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dpbo.obo
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format-version: 1.2
data-version: init/2020-12-01
saved-by: muehlhaus
default-namespace: DPBO
treat-xrefs-as-equivalent: MIAPPE
treat-xrefs-as-equivalent: NCBITaxon
treat-xrefs-as-equivalent: NCIT
treat-xrefs-as-equivalent: NFDI4PSO
remark: coverage: Missing Terms for the DataPLANT end-point repository templates
remark: creator: Dominik Brilhaus <dominik.brilhaus<-at->hhu.de>
remark: creator: Hajira Jabeen <hajira.jabeen<-at->uni-koeln.de>
remark: curator: Kathryn Dumschott <k.dumschott@fz-juelich.de>
remark: curator: Stella Eggels <s.eggels@fz-juelich.de>
ontology: dpbo
property_value: http://purl.org/dc/elements/1.1/creator "https://orcid.org/0000-0001-9021-3197" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "https://orcid.org/0000-0003-1476-2121" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "DataPLANT Biology Ontology" xsd:string
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))\n\n\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/BAO_0010013> \"\")\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/DPBO_0000041> \"\")\nAnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/DPBO_0000083> \"\")\nAnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/DPBO_1000006> \"\")\nAnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/DPBO_1000022> \"\")\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/dpbo#MCO_0000173> \"\")\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/dpbo#MCO_0000174> \"\")\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/dpbo#MCO_0000177> \"\")\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/dpbo#MCO_0000178> \"\")\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/dpbo#MCO_0000179> \"\")\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/dpbo#MCO_0000180> \"\")\n)
[Term]
id: AFP:0003774
name: imaging
def: "Imaging is a process that produces an image of something." []
[Term]
id: AFR:0000952
name: measurement time
def: "The date/time of the measurement." [Allotrope]
[Term]
id: AFR:0001255
name: temperature setting
def: "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." [Allotrope]
[Term]
id: AFR:0001577
name: injection volume setting
def: "The injection volume setting is an injection setting that specifies the volume of the fluid to be injected." []
[Term]
id: AFR:0002149
name: sample temperature
def: "A sample temperature result is a quality quantification facet that quantifies the temperature of the sample." []
[Term]
id: AGRO:00000006
name: irrigation process
def: "A planned process in which water is artificially supplied to plant or soil to sustain plants." []
[Term]
id: AGRO:00000007
name: desuckering
def: "A pruning process in which one or more suckers are removed." []
comment: Which suckers are removed depends on the criteria set by the agent of the desuckering process.
synonym: "desuckering process" EXACT []
is_a: AGRO:00000027 ! thinning
[Term]
id: AGRO:00000027
name: thinning
def: "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." [http://aims.fao.org/aos/agrovoc/c_6274, https://en.wikipedia.org/wiki/Pruning#Types_of_pruning]
synonym: "pruning" BROAD []
synonym: "thinning process" EXACT []
is_a: AGRO:00000566 ! pruning process
property_value: http://purl.org/dc/elements/1.1/creator "https://orcid.org/0000-0001-6284-4821" xsd:string
[Term]
id: AGRO:00000360
name: experimental site
def: "Location where the experiment is implemented." []
[Term]
id: AGRO:00000361
name: farmer field
def: "Experimental site in which the experiment is implemented on the field of a farmer." []
is_a: AGRO:00000360 ! experimental site
[Term]
id: AGRO:00000362
name: research station field
def: "Experimental site in which the experiment is done in a the field of a research station." []
synonym: "experimental station field" EXACT []
is_a: AGRO:00000360 ! experimental site
[Term]
id: AGRO:00000363
name: greenhouse
def: "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." [https://en.wikipedia.org/wiki/Greenhouse]
synonym: "glasshouse" EXACT []
synonym: "hothouse" BROAD []
synonym: "screenhouse" BROAD []
is_a: AGRO:00000360 ! experimental site
[Term]
id: AGRO:00000364
name: governmental forest
def: "Experimental site where the experiment is done in a forest owned by a government." []
is_a: AGRO:00000360 ! experimental site
[Term]
id: AGRO:00000365
name: private forest
def: "Experimental site where the experiment is done in a private forest." []
is_a: AGRO:00000360 ! experimental site
[Term]
id: AGRO:00000566
name: pruning process
def: "Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots." [https://en.wikipedia.org/wiki/Pruning]
synonym: "pruning" EXACT []
synonym: "pruning method" EXACT []
is_a: AGRO:00002071 ! agricultural process
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-6284-4821
[Term]
id: AGRO:00000572
name: GPS coordinates
def: "A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters" [https://whatis.techtarget.com/definition/GPS-coordinates]
synonym: "geo-location" EXACT []
synonym: "geographic coordinate system" BROAD []
synonym: "geolocation" EXACT []
synonym: "GPS coordinates measurement datum" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-6284-4821
[Term]
id: AGRO:00002071
name: agricultural process
def: "A planned process which occurs in an agricultural field." []
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8461-9745
[Term]
id: BAO:0000316
name: genomic DNA
def: "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." []
is_a: DPBO:0000012 ! bio entity
[Term]
id: BAO:0000513
name: 96 well plate
def: "This microplate contains 96 wells. It is suitable for a low throughput assay." []
[Term]
id: BAO:0002628
name: instrumentation manufacturer
def: "The role of a company as a creator of detection instrumentation." []
[Term]
id: BAO:0010013
name: 6 well plate
[Term]
id: BAO:0010026
name: protein profiling assay
def: "Protein profiling assays can be used to identify and quantify proteins together with their post-translational modifications" []
property_value: IAO:0000118 "protein profiling" xsd:string
property_value: IAO:0000118 "protein quantification assay" xsd:string
property_value: IAO:0000118 "protein quantification assay " xsd:string
[Term]
id: BAO:0010027
name: shotgun MS protein profiling assay
def: "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)" []
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BAO:0010028
name: SWATH MS protein profiling assay
def: "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" []
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BAO:0010029
name: P100 protein profiling assay
def: "A targeted phosphoproteomic assay that uses a data-driven approach to identify and quantify a set of 96 phosphopeptide probes" []
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BAO:0010030
name: RPPA protein profiling assay
def: "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" []
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BAO:0010049
name: Microwestern
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BAO:0010052
name: ELISA protein state assay
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BAO:0010070
name: Tandem Mass Tag (TMT) MS Protein Quantification
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BAO:0010071
name: Liquid Chromatography/Mass Spectroscopy (LC/MS) protein quantification
is_a: BAO:0010026 ! protein profiling assay
[Term]
id: BTO:0001899
name: stationary phase culture
namespace: BrendaTissueOBO
def: "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." [Biology_Dictionary_Hyperdictionary:http\://www.hyperdictionary.com/dictionary/Stationary+phase]
is_a: BTO:0001900 ! growth phase culture
[Term]
id: BTO:0001900
name: growth phase culture
namespace: BrendaTissueOBO
def: "The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time." [Biology_Dictionary_Hyperdictionary:http\://www.hyperdictionary.com/dictionary/Growth+phase]
[Term]
id: BTO:0001901
name: death phase culture
namespace: BrendaTissueOBO
def: "A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases." [Biology_Dictionary_Hyperdictionary:http\://www.hyperdictionary.com/dictionary/Death+phase]
is_a: BTO:0001900 ! growth phase culture
[Term]
id: BTO:0001902
name: lag phase culture
namespace: BrendaTissueOBO
def: "The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth." [Biology_Dictionary_Hyperdictionary:http\://www.hyperdictionary.com/dictionary/Lag+phase]
is_a: BTO:0001900 ! growth phase culture
[Term]
id: BTO:0001903
name: logarithmic phase culture
namespace: BrendaTissueOBO
def: "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." [Biology_Dictionary_Hyperdictionary:http\://www.hyperdictionary.com/dictionary/Logarithmic+phase]
synonym: "exponential growth phase culture" RELATED []
synonym: "log phase culture" RELATED []
is_a: BTO:0001900 ! growth phase culture
[Term]
id: CHEBI:36080
name: protein
def: " biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome." []
is_a: DPBO:0000012 ! bio entity
[Term]
id: CHMO:0000995
name: mobile phase
def: "A fluid that percolates through or along the stationary bed in chromatography." []
[Term]
id: CHMO:0001485
name: derivatisation
def: "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." [https://orcid.org/0000-0002-0640-0422]
synonym: "derivatization" EXACT []
is_a: OBI:0000094 ! material processing
[Term]
id: CHMO:0001549
name: sample drying
def: "The process of removing a solvent from a substance." [https://orcid.org/0000-0002-0640-0422]
synonym: "drying" RELATED non-mining_synonym []
is_a: OBI:0000094 ! material processing
[Term]
id: CHMO:0001557
name: vacuum drying
def: "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." [https://orcid.org/0000-0002-0640-0422]
is_a: CHMO:0001549 ! sample drying
[Term]
id: CHMO:0001577
name: extraction
def: "The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it." []
[Term]
id: CHMO:0001583
name: liquid-solid extraction
def: "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)." [ISBN:0-13-147835-4]
synonym: "liquid-solid extraction" EXACT []
synonym: "LSE" RELATED non-mining_synonym []
synonym: "solid phase extraction" EXACT []
synonym: "solid-phase extraction" EXACT []
synonym: "sorbent extraction" EXACT []
synonym: "sorptive extraction" EXACT []
synonym: "SPE" RELATED non-mining_synonym []
[Term]
id: CHMO:0001584
name: normal-phase solid-phase extraction
def: "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." [ISBN:0-13-147835-4]
synonym: "normal phase solid-phase extraction" EXACT []
synonym: "normal phase SPE" EXACT []
synonym: "normal-phase SPE" EXACT []
is_a: CHMO:0001583 ! liquid-solid extraction
[Term]
id: CHMO:0001585
name: reversed-phase solid-phase extraction
def: "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." [ISBN:0-13-147835-4]
synonym: "reverse phase solid-phase extraction" EXACT []
synonym: "reverse phase SPE" EXACT []
synonym: "reverse-phase solid-phase extraction" EXACT []
synonym: "reverse-phase SPE" EXACT []
synonym: "reversed phase SPE" EXACT []
synonym: "reversed-phase SPE" EXACT []
is_a: CHMO:0001583 ! liquid-solid extraction
[Term]
id: CHMO:0001586
name: solid-phase micro-extraction
def: "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)." [ISBN:0-13-147835-4]
synonym: "solid phase microextraction" EXACT []
synonym: "solid-phase microextraction" EXACT []
synonym: "SPME" EXACT []
is_a: CHMO:0001583 ! liquid-solid extraction
[Term]
id: CHMO:0001587
name: capillary micro-extraction
def: "The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary." [ISBN:0444505113]
synonym: "capillary microextraction" EXACT []
synonym: "CME" EXACT []
is_a: CHMO:0001586 ! solid-phase micro-extraction
[Term]
id: CHMO:0001588
name: sol–gel capillary micro-extraction
def: "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." [https://doi.org/10.1021/ac0109523]
synonym: "sgCME" EXACT []
synonym: "sol-gel capillary micro-extraction" EXACT []
synonym: "sol-gel capillary microextraction" EXACT []
synonym: "sol-gel CME" EXACT []
synonym: "solgel capillary microextraction" EXACT []
synonym: "solgel CME" EXACT []
is_a: CHMO:0001587 ! capillary micro-extraction
[Term]
id: CHMO:0001589
name: headspace solid-phase micro-extraction
def: "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." [https://orcid.org/0000-0002-0640-0422]
synonym: "headspace solid-phase micro-extraction" EXACT []
synonym: "headspace solid-phase microextraction" EXACT []
synonym: "headspace sorptive extraction" EXACT []
synonym: "HSPME" EXACT []
synonym: "hSPME" EXACT []
synonym: "HSSE" EXACT []
is_a: CHMO:0001586 ! solid-phase micro-extraction
[Term]
id: CHMO:0001590
name: micro-extraction in a packed syringe
def: "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." [https://doi.org/10.1002/jms.73]
synonym: "MEPS" EXACT []
synonym: "micro extraction by packed sorbent" EXACT []
synonym: "micro-extraction in packed syringe" EXACT []
synonym: "microextraction in a packed syringe" EXACT []
synonym: "microextraction in packed syringe" EXACT []
synonym: "packed syringe micro-extraction" EXACT []
synonym: "packed syringe microextraction" EXACT []
synonym: "packed-syringe micro-extraction" EXACT []
synonym: "packed-syringe microextraction" EXACT []
is_a: CHMO:0001586 ! solid-phase micro-extraction
[Term]
id: CHMO:0001598
name: solvent extraction
def: "The process of transferring a substance from any matrix to an appropriate liquid phase." [OrangeBook:9.4.1]
is_a: CHMO:0001577 ! extraction
[Term]
id: CHMO:0001652
name: grinding
def: "The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting." [https://doi.org/10.1351/goldbook.M03928]
synonym: "dry grinding" EXACT []
synonym: "milling" EXACT []
synonym: "solid-state grinding" EXACT []
synonym: "solvent-free grinding" EXACT []
is_a: OBI:0000094 ! material processing
[Term]
id: CHMO:0002757
name: methoxyamination derivatisation
def: "Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties." [https://doi.org/10.1039/9781847558107-00254, https://orcid.org/0000-0001-5985-7429]
comment: this typically happens prior to GC-MS, but not LC-MS
synonym: "methoxyamination derivatization" EXACT []
is_a: CHMO:0001485 ! derivatisation
is_a: DPBO:0000052 ! MS derivatization
[Term]
id: CHMO:0002758
name: trimethylsilyl derivatisation
def: "Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups." [https://doi.org/10.1039/9781847558107-00254, https://orcid.org/0000-0001-5985-7429]
comment: this typically happens prior to GC-MS, but not LC-MS
synonym: "TMS derivatisation" EXACT []
synonym: "trimethylsilyl derivatization" EXACT []
is_a: CHMO:0001485 ! derivatisation
is_a: DPBO:0000052 ! MS derivatization
[Term]
id: CHMO:0002863
name: dispersive solid phase extraction
synonym: "dispersive solid-phase extraction" EXACT []
is_a: CHMO:0001583 ! liquid-solid extraction
[Term]
id: CHMO:0002887
name: dispersive solid-phase microextraction
is_a: CHMO:0001586 ! solid-phase micro-extraction
[Term]
id: DPBO:0000001
name: growth plot design
def: "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" []
synonym: "Experimental Randomisation" RELATED []
disjoint_from: DPBO:0000002 ! read alignment software
[Term]
id: DPBO:0000002
name: read alignment software
def: "The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478" []
comment: “We might need to add the relationship with the class referenced above”
[Term]
id: DPBO:0000003
name: read alignment software version
def: "The version of the read alignment software (DPBO:0000002)." []
[Term]
id: DPBO:0000004
name: read alignment software parameters
def: "The parameters of the read alignment software (DPBO:0000002)." []
[Term]
id: DPBO:0000005
name: humidity day
def: "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)" []
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"
[Term]
id: DPBO:0000006
name: humidity night
def: "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)" []
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"
[Term]
id: DPBO:0000007
name: temperature day
def: "This term defines the air temperature at daytime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001)" []
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”
[Term]
id: DPBO:0000008
name: temperature night
def: "This term defines the air temperature at nighttime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001)" []
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”
[Term]
id: DPBO:0000009
name: sample collection method
def: "Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ”" []
[Term]
id: DPBO:0000010
name: metabolism quenching method
def: "Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.”" []
comment: “”
[Term]
id: DPBO:0000011
name: sample storage
def: "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”" []
comment: “”
[Term]
id: DPBO:0000012
name: bio entity
def: "The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.”" []
comment: “”
[Term]
id: DPBO:0000013
name: biosource amount
def: "The amount (typically in milligram) of material from which a bio entity (DPBO:0000012) is extracted.”" []
comment: “”
[Term]
id: DPBO:0000014
name: extraction kit
def: "The name of the commercial kit used for extraction of a bio entity (DPBO:0000012). Should include the company name.”" []
comment: “”
[Term]
id: DPBO:0000015
name: library layout
def: "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”" []
comment: “Adapted from http://purl.obolibrary.org/obo/NCIT_C150423"
[Term]
id: DPBO:0000016
name: library RNA amount
def: "Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)”" []
comment: “”
[Term]
id: DPBO:0000017
name: base-calling software
def: "The name of the software used for base-calling." []
comment: term description for base-calling http://edamontology.org/operation_3185
[Term]
id: DPBO:0000018
name: base-calling software version
def: "The version of the base-calling software (DPBO:0000017).”" []
comment: “”
[Term]
id: DPBO:0000019
name: base-calling software parameters
def: "The parameters of the base-calling software (DPBO:0000017).”" []
comment: “”
[Term]
id: DPBO:0000020
name: library strand
def: "Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (DPBO:0000015)”" []
comment: “”
[Term]
id: DPBO:0000021
name: raw data file format
def: "File format of the raw data file”" []
comment: “This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915"
[Term]
id: DPBO:0000022
name: raw data file checksum
def: "Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum" []
[Term]
id: DPBO:0000023
name: data filtering software
def: "Name of the software applied for data filtering" []
comment: “For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)”
[Term]
id: DPBO:0000024
name: data filtering software version
def: "The version of the data filtering software (DPBO:0000023).”" []
comment: “”
[Term]
id: DPBO:0000025
name: data filtering software parameters
def: "The parameters of the data filtering software (DPBO:0000023).”" []
comment: “”
[Term]
id: DPBO:0000026
name: genome reference sequence
def: "Name and version of the genome reference.”" []
comment: “See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644”
xref: MS:1002644
xref: NCIT:C16438
[Term]
id: DPBO:0000027
name: processed data file format
def: "File format of the processed data file”" []
comment: “”
[Term]
id: DPBO:0000028
name: processed data file name
def: "Name of the processed data file”" []
comment: “”
[Term]
id: DPBO:0000029
name: processed data file checksum
def: "Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum" []
[Term]
id: DPBO:0000030
name: isolation and growth condition
def: "Publication reference for isolation and growth condition specifications of the organism/material" []
comment: for submission to ENA
[Term]
id: DPBO:0000031
name: number of chromosomes
def: "The haploid chromosome count of a eukaryote" []
[Term]
id: DPBO:0000032
name: estimated genome size
def: "The estimated size of the genome prior to sequencing" []
comment: adapted from MIXS:0000024
[Term]
id: DPBO:0000033
name: plant age
def: "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)." []
comment: “This is a specialization of age (http://www.ebi.ac.uk/efo/EFO_0000246)"
[Term]
id: DPBO:0000034
name: plant health state
def: "Health status of the plant at the time of sample collection" []
[Term]
id: DPBO:0000035
name: Seurat
def: "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." []
is_a: DPBO:0000095 ! R package
is_obsolete: true
[Term]
id: SWO:1100130
name: Seurat
def: "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." []
is_a: DPBO:0000095 ! R package
xref: DPBO:0000035
[Term]
id: DPBO:0000036
name: obsolete_library selection
def: "The method used to select for or against, enrich, or screen the material being sequenced." []
comment: term is redundant, please use GENEPIO:0001940
xref: GENEPIO:0001940
is_a: ObsoleteClass ! Obsolete Class
is_obsolete: true
[Term]
id: DPBO:0000037
name: subspecific taxonomic rank
def: "Determination of the taxonomic ranking that is below species level i.e. variety, cultivar, ecotype, inbred line" []
[Term]
id: DPBO:0000038
name: rooting medium pH
def: "pH measurement of the culture rooting medium" []
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
[Term]
id: DPBO:0000039
name: rooting medium macronutrients
def: "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)" []
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
[Term]
id: DPBO:0000040
name: next generation sequencing instrument model
def: "Model name or number of next generation sequencing instrument" []
xref: EFO:0003739
[Term]
id: DPBO:0000041
name: growth day length
def: "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)" []
comment: “Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078"
synonym: "light duration" EXACT []
xref: PECO:0007078
xref: ZECO:0000147
[Term]
id: DPBO:0000042
name: biological replicate
def: "Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2')" []
xref: MS:1001809
[Term]
id: DPBO:0000043
name: MS sample post-extraction
def: "Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection)" []
[Term]
id: DPBO:0000044
name: MS sample resuspension
def: "Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile)" []
[Term]
id: DPBO:0000045
name: MS sample type
def: "Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control)" []
[Term]
id: DPBO:0000046
name: chromatography instrument model
def: "Company name, and instrument name or serial number of the chromatography instrument" []
comment: is_a chromatography device (http://purl.obolibrary.org/obo/OBI_0000048)
[Term]
id: DPBO:0000047
name: chromatography autosampler model
def: "Company name, and name or serial number of the chromatography autosampler model" []
comment: is_a autosampler (http://purl.obolibrary.org/obo/OBI_0000555)
[Term]
id: DPBO:0000048
name: chromatography column model
def: "Company name, and name or serial number of the chromatography column" []
[Term]
id: DPBO:0000049
name: chromatography guard column model
def: "Company name, and name or serial number of the chromatography guard column" []
comment: is_a http://purl.obolibrary.org/obo/OBI_0000614
[Term]
id: DPBO:0000050
name: extraction buffer
def: "Chemical buffer, solvent or solution used to extract a component from a biological sample." []
comment: “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884). DB"
[Term]
id: DPBO:0000051
name: extraction buffer volume
def: "Volume of the buffer (DPBO:0000050) used during extraction." []
comment: “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884)"
[Term]
id: DPBO:0000052
name: MS derivatization
def: "Derivatization for metabolomics mass spectrometry." []
xref: CHMO:0001485
is_a: OBI:0000094 ! material processing
[Term]
id: DPBO:0000053
name: chromatography column type
def: "Type of chromatography column (DPBO:0000048)" []
xref: CHMO:0001000
[Term]
id: DPBO:0000054
name: extraction method
def: "Method or kit that was used to extract DNA or RNA" []
comment: “More general than DPBO:0000014, because not everyone uses a kit for RNA/DNA extraction"
[Term]
id: DPBO:0000055
name: rooting medium micronutrients
def: "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)" []
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
[Term]
id: DPBO:0000056
name: library DNA amount
def: "Amount of DNA (microgram) used as starting material for library construction" []
comment: “"
[Term]
id: DPBO:0000057
name: next generation sequencing platform
def: "Name of the company that produces next generation sequencing instruments" []
xref: GENEPIO:0000071
[Term]
id: DPBO:0000058
name: rooting medium organic supplements
def: "Organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L)" []
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
[Term]
id: DPBO:0000059
name: sequence assembly method
def: "Strategy that was used to assemble reads into contigs" []
comment: “Just two options should be possible: de-novo assembly or mapping"
xref: GENEPIO:0000090
[Term]
id: DPBO:0000060
name: sequence assembly algorithm version
def: "The version of the sequence assembly algorithm (OBI_0001522)" []
comment: “"
[Term]
id: DPBO:0000061
name: genome status
def: "Status of the genome sequence that is uploaded" []
comment: “Just two options should be possible: full or partial"
[Term]
id: DPBO:0000062
name: RNA quality check
def: "Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis." []
[Term]
id: DPBO:0000063
name: BioProject accession number
def: "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." []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C175890
[Term]
id: DPBO:0000064
name: sample type
def: "Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C70713
[Term]
id: DPBO:0000065
name: rooting medium carbon source
def: "Source of organic carbon in the culture rooting medium; e.g. sucrose" []
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
[Term]
id: DPBO:0000066
name: rooting medium growth regulators
def: "Growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA" []
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
[Term]
id: DPBO:0000067
name: rooting medium solidifier
def: "Specification of the solidifying agent in the culture rooting medium; e.g. agar" []
comment: adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
[Term]
id: DPBO:0000068
name: obsolete_cell line
def: "A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [ NCI On-line Medical Dictionary ] " []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]"
xref: NCIT:C16403
is_a: ObsoleteClass ! Obsolete Class
is_obsolete: true
[Term]
id: DPBO:0000069
name: obsolete_cell type
def: "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]" []
comment: term is redundant, please use NCIT:C12508
is_a: ObsoleteClass ! Obsolete Class
is_obsolete: true
[Term]
id: DPBO:0000070
name: 5' partial CDS
def: "Incomplete CDS (coding sequence) with the start codon upstream of the submitted sequence." []
comment: adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences.
[Term]
id: DPBO:0000071
name: 3' partial CDS
def: "Incomplete CDS (coding sequence) with the stop codon downstream of the submitted sequence." []
comment: adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences.
[Term]
id: DPBO:0000072
name: plant disease stage
def: "Stage of plant disease at the time of sampling." []
[Term]
id: DPBO:0000073
name: phenotype
def: "Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C16977
[Term]
id: DPBO:0000074
name: geographic area
def: "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'" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C16632
[Term]
id: DPBO:0000075
name: 5' partial promoter
def: "Incomplete promoter with its 5' end upstream of the submitted sequence." []
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.
[Term]
id: DPBO:0000076
name: 3' partial promoter
def: "Incomplete promoter with its 3' end downstream of the submitted sequence." []
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.
[Term]
id: DPBO:0000077
name: metabolite assignment file
def: "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" []
comment: “[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title"
[Term]
id: DPBO:0000078
name: BioSample accession number
def: "BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]!" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C175889
[Term]
id: DPBO:0000079
name: promoter 5' end coordinate
def: "Coordinate of the 5' end of the promoter within the submitted sequence." []
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.
[Term]
id: DPBO:0000080
name: promoter 3' end coordinate
def: "Coordinate of the 3' end of the promoter within the submitted sequence." []
comment: adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.
[Term]
id: DPBO:0000081
name: chromatography gradient
def: "Settings of the gradient used during (e.g. liquid, gas or ion) chromatography" []
comment: "term was previously
[Term]
id: DPBO:0000082
name: rRNA depletion
def: "Method used for rRNA depletion during construction of the sequencing library." []
comment: "see also http://purl.obolibrary.org/obo/NCIT_C18685"
[Term]
id: DPBO:0000083
name: relative centrifugal force
def: "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." []
synonym: "RCF" EXACT []
is_a: UO:0000048 ! acceleration unit
equivalent_to: DPBO:0000084 ! g-force
[Term]
id: DPBO:0000084
name: g-force
def: "G-force is the force acting on an object as a result of acceleration or gravity." []
is_a: UO:0000048 ! acceleration unit
[Term]
id: DPBO:0000085
name: standard gravity
def: "The standard acceleration of an object in free fall at or near sea level equivalent to 9.807 m/s2." []
synonym: "g0" EXACT []
synonym: "standard acceleration due to gravity" EXACT []
synonym: "standard acceleration of free fall" EXACT []
is_a: UO:0000048 ! acceleration unit
[Term]
id: DPBO:0000086
name: single-end
def: "A library layout which describes that only one end of the library fragment is sequenced" []
comment: "Adapted from http://purl.obolibrary.org/obo/FBcv_0003220"
is_a: DPBO:0000015 ! library layout
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "RAW FILES_single or paired-end" xsd:string
[Term]
id: DPBO:0000087
name: library ID
def: "Short unique identifier for the sequencing library" []
comment: "Required for upload of next-generation sequencing data to SRA."
created_by: Angela Kranz | ORCID: 0000-0002-8000-0400
[Term]
id: DPBO:0000088
name: growth chamber
def: "A climatic chamber used for growing plants under controlled environmental conditions." []
is_a: MIAPPE:0095
[Term]
id: DPBO:0000089
name: SingleCellExperiment
def: "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." []
is_a: DPBO:0000095 ! R package
[Term]
id: DPBO:0000090
name: tidyverse
def: "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." []
is_a: DPBO:0000095 ! R package
[Term]
id: DPBO:0000091
name: Matrix
def: "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." []
is_a: DPBO:0000095 ! R package
[Term]
id: DPBO:0000092
name: scales
def: "Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends." []
is_a: DPBO:0000095 ! R package
[Term]
id: DPBO:0000093
name: cowplot
def: "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." []
is_a: DPBO:0000095 ! R package
[Term]
id: DPBO:0000094
name: RCurl
def: "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." []
is_a: DPBO:0000095 ! R package
[Term]
id: DPBO:0000095
name: R package