
comment: Definition from https://www.merriam-webster.com/dictionary/phenotyping

Zeiss Axioplan 2
type: Class
subclass of: microscope
definition: Axioplan series, imaging fluorescence microscope
created by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011
has_obo_namespace: DPBO
id: DPBO:1000225
comment: NOTE: This term's ID has been changed from DPBO:1000185 to DPBO:1000225 due to a discrepancy with the term ID: the ID DPBO:1000185 was already being used for another term within the ontology (incubation time)

student helper
type: Class
definition: A role of a student in a research project which is acknowledged in papers.
created by: Andrea Schrader | 0000-0002-3879-7057
has_obo_namespace: DPBO
id: DPBO:1000226

plant work helper
type: Class
definition: A person that helps at various steps of the plant growth cycle e.g. sowing seeds, separating plants at the correct age or collecting seeds.
has_obo_namespace: DPBO
id: DPBO:1000227
comment: Suggested by Andrea Schrader | 0000-0002-3879-7057

biolistic transformation
type: Class
definition: A method for physical delivery of DNA (likely also RNA) into cells. Gold or tungsten particles are coated with DNA and shot with a gene gun / particle gun on tissue like leaves, seedlings, callus or other types of tissue and cells. Often, in plant sciences, this method is used as a transient transformation method in protein or protein-protein interaction localization studies using binary vectors. Co-transformation of multiple vectors is possible.
has_exact_synonym: particle bombardment
has_obo_namespace: DPBO
id: DPBO:1000228
comment: Suggested by Andrea Schrader | 0000-0002-3879-7057

bioimaging protocol
type: Class
definition: A protocol describing the method of a bioimaging technique. Bioimaging is a biological imaging method causing as minimal interference to living processes as possible or getting a 3-D structure from the outside without physical interference e.g. of cells, tissues or other living matter. Usually, the method is non-invasive but also fixed biological material is covered by a wider definition. (adapted from https://cab.ku.dk/what_is_bioimaging/)
has_obo_namespace: DPBO
id: DPBO:1000229
comment: Suggested by Andrea Schrader | 0000-0002-3879-7057

transformation protocol
type: Class
definition: A protocol describing a transformation method of cell, tissues or organisms.
has_obo_namespace: DPBO
id: DPBO:1000230
comment: Suggested by Andrea Schrader | 0000-0002-3879-7057

Zeiss Axio Observer Z1
type: Class
subclass of: microscope
definition: Inverted fluorescence microscope
created by: suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074
has_obo_namespace: DPBO
id: DPBO:1000231
comment: https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research.html

Zeiss Imager M1
type: Class
subclass of: microscope
definition: Upright fluorescence microscope
created by: suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074
has_obo_namespace: DPBO
id: DPBO:1000232
comment: https://microscopy.ucsf.edu/instruments/zeiss-axioimager-m1, https://profcontrol.de/Zeiss-Axio-Imager-M1m-Fluorescence-DIC-Microscope-Fluoreszenz-Mikroskop

MG-RAST accession number field
type: Class
definition: A data field which describes the MG-RAST identifier linking raw read data, methodological metadata and quality control metrics submitted to the MG-RAST metagenomics analysis server.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000233
comment: https://www.mg-rast.org/mgmain.html

assembly software
type: Class
definition: Tool/Software used for assembly.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000234
comment: https://genomicsstandardsconsortium.github.io/mixs/0000058/

assembly parameters
type: Class
definition: Parameters used for assembly.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000235
comment: https://genomicsstandardsconsortium.github.io/mixs/0000058/

MISAG/MIMAG assembly quality
type: Class
definition: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000236
comment: https://genomicsstandardsconsortium.github.io/mixs/0000056/

binning software
type: Class
definition: Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000237
comment: https://genomicsstandardsconsortium.github.io/mixs/0000078/

binning parameters
type: Class
definition: The parameters that have been applied during the extraction of genomes from metagenomic datasets.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000238
comment: https://genomicsstandardsconsortium.github.io/mixs/0000077/

taxonomic identity marker
type: Class
definition: The phylogenetic marker(s) used to assign an organism name to the SAG or MAG.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000239
comment: https://genomicsstandardsconsortium.github.io/mixs/0000053/

completeness software
type: Class
definition: Tools used for completion estimate, i.e. checkm, anvi'o, busco.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000240
comment: https://genomicsstandardsconsortium.github.io/mixs/0000070/

completeness score
type: Class
definition: Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores.
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000241
comment: https://genomicsstandardsconsortium.github.io/mixs/0000069/

contamination score
type: Class
definition: The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases
created by: Angela Kranz | ORCID: 0000-0002-8000-0400
has_obo_namespace: DPBO
id: DPBO:1000242
comment: https://genomicsstandardsconsortium.github.io/mixs/0000072/

Soil Moisture Percentage
type: Class
definition: wetness caused by water
has_obo_namespace: DPBO
id: ECSO:00000517

NMR
type: Class
definition: An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.
has_broad_synonym: Spectroscopy
has_exact_synonym: NMR spectroscopy
has_exact_synonym: Nuclear magnetic resonance spectroscopy
has_narrow_synonym: HOESY
has_narrow_synonym: Heteronuclear Overhauser Effect Spectroscopy
has_narrow_synonym: NOESY
has_narrow_synonym: Nuclear Overhauser Effect Spectroscopy
has_narrow_synonym: ROESY
has_narrow_synonym: Rotational Frame Nuclear Overhauser Effect Spectroscopy
has_obo_namespace: DPBO
id: EDAM:0593

FASTQ
type: Class
subclass of: raw data file format
definition: FASTQ short read format ignoring quality scores.
has_obo_namespace: DPBO
id: EDAM:1930

ecotype
type: Class
subclass of: subspecific taxonomic rank
definition: A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
has_obo_namespace: DPBO
id: EFO:0000434

extraction protocol
type: Class
subclass of: sample processing protocol
has_obo_namespace: DPBO
id: EFO:0000490

light
type: Class
has_obo_namespace: DPBO
id: EFO:0000568

ChIP-seq
type: Class
subclass of: library strategy
definition: ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins.
has_obo_namespace: DPBO
id: EFO:0002692

experimental process
type: Class
definition: A process performed as part of an experiment or wider study, i.e. intentionally designed.
has_obo_namespace: DPBO
id: EFO:0002694

MRE-seq
type: Class
subclass of: library strategy
definition: An assay in which DNA us the input molecule derived from cleavage of DNA by use of methylation sensitive restriction enzymes to fragment DNA at methylation sites before sequencing
has_exact_synonym: Methylation-Sensitive Restriction Enzyme sequencing
has_obo_namespace: DPBO
id: EFO:0003748

MeDIP-seq
type: Class
subclass of: library strategy
definition: An assay in which DNA is the input molecule derived from an antibody based selection process using antibodies targeting methylated DNA, which is then sequenced using high throughput sequencing technology.
has_exact_synonym: Methylated DNA Immunoprecipitation sequencing
has_obo_namespace: DPBO
id: EFO:0003749

MBD-seq
type: Class
subclass of: library strategy
definition: An assay in which DNA is the input molecule derived from a selection process using methyl binding domain protein to enrich for methylated fractions of DNA, then sequenced using high throughput sequencing.
has_exact_synonym: methyl binding domain sequencing
has_obo_namespace: DPBO
id: EFO:0003750

MNase-seq
type: Class
subclass of: library strategy
definition: An assay in which DNA is the input molecule derived from a micrococcal nuclease digestion followed by high throughput sequencing, A method that distinguishes nucleosome positioning based on the ability of nucleosomes to protect associated DNA from digestion by micrococcal nuclease. Sequenced fragments reveal nucleosome location information about the input DNA.
has_obo_namespace: DPBO
id: EFO:0003751

Bisulfite-seq
type: Class
subclass of: library strategy
definition: An assay in which DNA is the input molecule derived from a bisulphite treatment of DNA to convert cytosine residues to uracil to determine methylation status.
has_obo_namespace: DPBO
id: EFO:0003753

growth protocol
type: Class
subclass of: protocol type
has_obo_namespace: DPBO
id: EFO:0003789

treatment protocol
type: Class
subclass of: protocol type
has_obo_namespace: DPBO
id: EFO:0003969

Illumina Genome Analyzer IIx
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0004202

Illumina HiSeq 2000
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina HiSeq 2000 is a sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0004203

Illumina MiSeq
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina MiSeq is a high-throughput sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions and 16S metagenomic sequencing.
has_obo_namespace: DPBO
id: EFO:0004205

454 GS 20 sequencer
type: Class
subclass of: next generation sequencing instrument model
definition: The 454 GS 20 is a GS20 high-throughput sequencing machine developed by 454 Life Sciences.
has_obo_namespace: DPBO
id: EFO:0004206

FAIRE-seq
type: Class
subclass of: library strategy
definition: FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) is an assay used for determining the sequences of DNA regions associated with regulatory activity. This is enabled by the isolation of nucleosome-depleted DNA from total genomic dna to access actively transcribed dna.
has_obo_namespace: DPBO
id: EFO:0004428

454 GS sequencer
type: Class
subclass of: next generation sequencing instrument model
definition: The 454 GS is a GS high-throughput sequencing machine developed by 454 Life Sciences.
has_obo_namespace: DPBO
id: EFO:0004431

454 GS FLX sequencer
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: EFO:0004432

454 GS FLX Titanium sequencer
type: Class
subclass of: next generation sequencing instrument model
definition: The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences.
has_obo_namespace: DPBO
id: EFO:0004433

454 GS Junior sequencer
type: Class
subclass of: next generation sequencing instrument model
definition: The 454 GS Junior is a GS high-throughput sequencing machine developed by 454 Life Sciences.
has_obo_namespace: DPBO
id: EFO:0004434

AB SOLiD PI System
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: EFO:0004437

AB SOLiD 4 System
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: EFO:0004438

AB SOLiD System 3.0
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: EFO:0004439

AB SOLiD 4hq System
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: EFO:0004441

AB SOLiD System 2.0
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: EFO:0004442

total RNA
type: Class
subclass of: bio entity
definition: An RNA extract that is the output of an extraction process in which total RNA from either whole cells or from specific cellular compartment(s)/organelle(s) are isolated from a specimen.
has_obo_namespace: DPBO
id: EFO:0004964

carbohydrate measurement
type: Class
definition: The quantification of some carbohydrate, typically obtained from an individual with the intention of using the measurement in some diagnostic process.
has_obo_namespace: DPBO
id: EFO:0004998

strain
type: Class
definition: A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
has_obo_namespace: DPBO
id: EFO:0005135

cultivar
type: Class
subclass of: subspecific taxonomic rank
definition: A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species.
has_obo_namespace: DPBO
id: EFO:0005136

RIP-seq
type: Class
subclass of: library strategy
definition: A method used for finding which RNA species interact with a particular RNA-binding protein. It involves immunoprecipitation with antibodies for the protein and then isolation of the RNAs associated with the protein. Unlike CLIP-seq, no cross-linking of RNAs and proteins is carried out prior to immunoprecipitation.
has_obo_namespace: DPBO
id: EFO:0005310

sample collection protocol
type: Class
subclass of: protocol type
has_obo_namespace: DPBO
id: EFO:0005518

ATAC-seq
type: Class
subclass of: library strategy
definition: Assay for transposase-accessible chromatin using sequencing (ATAC-seq), is a method based on direct in vitro transposition of sequencing adaptors into native chromatin, and is a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol.
definition citation: http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html
has_obo_namespace: DPBO
id: EFO:0007045

Hi-C
type: Class
subclass of: library strategy
definition: Hi-C is a method for analysing 3-dimensional organisation and interaction of chromatin, belonging to the class of techniques collectively called "Chromosome Conformation Capture", in which chromatin is crosslinked, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. Together with 5C, Hi-C does not limit to the study to a specific locus in the genome, and can be used to study chromatin interaction across the genome. To achieve high-throughput, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. Mapping the sequenced reads back to genome will reveal the origin of the fragments involved in the ligation events.
has_obo_namespace: DPBO
id: EFO:0007693

Illumina HiSeq 4000
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0008563

Illumina HiSeq 3000
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0008564

Illumina HiSeq 2500
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina HiSeq 2500 is a sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0008565

Illumina NextSeq 550
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina NextSeq 550 is a benchtop high-throughput sequencing machine developed by Illumina. Its primary applications include exome sequencing, targeted gene sequencing (amplicon, gene panel), whole-transcriptome sequencing and cytogenomic arrays.
has_obo_namespace: DPBO
id: EFO:0008566

PacBio RS II
type: Class
subclass of: next generation sequencing instrument model
definition: The PacBio RS II is a high-throughput sequencing machine developed by PacBio. Its primary applications are whole genome sequencing of smaller organisms and targeted sequencing of DNA and RNA.
has_obo_namespace: DPBO
id: EFO:0008631

ONT MinION
type: Class
subclass of: next generation sequencing instrument model
definition: The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies.
has_obo_namespace: DPBO
id: EFO:0008632

Illumina iSeq 100
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing.
has_obo_namespace: DPBO
id: EFO:0008635

Illumina MiniSeq
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0008636

Illumina NovaSeq 6000
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0008637

Chia-PET
type: Class
subclass of: library strategy
definition: ChIA-PET (chromatin interaction analysis by paired-end tag sequencing) is a type of chromosome conformation capture assay that uses chromatin immunoprecipitation to enrich for protein-specific chromatin complexes after digestion, followed by nuclear proximity ligation and high-throughput paired-end-tag sequencing.
database_cross_reference: PMID:20181287
has_exact_synonym: chromatin interaction analysis by paired-end tag sequencing
has_obo_namespace: DPBO
id: EFO:0008684

RNA-Seq
type: Class
subclass of: library strategy
definition: RNA-seq is a method that involves purifying RNA and making cDNA, followed by high-throughput sequencing.
IAO_0000117: Dani Welter
database_cross_reference: PMID:18516045
has_obo_namespace: DPBO
id: EFO:0008896

ssRNA-seq
type: Class
subclass of: library strategy
definition: Strand-specific RNA-seq (ssRNA-seq)
IAO_0000117: Dani Welter
database_cross_reference: PMID:19609351
has_obo_namespace: DPBO
id: EFO:0008950

TN-Seq
type: Class
subclass of: library strategy
definition: Transposon sequencing (TN-Seq)
IAO_0000117: Dani Welter
database_cross_reference: PMID:23712350
has_obo_namespace: DPBO
id: EFO:0008973

Illumina NextSeq 500
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0009173

RNA extraction protocol
type: Class
subclass of: extraction protocol
has_obo_namespace: DPBO
id: EFO:0010959

Illumina HiSeq 1500
type: Class
subclass of: next generation sequencing instrument model
definition: The Illumina HiSeq 1500 is a sequencing machine developed by Illumina.
has_obo_namespace: DPBO
id: EFO:0011027

protein extraction protocol
type: Class
subclass of: extraction protocol
has_obo_namespace: DPBO
id: EFO:0022383

DNA extraction protocol
type: Class
subclass of: extraction protocol
has_obo_namespace: DPBO
id: EFO:0022384

nuclear RNA
type: Class
subclass of: bio entity
has_obo_namespace: DPBO
id: EFO:0030052

geyser
type: Class
subclass of: environment (feature)
definition: A hot spring that erupts periodically, ejecting a column of hot water and steam into the air.
has_obo_namespace: DPBO
id: ENVO:00000050

cold seep
type: Class
subclass of: environment (feature)
definition: A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor.
has_obo_namespace: DPBO
id: ENVO:01000263

tropical mangrove
type: Class
subclass of: environment (feature)
definition: This class corresponds to the 'Tropical Mixed needleleaf / broadleaf forest' category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the 'tropical mixed needleleaf forest' class can be made. The relationship between this 'forest' class and the mangrove swamp must be clarified.
has_obo_namespace: DPBO
id: ENVO:01000403

image processing technique
type: Class
definition: Any form of signal processing for which the input is an image, such as a photograph or video frame; the output of image processing may be either an image or a set of characteristics or parameters related to the image.
has_obo_namespace: DPBO
id: ERO:0001788

plant material
type: Class
definition: Anatomical or other piece(s) or substance derived from one or more plants.
has_obo_namespace: DPBO
id: FOODON:00004331

read length
type: Class
definition: Numbers of base pairs per read
has_obo_namespace: DPBO
id: GENEPIO:0000076

adapter sequence
type: Class
definition: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters.
has_obo_namespace: DPBO
id: GENEPIO:0000083

library preparation kit
type: Class
definition: Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.
has_obo_namespace: DPBO
id: GENEPIO:0000085

library preparation kit version
type: Class
definition: The version identifier of a packaged kit tailored for specific sequencing workflows.
has_obo_namespace: DPBO
id: GENEPIO:0000149

SRA accession field
type: Class
IAO_0000112: SRR11177792
IAO_0000114: IAO_0000428
definition: A data field which describes the Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the International Nucleotide Sequence Database Collaboration (INSDC).
IAO_0000118: SRA accession
IAO_0000118: SRA_accession
contributor: https://orcid.org/0000-0002-1107-9135
contributor: https://orcid.org/0000-0002-8844-9165
contributor: https://orcid.org/0000-0002-9578-0788
date: 2021-04-24T00:42:14Z
has_exact_synonym: SRA accession slot
has_exact_synonym: Sequence Read Archive accession field
has_exact_synonym: Sequence Read Archive accession slot
has_obo_namespace: DPBO
id: GENEPIO:0001142
comment: DDBJ = DNA DataBank of Japan Example Guidance: Store the accession assigned to the submitted .run.. NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR.

sample collected by
type: Class
definition: The name of the agency that collected the original sample.
database_cross_reference: NCIT:C45262
has_obo_namespace: DPBO
id: GENEPIO:0001153

sample collection date
type: Class
definition: The date on which the sample was collected
database_cross_reference: NCIT:C81286
has_obo_namespace: DPBO
id: GENEPIO:0001174

laboratory sequencing datum
type: Class
has_obo_namespace: DPBO
id: GENEPIO:0001681

Complete Genomics platform
type: Class
subclass of: next generation sequencing instrument model
definition: Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: 'Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010).'
has_obo_namespace: DPBO
id: GENEPIO:0001924

SOLiD 4hq System
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: GENEPIO:0001928

SOLiD PI System
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: GENEPIO:0001931

SOLiD System 2.0
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: GENEPIO:0001932

SOLiD System 3.0
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: GENEPIO:0001933

454 Genome Sequencer FLX Titanium
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: GENEPIO:0001936

454 Genome Sequencer Junior
type: Class
subclass of: next generation sequencing instrument model
has_obo_namespace: DPBO
id: GENEPIO:0001938

library selection
type: Class
subclass of: laboratory sequencing datum
GENEPIO_0000005: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/
definition: Whether any method was used to select for or against, enrich, or screen the material being sequenced.
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: LIBRARY_SELECTION
has_obo_namespace: DPBO
id: GENEPIO:0001940

5-methylcytidine antibody method
type: Class
subclass of: library selection
definition: Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
database_cross_reference: NCBI SRA: 5-methylcytidine antibody
has_obo_namespace: DPBO
id: GENEPIO:0001941

CAGE method
type: Class
subclass of: library selection
definition: Cap-analysis gene expression.
database_cross_reference: NCBI SRA: CAGE
has_obo_namespace: DPBO
id: GENEPIO:0001942

CF-H method
type: Class
subclass of: library selection
definition: Cot-filtered highly repetitive genomic DNA
database_cross_reference: NCBI SRA: CF-H
has_obo_namespace: DPBO
id: GENEPIO:0001943

CF-M method
type: Class
subclass of: library selection
definition: Cot-filtered moderately repetitive genomic DNA
database_cross_reference: NCBI SRA: CF-M
has_obo_namespace: DPBO
id: GENEPIO:0001944

CF-S method
type: Class
subclass of: library selection
definition: Cot-filtered single/low-copy genomic DNA
database_cross_reference: NCBI SRA: CF-S
has_obo_namespace: DPBO
id: GENEPIO:0001945

CF-T method
type: Class
subclass of: library selection
definition: Cot-filtered theoretical single-copy genomic DNA
database_cross_reference: NCBI SRA: CF-T
has_obo_namespace: DPBO
id: GENEPIO:0001946

ChIP method
type: Class
subclass of: library selection
definition: Chromatin immunoprecipitation
database_cross_reference: NCBI SRA: ChIP
has_obo_namespace: DPBO
id: GENEPIO:0001947

DNAse method
type: Class
subclass of: library selection
definition: Deoxyribonuclease (MNase) digestion
database_cross_reference: NCBI SRA: DNAse
has_obo_namespace: DPBO
id: GENEPIO:0001948

HMPR method
type: Class
subclass of: library selection
definition: Hypo-methylated partial restriction digest
database_cross_reference: NCBI SRA: HMPR
has_obo_namespace: DPBO
id: GENEPIO:0001949

Hybrid Selection method
type: Class
subclass of: library selection
definition: Selection by hybridization in array or solution.
database_cross_reference: NCBI SRA: Hybrid Selection
has_obo_namespace: DPBO
id: GENEPIO:0001950

MBD2 protein methyl-CpG binding domain method
type: Class
subclass of: library selection
definition: Enrichment by methyl-CpG binding domain.
database_cross_reference: NCBI SRA: MBD2 protein methyl-CpG binding domain
has_obo_namespace: DPBO
id: GENEPIO:0001951

MF method
type: Class
subclass of: library selection
definition: Methyl Filtrated
database_cross_reference: NCBI SRA: MF
has_obo_namespace: DPBO
id: GENEPIO:0001952

MNase method
type: Class
subclass of: library selection
definition: Micrococcal Nuclease (MNase) digestion
database_cross_reference: NCBI SRA: MNase
has_obo_namespace: DPBO
id: GENEPIO:0001953

MSLL method
type: Class
subclass of: library selection
definition: Methylation Spanning Linking Library
database_cross_reference: NCBI SRA: MSLL
has_obo_namespace: DPBO
id: GENEPIO:0001954

PCR method
type: Class
subclass of: library selection
definition: Source material was selected by designed primers.
database_cross_reference: NCBI SRA: PCR
has_obo_namespace: DPBO
id: GENEPIO:0001955

RACE method
type: Class
subclass of: library selection
definition: Rapid Amplification of cDNA Ends.
database_cross_reference: NCBI SRA: RACE
has_obo_namespace: DPBO
id: GENEPIO:0001956

RANDOM PCR method
type: Class
subclass of: library selection
definition: Source material was selected by randomly generated primers.
database_cross_reference: NCBI SRA: RANDOM PCR
has_obo_namespace: DPBO
id: GENEPIO:0001957

RANDOM method
type: Class
subclass of: library selection
definition: Random selection by shearing or other method.
database_cross_reference: NCBI SRA: RANDOM
has_obo_namespace: DPBO
id: GENEPIO:0001958

RT-PCR method
type: Class
subclass of: library selection
definition: Source material was selected by reverse transcription PCR
database_cross_reference: NCBI SRA: RT-PCR
has_obo_namespace: DPBO
id: GENEPIO:0001959

Reduced Representation method
type: Class
subclass of: library selection
definition: Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.
database_cross_reference: NCBI SRA: Reduced Representation
has_obo_namespace: DPBO
id: GENEPIO:0001960

Restriction Digest method
type: Class
subclass of: library selection
definition: DNA fractionation using restriction enzymes.
database_cross_reference: NCBI SRA: Restriction Digest
has_obo_namespace: DPBO
id: GENEPIO:0001961

cDNA method
type: Class
subclass of: library selection
definition: PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA.
database_cross_reference: NCBI SRA: cDNA
has_obo_namespace: DPBO
id: GENEPIO:0001962

size fractionation method
type: Class
subclass of: library selection
definition: Physical selection of size appropriate targets.
database_cross_reference: NCBI SRA: size fractionation
has_obo_namespace: DPBO
id: GENEPIO:0001963

other library method
type: Class
subclass of: library selection
definition: Other library enrichment, screening, or selection process.
database_cross_reference: NCBI SRA: other
has_obo_namespace: DPBO
id: GENEPIO:0001964

library source
type: Class
subclass of: laboratory sequencing datum
definition: The library source specifies the type of source material that is being sequenced.
has_obo_namespace: DPBO
id: GENEPIO:0001965

genomic source
type: Class
subclass of: library source
definition: Genomic DNA (includes PCR products from genomic DNA).
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: GENOMIC
has_obo_namespace: DPBO
id: GENEPIO:0001966

metagenomic source
type: Class
subclass of: library source
definition: Mixed material from metagenome.
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: METAGENOMIC
has_obo_namespace: DPBO
id: GENEPIO:0001967

metatranscriptomic source
type: Class
subclass of: library source
definition: Transcription products from community targets
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: METATRANSCRIPTOMIC
has_obo_namespace: DPBO
id: GENEPIO:0001968

other library source
type: Class
subclass of: library source
definition: Other, unspecified, or unknown library source material.
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: OTHER
has_obo_namespace: DPBO
id: GENEPIO:0001969

synthetic source
type: Class
subclass of: library source
definition: Synthetic DNA.
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: SYNTHETIC
has_obo_namespace: DPBO
id: GENEPIO:0001970

transcriptomic source
type: Class
subclass of: library source
definition: Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: TRANSCRIPTOMIC
has_obo_namespace: DPBO
id: GENEPIO:0001971

viral RNA source
type: Class
subclass of: library source
definition: Viral RNA.
IAO_0000117: Damion Dooley
database_cross_reference: NCBI SRA: VIRAL RNA
has_obo_namespace: DPBO
id: GENEPIO:0001972

library strategy
type: Class
subclass of: laboratory sequencing datum
definition: Sequencing technique intended for this library.
IAO_0000117: Damion Dooley
IAO_0000119: https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/
has_obo_namespace: DPBO
id: GENEPIO:0001973

Illumina HiScanSQ
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an 'SQ Module' to support microfluidics.
has_obo_namespace: DPBO
id: GENEPIO:0100109

Illumina HiSeq X Five
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.
has_obo_namespace: DPBO
id: GENEPIO:0100112

Illumina HiSeq X Ten
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
has_obo_namespace: DPBO
id: GENEPIO:0100113

Illumina HiSeq 1500
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day.
has_obo_namespace: DPBO
id: GENEPIO:0100115

Illumina iSeq 100
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.
has_obo_namespace: DPBO
id: GENEPIO:0100121

Illumina NovaSeq 6000
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.
has_obo_namespace: DPBO
id: GENEPIO:0100123

Illumina MiniSeq
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.
has_obo_namespace: DPBO
id: GENEPIO:0100124

Illumina NextSeq 550
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.
has_obo_namespace: DPBO
id: GENEPIO:0100128

PacBio RS
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes 'SMRT Cells' for single-molecule real-time sequencing. The RS was the first model made by the company.
has_obo_namespace: DPBO
id: GENEPIO:0100131

PacBio Sequel
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation
has_obo_namespace: DPBO
id: GENEPIO:0100133

PacBio Sequel II
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation.
has_obo_namespace: DPBO
id: GENEPIO:0100134

Ion Torrent PGM
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.
has_obo_namespace: DPBO
id: GENEPIO:0100136

Ion Torrent Proton
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.
has_obo_namespace: DPBO
id: GENEPIO:0100137

Ion Torrent S5 XL
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.
has_obo_namespace: DPBO
id: GENEPIO:0100138

Ion Torrent S5
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.
has_obo_namespace: DPBO
id: GENEPIO:0100139

Oxford Nanopore GridION
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual
has_obo_namespace: DPBO
id: GENEPIO:0100141

Oxford Nanopore MinION
type: Class
subclass of: next generation sequencing instrument model
definition: A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.
has_obo_namespace: DPBO
id: GENEPIO:0100142

Oxford Nanopore PromethION
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.
has_obo_namespace: DPBO
id: GENEPIO:0100143

BGI Genomics BGISEQ-500
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and 'DNA Nanoballs'.
has_obo_namespace: DPBO
id: GENEPIO:0100145

MGI DNBSEQ-T7
type: Class
subclass of: next generation sequencing instrument model
definition: A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day.
has_obo_namespace: DPBO
id: GENEPIO:0100147

MGI DNBSEQ-G400
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run.
has_obo_namespace: DPBO
id: GENEPIO:0100148

MGI DNBSEQ-G50
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.
has_obo_namespace: DPBO
id: GENEPIO:0100150

gene symbol
type: Class
definition: A sequence data which is the short name of a gene typically derived from the gene name.
has_obo_namespace: DPBO
id: GENEPIO:0100598

geographical entity
type: Class
has_obo_namespace: DPBO
id: GEO:000000370

geographical region
type: Class
subclass of: geographical entity
definition: A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface.
IAO_0000117: François Modave
IAO_0000117: Mathias Brochhausen
IAO_0000117: Matt Diller
IAO_0000117: William R. Hogan
has_obo_namespace: DPBO
id: GEO:000000372

overexpression mutant
type: Class
subclass of: mutant
definition: A mutant in which a gene ore genes are expressed at higher levels than the wild type.
has_obo_namespace: DPBO
id: MCO:0000041

gene variant mutant
type: Class
subclass of: mutant
definition: A mutant genotype in which one or more genes can have modifications (subtitutions, indels, partial truncations, etc), but they conserve functionality.
has_obo_namespace: DPBO
id: MCO:0000042

knockout mutant
type: Class
subclass of: mutant
definition: A mutant in which the function of a target gene has been disrupted within its normal biological context. Utilized to examine the involvement of a gene in a complex biological process.
has_obo_namespace: DPBO
id: MCO:0000051

plasmid mutant
type: Class
subclass of: mutant
definition: a mutant in which a foreign DNA sequence is introduced to cell in an extrachromosomal unit of replication.
has_obo_namespace: DPBO
id: MCO:0000052

OD600
type: Class
subclass of: optical density
definition: An optical density that specifies the amount of light of 600 nm of wavelenght the bearer is able to transmit.
has_obo_namespace: DPBO
id: MCO:0000059

optical density
type: Class
definition: A physical quality that inheres in a bearer by virtue of the amount of light that the bearer of the quality is able to transmit.
has_obo_namespace: DPBO
id: MCO:0000077

nutrient availability stress treatment
type: Class
subclass of: treatment
has_obo_namespace: DPBO
id: MCO:0000173

nutrient depletion treatment
type: Class
subclass of: nutrient availability stress treatment
has_obo_namespace: DPBO
id: MCO:0000174

iron depletion
type: Class
subclass of: nutrient availability stress treatment
has_obo_namespace: DPBO
id: MCO:0000177

carbon starvation
type: Class
subclass of: nutrient availability stress treatment
has_obo_namespace: DPBO
id: MCO:0000178

nitrogen starvation
type: Class
subclass of: nutrient availability stress treatment
has_obo_namespace: DPBO
id: MCO:0000179

phosphate starvation
type: Class
subclass of: nutrient availability stress treatment
has_obo_namespace: DPBO
id: MCO:0000180

genotype
type: Class
definition: A biological quality that inheres in specific organisms and that describes its total genetic content
has_obo_namespace: DPBO
id: MCO:0000851

treatment
type: Class
definition: A process in which the act is intended to modify or alter some other material entity.
has_obo_namespace: DPBO
id: MCO:0000866

Biological material preprocessing
type: Class
has_obo_namespace: DPBO
id: MIAPPE:0049

Growth facility
type: Class
has_obo_namespace: DPBO
id: MIAPPE:0095

gene product
type: Class
definition: Reference of a protein object pointing to its genomic or nucleic acid sequence.
has_obo_namespace: DPBO
id: MI:0251

tag
type: Class
definition: Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
has_obo_namespace: DPBO
id: MI:0507

Axiom
annotated source: tag
annotated property: definition
annotated target: Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
database_cross_reference: PMID:14755292

Healthy
type: Class
subclass of: plant health state
definition: Having no significant health-related issues.
has_obo_namespace: DPBO
id: NCIT:C115935

Cover Slip
type: Class
has_obo_namespace: DPBO
id: NCIT:C126370

BGISEQ-500 Sequencing
type: Class
subclass of: next generation sequencing instrument model
definition: A proprietary next-generation DNA sequencing system from BGI Genomics using combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB) technology. The cPAS chemistry works by incorporating a fluorescent probe to a DNA anchor on the DNB, followed by high-resolution digital imaging.
has_obo_namespace: DPBO
id: NCIT:C146812

Complete Genomics Sequencing
type: Class
subclass of: next generation sequencing instrument model
definition: A next-generation DNA sequencing service offered by Complete Genomics. Unamplified human genomic DNA is sheared into 500bp fragments and then amplified to create DNA nano-balls (DNBs). The DNBs are arrayed on a substrate and their sequence is determined by Combinatorial Probe-Anchor Ligation (cPAL) sequencing.
has_obo_namespace: DPBO
id: NCIT:C146815

Illumina Sequencing
type: Class
subclass of: sequencing method
definition: A proprietary next-generation DNA sequencing system from Solexa that uses reversible terminator nucleotides. The genomic DNA to be sequenced is fragmented and ligated to adapter molecules on both ends to construct an Illumina-specific adapter library. PCR amplification of the DNA fragments is then performed using the adapter sequence as primer. Sequencing is carried out by repeated cycles of adding reversible fluorescent-labelled nucleotide and incorporation of the nucleotides to the complementary strand. The fluorescence of the incorporated nucleotides is detected.
has_obo_namespace: DPBO
id: NCIT:C146817

Nanopore Sequencing
type: Class
subclass of: sequencing method
definition: A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis.
has_obo_namespace: DPBO
id: NCIT:C146818

Environmental DNA
type: Class
definition: DNA obtained directly from environmental samples (soil, sediment, water, etc.) without any obvious signs of biological source material. It originates from cellular material shed by organisms (via skin, excrement, etc.) into aquatic or terrestrial environments.
has_obo_namespace: DPBO
id: NCIT:C169106

Diseased
type: Class
subclass of: plant health state
definition: An indication that an anatomic structure has detectable aberrations.
has_obo_namespace: DPBO
id: NCIT:C175249

Imaging Software Name
type: Class
definition: The name of the software program capture and/or process imaging data.
has_obo_namespace: DPBO
id: NCIT:C175898

Axiom
annotated source: Imaging Software Name
annotated property: definition
annotated target: The name of the software program capture and/or process imaging data.
P378: NCI

Objective Lens
type: Class
has_obo_namespace: DPBO
id: NCIT:C181919

mutant
type: Class
subclass of: genotype
definition: An altered form of an individual, organism, population, or genetic character that differs from the corresponding wild type due to one or more alterations (mutations).
has_obo_namespace: DPBO
id: NCIT:C25360

Species
type: Class
database_cross_reference: MIAPPE:0043
database_cross_reference: NCBITaxon:species
has_obo_namespace: DPBO
id: NCIT:C45293

No
type: Class
subclass of: 5' partial CDS
subclass of: 3' partial CDS
subclass of: 5' partial promoter
subclass of: 3' partial promoter
subclass of: Environmental DNA
subclass of: bidirectional_promoter
definition: The non-affirmative response to a question.
has_obo_namespace: DPBO
id: NCIT:C49487

Yes
type: Class
subclass of: 5' partial CDS
subclass of: 3' partial CDS
subclass of: 5' partial promoter
subclass of: 3' partial promoter
subclass of: Environmental DNA
subclass of: bidirectional_promoter
definition: The affirmative response to a question.
has_obo_namespace: DPBO
id: NCIT:C49488

wild type
type: Class
subclass of: genotype
definition: The naturally-occurring, normal, non-mutated version of a gene or genome.
has_obo_namespace: DPBO
id: NCIT:C62195

Variety
type: Class
subclass of: subspecific taxonomic rank
definition: In botanical nomenclature, a rank below subspecies but above forma.
has_obo_namespace: DPBO
id: NCIT:C62709

Cytoplasmic RNA
type: Class
subclass of: bio entity
definition: RNA present in the cytoplasm. It is involved in the protein export process from the cells.
has_obo_namespace: DPBO
id: NCIT:C84512

sample pH
type: Class
subclass of: pH
has_obo_namespace: DPBO
id: NMR:1000019

NMR acquisition parameter
type: Class
definition: Parameters used in the NMR spectrometry acquisition.
has_obo_namespace: DPBO
id: NMR:1001954

pH
type: Class
has_obo_namespace: DPBO
id: NMR:1002011

field strength
type: Class
definition: The intensity of an electric, magnetic, or other field.
has_obo_namespace: DPBO
id: NMR:1400027

number of scans
type: Class
subclass of: NMR acquisition parameter
definition: The number of repeat scans performed and summed to create the data set for an NMR sample.
has_obo_namespace: DPBO
id: NMR:1400087

magnetic field strength
type: Class
subclass of: field strength
has_obo_namespace: DPBO
id: NMR:1400253
comment: defneed

culture medium
type: Class
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
has_obo_namespace: DPBO
id: OBI:0000079

material processing
type: Class
definition: A planned process which results in physical changes in a specified input material
has_obo_namespace: DPBO
id: OBI:0000094

454 Genome Sequencer FLX
type: Class
subclass of: next generation sequencing instrument model
definition: Is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.
has_obo_namespace: DPBO
id: OBI:0000702

HeliScope Single Molecule Sequencer
type: Class
subclass of: next generation sequencing instrument model
definition: Is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
has_obo_namespace: DPBO
id: OBI:0000717

container
type: Class
has_obo_namespace: DPBO
id: OBI:0000967

digital camera
type: Class
definition: An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
has_obo_namespace: DPBO
id: OBI:0001048

microplate reader
type: Class
definition: A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
has_obo_namespace: DPBO
id: OBI:0001058

Genome Analyzer IIx
type: Class
subclass of: next generation sequencing instrument model
definition: An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.
has_obo_namespace: DPBO
id: OBI:0002000

Illumina HiSeq 2000
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.
has_obo_namespace: DPBO
id: OBI:0002001

Illumina HiSeq 2500
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.
has_obo_namespace: DPBO
id: OBI:0002002

SOLiD 3 Plus System
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.
has_obo_namespace: DPBO
id: OBI:0002007

PacBio RS II
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.
has_obo_namespace: DPBO
id: OBI:0002012

Illumina HiSeq 1000
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.
has_obo_namespace: DPBO
id: OBI:0002022

Illumina HiSeq 3000
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
has_obo_namespace: DPBO
id: OBI:0002048

Illumina HiSeq 4000
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
has_obo_namespace: DPBO
id: OBI:0002049

Illumina HiSeq X Ten
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
has_obo_namespace: DPBO
id: OBI:0002129

Illumina NovaSeq 6000
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.
has_obo_namespace: DPBO
id: OBI:0002630

PacBio Sequel
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation
has_obo_namespace: DPBO
id: OBI:0002632

PacBio Sequel II
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation.
has_obo_namespace: DPBO
id: OBI:0002633

Oxford Nanopore MinION
type: Class
subclass of: next generation sequencing instrument model
definition: A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.
has_obo_namespace: DPBO
id: OBI:0002750

Oxford Nanopore PromethION
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.
has_obo_namespace: DPBO
id: OBI:0002752

Illumina MiniSeq
type: Class
subclass of: next generation sequencing instrument model
definition: A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run.
has_obo_namespace: DPBO
id: OBI:0003114

Illumina HiSeq 1500
type: Class
subclass of: next generation sequencing instrument model
definition: A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option.
has_obo_namespace: DPBO
id: OBI:0003386

organism
type: Class
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
database_cross_reference: MIAPPE:0041
database_cross_reference: NCIT:C14250
database_cross_reference: NFDI4PSO:0000030
has_obo_namespace: DPBO
id: OBI:0100026

microscope
type: Class
definition: A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
has_obo_namespace: DPBO
id: OBI:0400169

microscope slide
type: Class
definition: A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
has_obo_namespace: DPBO
id: OBI:0400170

obsolete_Objective
type: Class
subclass of: Obsolete Class
has_obo_namespace: DPBO
id: OME:Objective
comment: Class "Objective" is microscopes' objective lens. 19.02.2024: term has been deprecated, please use REPR:Objective
deprecated: true

volume
type: Class
has_obo_namespace: DPBO
id: PATO:0000918

contamination
type: Class
definition: The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity.
has_obo_namespace: DPBO
id: PATO:0015031

Axiom
annotated source: contamination
annotated property: definition
annotated target: The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity.
database_cross_reference: https://en.wikipedia.org/wiki/Contamination
database_cross_reference: https://github.com/pato-ontology/pato/issues/420

plant exposure
type: Class
subclass of: Biological material preprocessing
definition: A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (biotic plant exposurePECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357plant experimental condition) or set of conditions describing the application of an abiotic (abiotic plant exposure) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof.
has_obo_namespace: DPBO
id: PECO:0001001

fruit
type: Class
subclass of: Tissue
has_obo_namespace: DPBO
id: PO:0009001

plant organ
type: Class
subclass of: Tissue
has_obo_namespace: DPBO
id: PO:0009008

seed
type: Class
subclass of: Tissue
has_obo_namespace: DPBO
id: PO:0009010

cardinal part of multi-tissue plant structure
type: Class
subclass of: Tissue
has_obo_namespace: DPBO
id: PO:0025498

Quantification method
type: Class
created by: jg
creation date: 2011-07-22T09:15:33Z
has_obo_namespace: PRIDE
id: PRIDE:0000307
comment: Defines various quantification methods

Gel-based quantification method
type: Class
subclass of: Quantification method
created by: jg
creation date: 2011-07-22T09:16:24Z
has_obo_namespace: PRIDE
id: PRIDE:0000308
comment: Describes gel-based quantification methods

Gel-free quantification method
type: Class
subclass of: Quantification method
created by: jg
creation date: 2011-07-22T09:17:03Z
has_obo_namespace: PRIDE
id: PRIDE:0000309
comment: Describes gel-free quantification methods

Isotope labeling
type: Class
subclass of: Gel-free quantification method
created by: jg
creation date: 2011-07-22T09:17:34Z
has_obo_namespace: PRIDE
id: PRIDE:0000310
comment: Describes quantification techniques using isotope labeling

Selected Reaction Monitoring
type: Class
subclass of: Gel-free quantification method
created by: jg
creation date: 2011-07-22T09:18:39Z
has_obo_namespace: PRIDE
id: PRIDE:0000311
comment: Describes quantification techniques based on selected / multiple reaction monitoring

Label free
type: Class
subclass of: Gel-free quantification method
created by: jg
creation date: 2011-07-22T09:19:54Z
has_obo_namespace: PRIDE
id: PRIDE:0000312
comment: Describes label free quantification techniques.

iTRAQ
type: Class
subclass of: MS2 based isotope labeling
created by: jg
creation date: 2011-07-22T09:20:23Z
has_obo_namespace: PRIDE
id: PRIDE:0000313
comment: Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level

TMT
type: Class
subclass of: MS2 based isotope labeling
created by: jg
creation date: 2011-07-22T09:23:12Z
has_exact_synonym: Tandem Mass Tag
has_obo_namespace: PRIDE
id: PRIDE:0000314
comment: Tandem Mass Tag is a MS2 based isotope labeling quantification technique

SILAC
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:25:50Z
has_exact_synonym: Stable isotope labeling with amino acids in cell culture
has_obo_namespace: PRIDE
id: PRIDE:0000315
comment: Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification

MS1 based isotope labeling
type: Class
subclass of: Isotope labeling
created by: jg
creation date: 2011-07-22T09:28:05Z
has_obo_namespace: PRIDE
id: PRIDE:0000316
comment: Describes isotope labeling quantification techniques detectable at MS1 level.

MS2 based isotope labeling
type: Class
subclass of: Isotope labeling
created by: jg
creation date: 2011-07-22T09:29:15Z
has_obo_namespace: PRIDE
id: PRIDE:0000317
comment: Describes isotope labeling quantification techniques detectable at MS1 level.

18O
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:30:12Z
has_obo_namespace: PRIDE
id: PRIDE:0000318
comment: The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen.

ICAT
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:31:24Z
has_exact_synonym: Isotope-Coded Affinity Tags
has_obo_namespace: PRIDE
id: PRIDE:0000319
comment: Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements.

AQUA
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:32:46Z
has_obo_namespace: PRIDE
id: PRIDE:0000320
comment: AQUA is an isotope labeling based quantification technique that uses known peptides.

ICPL
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:34:37Z
has_exact_synonym: Isotope-coded protein label
has_obo_namespace: PRIDE
id: PRIDE:0000321
comment: Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses.

emPAI
type: Class
subclass of: Label free
created by: jg
creation date: 2011-07-22T09:36:57Z
has_exact_synonym: Exponentially Modified Protein Abundance Index
has_obo_namespace: PRIDE
id: PRIDE:0000322
comment: The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result.

TIC
type: Class
subclass of: Label free
created by: jg
creation date: 2011-07-22T09:38:17Z
has_exact_synonym: Total Ion Current
has_obo_namespace: PRIDE
id: PRIDE:0000323
comment: The Total Ion Current (TIC) can be measured or calculated in order to target specific ions.

MS1 intensity based label-free quantification method
type: Class
subclass of: Gel-free quantification method
created by: rw
has_obo_namespace: PRIDE
id: PRIDE:0000425

Peptide counting
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000435
comment: Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140.

Spectrum counting
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000436
comment: Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140

Protein Abundance Index - PAI
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000437
comment: Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140

Spectrum count/molecular weight
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000438
comment: Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140

Spectral Abundance Factor - SAF
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000439
comment: The spectrum count is normalized for protein length. Method reviewed in PMID 22772140

Normalized Spectral Abundance Factor - NSAF
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000440
comment: Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140

APEX - Absolute Protein Expression
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000441
comment: Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140

Experiment Type
type: Class
definition: Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method.
has_obo_namespace: DPBO
id: PRIDE:0000457

Parallel Reaction Monitoring (PRM)
type: Class
subclass of: Selected Reaction Monitoring
definition: Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis.
has_obo_namespace: PRIDE
id: PRIDE:0000463

Axiom
annotated source: Parallel Reaction Monitoring (PRM)
annotated property: definition
annotated target: Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis.
database_cross_reference: PRIDE:PRIDE

Dimethyl Labeling
type: Class
subclass of: Isotope labeling
definition: Dimethyl Labeling (DML)
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000513

Axiom
annotated source: Dimethyl Labeling
annotated property: definition
annotated target: Dimethyl Labeling (DML)
database_cross_reference: PRIDE:PRIDE

diaPASEF
type: Class
definition: Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825
created by: yperez
has_obo_namespace: DPBO
id: PRIDE:0000650

Axiom
annotated source: diaPASEF
annotated property: definition
annotated target: Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825
database_cross_reference: PRIDE:PRIDE

plant disease
type: Class
definition: A biotic plant stress caused by exposure to an environment containing a biological stress agent.
has_obo_namespace: DPBO
id: PSO:0000013

Objective
type: Class
definition: The microscope's objective lens.
has_obo_namespace: DPBO
id: REPR:Objective

Well
type: Class
definition: A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well.
has_obo_namespace: DPBO
id: REPR:Well

cover slip preparation (procedure)
type: Class
has_obo_namespace: DPBO
id: SCTID:71661000

longitude
type: Class
definition: Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point.
has_obo_namespace: DPBO
id: SIO:000318

latitude
type: Class
definition: Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane
has_obo_namespace: DPBO
id: SIO:000319

data analysis
type: Class
definition: data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making
has_obo_namespace: DPBO
id: SIO:001051

nucleic acid sequence
type: Class
definition: A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid.
has_obo_namespace: DPBO
id: SIO:010016

Microscope slide mounting medium (substance)
type: Class
has_obo_namespace: DPBO
id: SNOMED:430862008

terminator
type: Class
definition: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
has_broad_synonym: INSDC_feature:regulatory
database_cross_reference: http://en.wikipedia.org/wiki/Terminator_(genetics)
has_exact_synonym: INSDC_qualifier:terminator
has_exact_synonym: terminator sequence
has_obo_namespace: DPBO
id: SO:0000141
comment: Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.

Axiom
annotated source: terminator
annotated property: definition
annotated target: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
database_cross_reference: http://www.insdc.org/files/feature_table.html

wiki
type: Axiom
annotated source: terminator
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Terminator_(genetics)

promoter
type: Class
definition: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.
has_obo_namespace: DPBO
id: SO:0000167

coding_start
type: Class
subclass of: CDS_region
definition: The first base to be translated into protein.
has_exact_synonym: coding start
has_exact_synonym: translation initiation site
has_obo_namespace: sequence
has_related_synonym: translation start
id: SO:0000323

Axiom
annotated source: coding_start
annotated property: definition
annotated target: The first base to be translated into protein.
database_cross_reference: SO:ke

coding_end
type: Class
subclass of: CDS_region
definition: The last base to be translated into protein. It does not include the stop codon.
has_exact_synonym: coding end
has_exact_synonym: translation termination site
has_exact_synonym: translation_end
has_obo_namespace: sequence
id: SO:0000327

Axiom
annotated source: coding_end
annotated property: definition
annotated target: The last base to be translated into protein. It does not include the stop codon.
database_cross_reference: SO:ke

bidirectional_promoter
type: Class
subclass of: promoter
definition: A promoter that can allow for transcription in both directions.
has_exact_synonym: bidirectional promoter
has_obo_namespace: sequence
id: SO:0000568
comment: Definition updated in Aug 2020 by Dave Sant.

Axiom
annotated source: bidirectional_promoter
annotated property: definition
annotated target: A promoter that can allow for transcription in both directions.
database_cross_reference: PMID:21601935
database_cross_reference: SO:ke

CDS_region
type: Class
definition: A region of a CDS.
has_obo_namespace: DPBO
id: SO:0000851

Seurat
type: Class
subclass of: R package
definition: Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
database_cross_reference: DPBO:0000035
has_obo_namespace: DPBO
id: SWO:1100130

unit
type: Class
has_obo_namespace: DPBO
id: UO:0000000

acceleration unit
type: Class
subclass of: unit
definition: A unit which is a standard measure of the rate of change of velocity in either speed or direction.
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000048
in_subset: unit group slim

Axiom
annotated source: acceleration unit
annotated property: definition
annotated target: A unit which is a standard measure of the rate of change of velocity in either speed or direction.
database_cross_reference: Wikipedia:Wikipedia

ratio
type: Class
has_obo_namespace: DPBO
id: UO:0010006

Small molecule report
type: Class
has_obo_namespace: DPBO

Molecule identifier
type: Class
has_obo_namespace: DPBO

Molecule name
type: Class
has_obo_namespace: DPBO

Compound name
type: Class
subclass of: Molecule name
subclass of: Compound identifier
definition: Unique name of a chemical compound.
created in: beta12orEarlier
has_exact_synonym: Chemical name
has_obo_namespace: DPBO
in_subset: data
in_subset: edam
in_subset: identifiers

Compound identifier
type: Class
subclass of: Molecule identifier
subclass of: Restriction
  on property: is identifier of
  some values from: Small molecule report
not recommended for annotation: true
definition: Identifier of an entry from a database of chemicals.
created in: beta12orEarlier
has_exact_synonym: Chemical compound identifier
has_exact_synonym: Compound ID
has_exact_synonym: Small molecule identifier
has_obo_namespace: DPBO
in_subset: data
in_subset: edam
in_subset: identifiers

ORF identifier
type: Class
definition: An identifier of an open reading frame.
has_obo_namespace: DPBO

library strategy
type: Class
subclass of: Obsolete Class
definition: Sequencing technique intended for a next generation sequencing library.
database_cross_reference: GENEPIO:0001973
has_obo_namespace: DPBO
id: obsolete_DPBO:0000035
comment: term is redundant, please use GENEPIO:0001973
deprecated: true

Read mapping
type: Class
created in: 1.1
has definition: Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.
has_exact_synonym: Oligonucleotide alignment
has_exact_synonym: Oligonucleotide alignment construction
has_exact_synonym: Oligonucleotide alignment generation
has_exact_synonym: Oligonucleotide mapping
has_exact_synonym: Read alignment
has_exact_synonym: Short oligonucleotide alignment
has_exact_synonym: Short read alignment
has_exact_synonym: Short read mapping
has_exact_synonym: Short sequence read mapping
has_obo_namespace: DPBO
id: operation:3198
in_subset: edam
in_subset: operations
comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.

Nucleic acids
type: Class
has_obo_namespace: DPBO
id: topic:0077

RNA
type: Class
subclass of: Nucleic acids
definition: RNA sequences and structures.
created in: beta12orEarlier
has human readable id: RNA
see also: RNA
has_narrow_synonym: Small RNA
has_obo_namespace: DPBO
id: topic:0099
in_subset: edam
in_subset: topics

polyA RNA
type: Class
subclass of: bio entity
definition: A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
has_obo_namespace: DPBO
id: OBI_0000869

Obsolete Class
type: Class
has_obo_namespace: DPBO
id: ObsoleteClass