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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 <[email protected]>
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 "The DataPlant 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(owl:deprecated <http://purl.obolibrary.org/obo/DPBO_1000022> \"\")\n)
[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:0000513
name: 96 well plate
def: "This microplate contains 96 wells. It is suitable for a low throughput assay." []
[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: 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: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: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: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: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: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: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: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: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:0000072
name: plant disease stage
def: "Stage of plant disease (DPBO:0000071) 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: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: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:0002000
name: alias
def: "Unique identificator for a study. This is used to link experiments to the study." []
[Term]
id: DPBO:0002001
name: study abstract
def: "Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication." []
[Term]
id: DPBO:0002002
name: title
def: "Title of the study as would be used in a publication." []
[Term]
id: DPBO:0002005
name: project name
def: "Name of the project within which the experiment was organized." []
[Term]
id: DPBO:0002006
name: sequencing method
def: "Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid." []
[Term]
id: DPBO:0002007
name: investigation type
def: "Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium" []
[Term]
id: DPBO:0002008
name: environment (feature)
def: "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. " []
comment: EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []
xref: ENVO:01000813
[Term]
id: DPBO:0002009
name: environment (material)
def: "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. " []
comment: EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []
xref: ENVO:00010483
[Term]
id: DPBO:0002010
name: plant-associated environmental package
def: "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" []
[Term]
id: DPBO:0010000
name: ENA
def: "The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data." []
comment: https://www.ebi.ac.uk/ena/
xref: ENSGLOSSARY:0000217
is_a: DPBO:1000095 ! endpoint repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date "2022-02-02T08:33:08Z" xsd:dateTime
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010002
name: BioSample
def: "The BioSample database contains descriptions of biological source materials used in experimental assays." []
comment: https://www.ncbi.nlm.nih.gov/biosample/
is_a: DPBO:1000095 ! endpoint repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date "2022-02-02T08:33:08Z" xsd:dateTime
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010004
name: BioProject
def: "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." []
comment: https://www.ncbi.nlm.nih.gov/bioproject/
xref: GENEPIO:0001836
is_a: DPBO:1000095 ! endpoint repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date "2022-02-02T08:58:37Z" xsd:dateTime
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010005
name: GenBank
def: "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." []
comment: https://www.ncbi.nlm.nih.gov/genbank/
xref: NCIT:C43818
is_a: DPBO:1000095 ! endpoint repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date "2022-02-02T08:59:49Z" xsd:dateTime
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010006
name: SRA
def: "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." []
comment: https://www.ncbi.nlm.nih.gov/sra/
is_a: DPBO:1000095 ! endpoint repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date "2022-02-02T09:02:27Z" xsd:dateTime
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010007
name: PGP
def: "Plant Genomics & Phenomics Research Data Repository" []
comment: https://edal-pgp.ipk-gatersleben.de
is_a: DPBO:1000095 ! endpoint repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date "2022-02-02T09:03:35Z" xsd:dateTime
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010008
name: BIA
def: "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." []
comment: https://www.ebi.ac.uk/bioimage-archive/
is_a: DPBO:1000095 ! endpoint repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date "2022-02-02T09:04:46Z" xsd:dateTime
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010009
name: biosource material state
def: "The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay." []
comment: "Relates to DPBO:0000013"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010010
name: fresh material
def: "Fresh (non-dry) biosource material" []
comment: "Relates to https://cropontology.org/rdf/CO_347:0000193
is_a: DPBO:0010009 ! biosource material state
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010011
name: dry material
def: "Dry biosource material" []
comment: "Relates to https://cropontology.org/rdf/CO_347:0000196
is_a: DPBO:0010009 ! biosource material state
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010012
name: internal standard
def: "Internal standard added in known amount to an analytical sample" []
comment: "Similar to http://purl.obolibrary.org/obo/MSIO_0000005
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010013
name: sample volume
def: "Volume taken from the sample to be assayed (measured)." []
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010014
name: chromatography injection volume
def: "Volume of the sample injected during chromatography" []
comment: "Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
[Term]
id: DPBO:0010015
name: chromatography injection mode
def: "This is to specify split / splitless runs during e.g. gas-chromatography." []
comment: "Compare to http://purl.obolibrary.org/obo/OBI_0000525
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
[Term]
id: DPBO:1000003
name: obsolete_RNA-seq
def: "placeholder def of RNA-Seq" []
comment: To be transformed to an instance. DB
is_a: ObsoleteClass ! Obsolete Class
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: DPBO:1000004
name: miRNA-seq
def: "A library strategy that can identify and quantify the microRNA sequences present in a biological sample." []
comment: "Adapted from http://purl.obolibrary.org/obo/NCIT_C156057"
is_a: GENEPIO:0001973 ! library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
[Term]
id: DPBO:1000005
name: ncRNA-seq
def: "A next-generation sequencing library strategy that can determine the small and large non-protein coding RNA transcripts in a sample." []
comment: "Adapted from http://purl.obolibrary.org/obo/NCIT_C172858"
is_a: GENEPIO:0001973 ! library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
[Term]
id: DPBO:1000006
name: RNA-seq (size fractionation)
def: "placeholder def of RNA-Seq (size fractionation)" []
comment: To be transformed to an instance. DB
is_a: GENEPIO:0001973 ! library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
[Term]
id: DPBO:1000007
name: RNA-seq (CAGE)
def: "placeholder def of RNA-Seq (CAGE)" []
comment: To be transformed to an instance. DB
is_a: GENEPIO:0001973 ! library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string