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 hhu.de> remark: creator: Hajira Jabeen uni-koeln.de> remark: curator: Kathryn Dumschott remark: curator: Stella Eggels idspace: DPBO https://purl.org/nfdi4plants/ontology/dpbo/DPBO_ "DataPLANT Biology Ontology" 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:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"\")\nAnnotationAssertion( \"\")\nAnnotationAssertion(rdfs:comment \"\")\nAnnotationAssertion(rdfs:comment \"\")\nAnnotationAssertion(owl:deprecated \"\")\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: AFM:0000341 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CL] is_a: DPBO:0000177 ! plant material type [Term] id: AFP:0003774 name: imaging def: "Imaging is a process that produces an image of something." [] [Term] id: AFQ:0000029 name: detection wavelength def: "A detection wavelength quality is a device setting which determines the wavelength range that a detector of electromagnetic radiation detects." [Allotrope] [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: AFR:0002229 name: experiment type def: "An experiment type is a classification datum that classifies the type of experiment performed." [Allotrope] [Term] id: AFR:0002311 name: cycle count def: "A cycle count is a count of the number of iterations of a repeated process." [Allotrope] [Term] id: AFRL:0000035 name: sample role def: "A sample role is a type of role whose bearer is a material entity that is the output of a sampling." [Allotrope] [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 is_a: MIAPPE:0095 ! Growth facility [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 is_a: MIAPPE:0095 ! Growth facility [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 is_a: MIAPPE:0095 ! Growth facility [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 is_a: MIAPPE:0095 ! Growth facility [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 is_a: MIAPPE:0095 ! Growth facility [Term] id: AGRO:00000372 name: farmer def: "A person engaged in agriculture, raising living organisms for food or raw materials." [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000373 name: researcher def: "A person who conducts research." [] synonym: "scientist" EXACT [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000374 name: student def: "A person that is enrolled or attends classes at a school, college, or university." [] synonym: "intern" RELATED [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000375 name: research station employee def: "A person that works in a research station." [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000376 name: extension agent def: "A person that is employed by the government to assist people in rural areas with methods of farming and home economics." [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000377 name: faculty member def: "A person that is an educator who works at a college or university." [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000378 name: person role within the experiment def: "Roled performed by a person during an experiment." [] [Term] id: AGRO:00000379 name: data collector def: "A person that has a role of collecting data related to the experiment." [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000380 name: principal investigator def: "A person that is the holder of an independent grant and the lead researcher for the grant project." [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000381 name: experiment manager def: "A person that has a role of managing the experiment." [] is_a: AGRO:00000378 ! person role within the experiment [Term] id: AGRO:00000382 name: field laborer def: "A person that has a role of performing the operations required to run the experiment in the field." [] is_a: AGRO:00000378 ! person role within the experiment [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:00000659 name: field owner def: "A person that own an agricultural field." [] is_a: AGRO:00000378 ! person role within the experiment [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:0000269 name: DNA def: "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." [] is_a: DPBO:0000012 ! bio entity is_a: NCIT:C63816 [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 is_a: NCIT:C63816 [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: C:86F26167 name: genotyping-by-sequencing is_a: GENEPIO:0001973 ! library strategy [Term] id: CHEBI:2509 name: agar def: "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." [] is_a: DPBO:0000067 ! rooting medium solidifier [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 is_a: NCIT:C63816 [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 [] xref: AGRO:00000343 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: obsolete_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: ObsoleteClass ! Obsolete Class is_obsolete: true [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 xref: PATO:0001428 [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: EO:0007153 xref: PECO:0007078 xref: ZECO:0000147 [Term] id: DPBO:0000042 name: biological replicate identifier 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" [] [Term] id: DPBO:0000047 name: chromatography autosampler model def: "Company name, and name or serial number of the chromatography autosampler model" [] [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" [] [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" [] [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 dependent 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 ! Growth facility [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' 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 def: "Packages are collections of R functions, data, and compiled code in a well-defined format, created to add specific functionality." [] [Term] id: DPBO:0000096 name: package version def: "The version of the software package or library that was used in the analysis." [] [Term] id: DPBO:0000097 name: prm-PASEF def: "Targeted proteomics method that combines parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF)." [] comment: Bruker Corporation term. Definition from https://www.bruker.com/ [Term] id: DPBO:0000098 name: dda-PASEF def: "Data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF) technology for proteomics analysis." [] comment: Bruker Corporation term. Definition from https://www.bruker.com/ [Term] id: DPBO:0000099 name: antibiotic concentration def: "Concentration of an antibiotic that was added to a growth medium." [] [Term] id: DPBO:0000100 name: growth time def: "Duration of a bacterial cultivation." [] [Term] id: DPBO:0000101 name: start OD600 def: "The OD600 that was used to inoculate a bacterial culture." [] [Term] id: DPBO:0000102 name: harvesting method def: "Method that was used to harvest bacterial cells." [] [Term] id: DPBO:0000103 name: dissolved oxygen (DO) def: "Constant percentage of dissolved oxygen in a culture medium." [] [Term] id: DPBO:0000104 name: oxygen limitation experiment def: "An experiment that is used to grow bacterial cells under oxygen limitation conditions. " [] is_a: EFO:0002694 ! experimental process [Term] id: DPBO:0000105 name: oxygen concentration def: "Percent of oxygen that is added to a culture medium via gassing." [] [Term] id: DPBO:0000106 name: nitrogen concentration def: "Percent of nitrogen that is added to a culture medium via gassing." [] [Term] id: DPBO:0000107 name: oxygen excess experiment def: "An experiment that is used to grow bacterial cells under oxygen excess conditions." [] is_a: EFO:0002694 ! experimental process [Term] id: DPBO:0000108 name: transcriptional binding site identification def: "A measurement that is used to identify transcriptional binding sites in a genome." [] [Term] id: DPBO:0000109 name: leaf gas exchange def: "Exchange of carbon dioxide, oxygen and water vapor between the plant leaf and the ambient air through stomata." [] created_by: Stella Eggels [Term] id: DPBO:0000110 name: infrared gas analyzer def: "Analyzer that measures the concentration of gases in air based on their absorption of infrared radiation." [] created_by: Stella Eggels [Term] id: DPBO:0000111 name: Explication def: "A word, term or short statement that clarifies the cause, context and/or consequence of another entity." [] [Term] id: DPBO:0000112 name: tissue def: "Multicellular structure comprising similar cells with some specific function." [] comment: adapted from FBcv:0003046 [Term] id: DPBO:0000113 name: sampling depth def: "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." [] comment: adapted from MIXS:0000018 [Term] id: DPBO:0000114 name: number of injections def: "Number of injections of a sample into a mass spectrometer or chromatograph." [] [Term] id: DPBO:0000115 name: inbred line def: "Nearly identical and homozygous genotypes, resulting from repeated selfing over several generations." [] is_a: DPBO:0000037 ! subspecific taxonomic rank [Term] id: DPBO:0000116 name: Infinite M200 plate reader (Tecan) def: "A microtiter plate reader by the brand Tecan." [] xref: BAO:0150076 is_a: OBI:0001058 ! microplate reader [Term] id: DPBO:0000117 name: obsolete_buffer volume def: "Volume of the buffer in which the sample is diluted." [] comment: Suggested by Lukas Weil | 0000-0003-1945-6342; term is redundant, please use EFO:0920056 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true xref: EFO:0920056 [Term] id: DPBO:0000118 name: mortar and pestle def: "Combination of two tools used for grinding or shearing substances to a fine paste or powder." [] comment: Suggested by Lukas Weil | 0000-0003-1945-6342 is_a: DPBO:0000119 ! grinding device [Term] id: DPBO:0000119 name: grinding device def: "Device used for the mechanical reduction of the particle size of a solid sample." [] comment: definition adapted from CHMO:0001652 [Term] id: DPBO:0000120 name: sugar measurement def: "The quantification of some sugar." [] comment: Suggested by Lukas Weil | 0000-0003-1945-6342 is_a: EFO:0004998 ! carbohydrate measurement [Term] id: DPBO:0000121 name: TAP medium def: "Tris-Acetate-Phosphate medium for the growth of Chlamydomonas." [] comment: Medium composition can be found at doi.org/10.1101/pdb.rec560 is_a: OBI:0000079 ! culture medium [Term] id: DPBO:0000122 name: imaging signal mechanism def: "Mechanism by which the imaging signal is generated by the sample, e.g. fluorescent protein, fluorescent dye, antibody." [] xref: SHARELOC:000004 [Term] id: DPBO:0000123 name: imaging signal molecule def: "Name of the molecule used to visualize a specific target in a cell or tissue, e.g. GFP." [] [Term] id: DPBO:0000124 name: excitation method def: "The type of excitation used for imaging purposes." [] [Term] id: DPBO:0000125 name: whole genome amplification def: "Whole genome amplification followed by random sequencing." [] comment: from the ENA (European Nucleotide Archive) Read submission permitted values. is_a: GENEPIO:0001973 ! library strategy [Term] id: DPBO:0000126 name: single cell genomic source def: "Genomic DNA that can be traced to a single cell of origin." [] comment: adapted from http://purl.obolibrary.org/obo/OBI_0002631 is_a: GENEPIO:0001965 ! library source [Term] id: DPBO:0000127 name: single cell transcriptomic source def: "Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries) that can be traced to a single cell of origin." [] comment: adapted from http://purl.obolibrary.org/obo/OBI_0002631 and the ENA (European Nucleotide Archive) Read submission permitted values is_a: GENEPIO:0001965 ! library source [Term] id: DPBO:0000128 name: repeat fractionation def: "Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation techniques based on DNA kinetics." [] comment: from the ENA (European Nucleotide Archive) Read submission permitted values is_a: GENEPIO:0001940 ! library selection [Term] id: DPBO:0000129 name: oligo-dT selection def: "Enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT." [] comment: from the ENA (European Nucleotide Archive) Read submission permitted values xref: FBcv:0003203 is_a: GENEPIO:0001940 ! library selection [Term] id: DPBO:0000130 name: inverse rRNA selection def: "Depletion of ribosomal RNA by inverse oligo hybridization." [] comment: from the ENA (European Nucleotide Archive) Read submission permitted values is_a: GENEPIO:0001940 ! library selection [Term] id: DPBO:0000131 name: padlock probes capture method def: "Targeted sequence capture protocol covering an arbitrary set of nonrepetitive genomics targets. An example is capture bisulfite sequencing using padlock probes (BSPP)." [] comment: from the ENA (European Nucleotide Archive) Read submission permitted values is_a: GENEPIO:0001940 ! library selection [Term] id: DPBO:0000132 name: cell lysis approach def: "Name of the kit or standard protocol used for cell(s) lysis." [] comment: adapted from the MIxS checklists, MIXS:0000054 [Term] id: DPBO:0000133 name: cell sorting technology def: "Method used to sort/isolate cells of interest." [] comment: adapted from the MIxS checklists, MIXS:0000075 [Term] id: DPBO:0000134 name: whole genome amplification approach def: "Method used to amplify genomic DNA in preparation for sequencing." [] comment: adapted from the MIxS checklists, MIXS:0000055 [Term] id: DPBO:0000135 name: instrument customizations def: "Any significant (i.e. affecting behaviour) deviations from the manufacturer’s specification for the instrument." [] comment: adapted from the MIAPE-MS checklist [Term] id: DPBO:0000136 name: ion source description def: "Description of the ion source of a mass spectrometer and relevant and discriminating parameters for its use." [] comment: adapted from the MIAPE-MS checklist [Term] id: DPBO:0000137 name: activation component def: "Instrument component of a mass spectrometer, where the activation and/or dissociation occurs." [] comment: adapted from the MIAPE-MS checklist [Term] id: DPBO:0000138 name: chromatography column accessories def: "Details of any guards or traps used in conjunction with the chromatography column." [] comment: adapted from the MIAPE-CC checklist [Term] id: DPBO:0000139 name: mobile phase constituents def: "A description, the concentration, pH (including how it was adjusted) and date prepared of each consistuent of the mobile phase." [] comment: adapted from the MIAPE-CC checklist [Term] id: DPBO:0000140 name: column run time def: "The total time of the chromatography column run with appropriate units." [] comment: adapted from the MIAPE-CC checklist [Term] id: DPBO:0000141 name: detector model def: "Manufacturer and model name, or description of the equipment used for detection." [] comment: adapted from the MIAPE-CC checklist [Term] id: DPBO:0000142 name: pre and post chromatography run processes def: "Description of the purpose, reagents used, duration and flow rate of processes pre or post chromatography run, such as equilibration, calibration or washing." [] comment: adapted from the MIAPE-CC checklist [Term] id: DPBO:0000143 name: gel electrophoresis dimension type def: "The type of gel electrophoresis with respect to the number of dimensions." [] [Term] id: DPBO:0000144 name: loading buffer def: "The components, with concentrations (excluding the sample) of the loading buffer that is to be loaded onto the gel matrix for gel electrophoresis." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000145 name: gel electrophoresis separation method def: "Name of the separation technique employed for each dimension of gel electrophoresis." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000146 name: gel matrix type def: "Name and type of the gel matrix used for gel electrophoresis." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000147 name: gel manufacture def: "Description of how the gel used for gel electrophoresis was produced. For purchased gels, model name, model number, batch number and manufacturer, for self-prepared gels, a reference to the recipe or published protocol should be given." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000148 name: physical dimensions of the gel def: "The physical dimensions of the gel matrix and of any sub-matrices. The measurements should be in the form of the Cartesian Coordinate system (x,y,z)." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000149 name: physicochemical property range and distribution of the gel def: "The details of the pH distribution of the matrix, including the overall pH range of the gel, and details of the molecular weight distribution of matrix with appropriate measurement unit." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000150 name: acrylamide concentration def: "The acrylamide concentration of the gel, or each matrix. For gradients include the gradient distribution if appropriate, (e.g. fixed, stepped or linear)." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000151 name: acrylamide crosslinker ratio def: "The acrylamide to crosslinker ratio of the gel." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000152 name: additional gel ingredients def: "The details of any additional substances or reagents contained within the gel, recording the concentration or molarities for each (and pH if appropriate)." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000153 name: gel lane number def: "The number of lanes on the gel matrix." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000154 name: gel electrophoresis sample application def: "Description of how the sample was applied to the gel for electrophoresis, including method and volume of loading buffer and sample." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000155 name: electrophoresis conditions def: "The running conditions applied to the gel. To be given in terms of voltages versus time/kilovolt hours (or appropriate measurements) and temperature. Include voltage mode profile (step and hold, or gradient).." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000156 name: interdimension process def: "Description of any process applied to, or carried out between the dimensions of gel electrophoresis, including processes such as equilibration, reduction and alkylation." [] comment: adapted from the MIAPE-GE checklist [Term] id: DPBO:0000157 name: molecular interaction host system def: "The host organism in which the studies molecular interaction took place." [] comment: adapted from the MIMIx checklist [Term] id: DPBO:0000158 name: molecular interaction participant accession number def: "The accession number from a database for a molecule that is part of a molecular interaction." [] comment: adapted from the MIMIx checklist [Term] id: DPBO:0000159 name: skimmer and focusing lens voltages def: "Voltages of the skimmer and the focusing lens in a mass spectrometer." [] comment: term from CIMR [Term] id: DPBO:0000160 name: ionization gas flows def: "Controlled introduction of gases used for ionization in mass spectrometry such as nebulization gas or cone gas." [] [Term] id: DPBO:0000161 name: data acquisition date def: "The date that data was acquired for a sample." [] [Term] id: DPBO:0000162 name: data acquisition rate def: "The rate at which data was measured." [] [Term] id: DPBO:0000163 name: mass spectrometer lock spray def: "Sprayer used in mass spectrometry that provides a continuous calibrant to ensure high mass accuracy throughout an analysis." [] [Term] id: DPBO:0000164 name: autosampler wash cycles def: "Number and volume of washing steps in a chromatography autosampler." [] [Term] id: DPBO:0000165 name: physical column parameters def: "Physical characteristics of a chromatography column, such as pore size, particle size or coating thickness." [] [Term] id: DPBO:0000166 name: chromatography pressure def: "Pressure used during chromatographic separation." [] [Term] id: DPBO:0000167 name: chromatography injection mode def: "Method of how the sample is introduced into the chromatography system." [] [Term] id: DPBO:0000168 name: post-column split def: "Chromatography setup where the flow coming out of the column is split into two or more paths after the separation has occurred." [] [Term] id: DPBO:0000169 name: sample resuspension def: "Description of what solution a sample was resuspended in after extraction." [] [Term] id: DPBO:0000170 name: sample wash method def: "Wash method for removing unwanted external components from the sample." [] comment: adapted from CIMR [Term] id: DPBO:0000171 name: concentration adjustment def: "The process of concentrating, diluting and/or resuspending an extract to obtain a desired concentration." [] [Term] id: DPBO:0000172 name: extract cleanup def: "Method for removing unwanted components from an extract, such as ultrafiltration, removal of paramagnetic ions or addition of metal chelators." [] comment: adapted from CIMR [Term] id: DPBO:0000173 name: extract storage def: "Storage conditions prior to and during analysis of an extract." [] comment: adapted from CIMR [Term] id: DPBO:0000174 name: gel electrophoresis dimension def: "Specification of whether the first or second dimension of a one- or two-dimensional gel electrophoresis is described." [] [Term] id: DPBO:0000175 name: sample description def: "Description of the sample." [] [Term] id: DPBO:0000176 name: shaker type def: "Type of laboratory device used to agitate or mix biological samples, typically in liquid form, to promote aeration, cell growth, or chemical reactions. Different types are available." [] xref: SNOMED:470694005 [Term] id: DPBO:0000177 name: plant material type def: "The level at which the plant material is investigated (e.g. whole organism, organism part, cell, DNA)." [] [Term] id: DPBO:0000178 name: stock solution protocol def: " A protocol that details how a stock solution is mixed from various chemical compounds. This can be from the same or different methodologies." [] is_a: DPBO:1000161 ! protocol type [Term] id: DPBO:0000179 name: Source Name def: "Sources are considered as the starting biological material used in a study." [] comment: https://isa-specs.readthedocs.io/en/latest/isamodel.html is_a: DPBO:0000182 ! Material [Term] id: DPBO:0000180 name: Sample Name def: "Samples are a kind of material and represent major outputs resulting from a protocol application." [] comment: https://isa-specs.readthedocs.io/en/latest/isamodel.html is_a: DPBO:0000182 ! Material [Term] id: DPBO:0000181 name: data file name def: "Name of the data file resulting from a protocol application that corresponds to some process that produces data." [] comment: https://isa-specs.readthedocs.io/en/latest/isamodel.html [Term] id: DPBO:0000182 name: Material def: "Name of the material consumed or produced during an experimental workflow." [] comment: https://isa-specs.readthedocs.io/en/latest/isamodel.html [Term] id: DPBO:0000183 name: NMR sample protocol def: "Column marking the start of metadata describing the NMR sample." [] comment: as required by MetaboLights [Term] id: DPBO:0000184 name: NMR spectroscopy protocol def: "Column marking the start of metadata describing the NMR spectroscopy." [] comment: as required by MetaboLights [Term] id: DPBO:0000185 name: NMR assay protocol def: "Column marking the start of metadata describing the NMR assay." [] comment: as required by MetaboLights [Term] id: DPBO:0000186 name: metabolite identification protocol def: "Column marking the start of metadata describing the metabolite identification." [] comment: as required by MetaboLights [Term] id: DPBO:0000187 name: chromatography protocol def: "Column marking the start of metadata describing the chromatography." [] comment: as required by MetaboLights [Term] id: DPBO:0000188 name: mass spectrometry protocol def: "Column marking the start of metadata describing the mass spectrometry." [] comment: as required by MetaboLights [Term] id: DPBO:00002008 name: obsolete_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. " [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [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:0002011 name: cultivation container def: "A container that is used for the cultivation of cells." [] [Term] id: DPBO:0002012 name: shake flask def: "A shake flask is a common piece of laboratory equipment used for growing microorganisms or cells in a liquid culture. " [] is_a: DPBO:0002011 ! cultivation container [Term] id: DPBO:0002013 name: CGXII medium def: "A defined medium for Corynebacterium glutamicum according to Keilhauer et al., 1993. " [] is_a: OBI:0000079 ! culture medium [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 xref: AFRL:0000432 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: obsolete_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 comment: term is redundant, please use EFO:0920055 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true xref: EFO:0920055 [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: "A library strategy with an additional size fractionation step after RNA-seq library preparation" [] 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: "A library strategy that is used to sequence the 5' capped transcripts, using CAGE to biotinylate and isolate the 7-methylguanosine cap." [] comment: "Adapted from http://purl.obolibrary.org/obo/FBcv_0003051" 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:1000008 name: RNA-seq (RACE) def: "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." [] comment: "Adapted from http://www.ebi.ac.uk/efo/EFO_0004182." 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:1000009 name: obsolete_ssRNA-seq def: "placeholder def of ssRNA-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:1000010 name: obsolete_ChIP-seq def: "placeholder def of ChIP-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:1000011 name: obsolete_MNase-seq def: "placeholder def of MNase-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:1000012 name: obsolete_MBD-seq def: "placeholder def of MBD-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:1000013 name: obsolete_MRE-seq def: "placeholder def of MRE-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:1000014 name: obsolete_Bisulfite-seq def: "placeholder def of Bisulfite-Seq" [] comment: Replaced by EFO term Bisulfite-seq (id:0003753) 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:1000015 name: Bisulfite-seq (reduced representation) def: "A library strategy that uses one or more restriction enzymes on a genomic DNA sample prior to sequencing to produce sequence-specific fragmentation" [] comment: To be transformed to an instance. DB synonym: "reduced-representation bisulfite sequencing" EXACT [] synonym: "RRBS-Seq" EXACT [] 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:1000016 name: obsolete_MeDIP-seq def: "placeholder def of MeDIP-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:1000017 name: DNase hypersensitivity def: "A library strategy that is used to characterize the DNase hypersensitivity of a genome by treatment with DNase before library preparation." [] comment: "Adapted from FBcv:0003058." 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:1000018 name: Tn-seq def: "A library strategy that is used to sequence transposons." [] comment: "Adapted from http://www.ebi.ac.uk/efo/EFO_0008973." 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:1000019 name: obsolete_FAIRE-seq def: "placeholder def of FAIRE-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:1000020 name: SELEX def: "A library strategy for high-througput sequencing that is based on Systematic evolution of ligands by exponential enrichment." [] comment: "Adapted from http://www.ebi.ac.uk/efo/EFO_0008918." 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:1000021 name: obsolete_RIP-seq def: "placeholder def of RIP-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:1000022 name: obsolete_ATAC-seq def: "placeholder def of ATAC-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:1000023 name: obsolete_ChIA-PET def: "placeholder def of ChIA-PET" [] 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:1000024 name: obsolete_Hi-C def: "placeholder def of Hi-C" [] 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:1000025 name: OTHER: specify def: "Any other possible library strategy that can be used for RNA-seq" [] 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." 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:1000026 name: obsolete_fastq def: "placeholder def of fastq" [] 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 "RAW FILES_file type" xsd:string is_obsolete: true [Term] id: DPBO:1000027 name: bam def: "Binary format for storing of sequencing data" [] comment: Adapted from http://purl.obolibrary.org/obo/NGBO_6000021. is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000028 name: Illumina_native_qseq def: "Illumina´s native QSEQ format" [] is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000029 name: Illumina_native def: "Illumina´s native sequencing format" [] is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000030 name: SOLiD_native_csfasta def: "SOLID´s native csfasta sequencing format" [] is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000031 name: SOLiD_native_qual def: "SOLI´s native quality sequencing format" [] is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000032 name: sff def: "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." [] comment: http://edamontology.org/format_3284 is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000033 name: 454_native_seq def: "454 pyrosequencing native sequencing file format" [] is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000034 name: 454_native_qual def: "454 pyrosequencing native quality sequencing file format" [] is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000035 name: Helicos_native def: "Helicos native file format" [] is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000036 name: srf def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [] comment: http://edamontology.org/format_3017 is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000037 name: PacBio_HDF5 def: "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." [] comment: Adapted from http://purl.obolibrary.org/obo/NCIT_C184763 is_a: DPBO:0000021 ! raw data file format property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_file type" xsd:string [Term] id: DPBO:1000038 name: obsolete_Illumina Genome Analyzer IIx comment: term is redundant, use EFO:0004202 or OBI:0002000 instead is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000039 name: obsolete_Illumina HiSeq 1000 comment: term is redundant, use EFO:0004204 or OBI:0002022 instead is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000040 name: obsolete_Illumina HiSeq 1500 comment: term is redundant, use GENEPIO:0100115, OBI:0003386 or EFO:0011027 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000041 name: obsolete_Illumina HiSeq 2000 comment: Term is redundant, please use OBI:0002001 or EFO:0004203 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000042 name: obsolete_Illumina HiSeq 2500 comment: Term is redundant, please use OBI:0002002 or EFO:0008565 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000043 name: obsolete_Illumina HiSeq 3000 comment: Term is redundant, please use OBI:0002048 or EFO:0008564 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000044 name: obsolete_Illumina HiSeq 4000 comment: Term is redundant, please use OBI:0002049 or EFO:0008563 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000045 name: obsolete_Illumina NextSeq 500 comment: Term is redundant, please use EFO:0009173 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000046 name: obsolete_Illumina NextSeq 550 comment: Term is redundant, please use GENEPIO:0100128 or EFO:0008566 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000047 name: obsolete_Illumina HiSeq X Ten comment: Term is redundant, please use GENEPIO:0100113 or OBI:0002129 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000048 name: obsolete_Illumina HiSeq X Five comment: Term is redundant, please use GENEPIO:0100112 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000049 name: obsolete_Illumina NovaSeq 6000 comment: Term is redundant, please use GENEPIO:0100123, OBI:0002630 or EFO:0008637 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000050 name: obsolete_Illumina MiSeq comment: Redundant term, please use EFO:0004205 instead is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000051 name: obsolete_Illumina HiScanSQ comment: Redundant term, please use GENEPIO:0100109 instead is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000052 name: obsolete_Illumina MiniSeq comment: Term is redundant, please use GENEPIO:0100124, OBI:0003114 or EFO:0008636 instead. is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000053 name: obsolete_Illumina iSeq 100 comment: Term is redundant, please use GENEPIO:0100121 or EFO:0008635 instead is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000054 name: obsolete_BGISEQ-500 comment: Term is redundant, please use NCIT:C146812 or GENEPIO:0100145 instead is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000055 name: obsolete_DNBSEQ-G400 comment: Term is redundant, please use GENEPIO:0100148 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000056 name: obsolete_DNBSEQ-T7 comment: Term is redundant, please use GENEPIO:0100147 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000057 name: obsolete_DNBSEQ-G50 comment: Term is redundant, please use GENEPIO:0100150 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000058 name: obsolete_Ion Torrent PGM comment: Term is redundant, please use GENEPIO:0100136 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000059 name: obsolete_Ion Torrent Proton comment: Term is redundant, please use GENEPIO:0100137 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000060 name: obsolete_Ion Torrent S5 comment: Term is redundant, please use GENEPIO:0100139 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000061 name: obsolete_Ion Torrent S5 XL comment: Term is redundant, please use GENEPIO:0100138 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000062 name: obsolete_PacBio RS comment: Term is redundant, please use GENEPIO:0100131 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000063 name: obsolete_PacBio RS II comment: Term is redundant, please use OBI:0002012 or EFO:0008631 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000064 name: obsolete_Sequel comment: Term is redundant, please use GENEPIO:0100133 or OBI:0002632 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000065 name: obsolete_Sequel II comment: Term is redundant, please use GENEPIO:0100134 or OBI:0002633 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000066 name: obsolete_AB SOLiD System 2.0 comment: Term is redundant, please use GENEPIO:0001932 or EFO:0004442 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000067 name: obsolete_AB SOLiD System 3.0 comment: Term is redundant, please use EFO:0004439 or GENEPIO:0001933 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000068 name: obsolete_AB SOLiD 3 Plus System comment: Term is redundant, please use OBI:0002007. is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000069 name: obsolete_AB SOLiD 4 System comment: Term is redundant, please use EFO:0004438 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000070 name: obsolete_AB SOLiD 4hq System comment: Term is redundant, please use GENEPIO:0001928 or EFO:0004441 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000071 name: obsolete_AB SOLiD PI System comment: Term is redundant, please use EFO:0004437 or GENEPIO:0001931 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000072 name: AB 5500 Genetic Analyzer is_a: DPBO:0000040 ! next generation sequencing instrument model property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string [Term] id: DPBO:1000073 name: AB 5500xl Genetic Analyzer is_a: DPBO:0000040 ! next generation sequencing instrument model property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string [Term] id: DPBO:1000074 name: AB 5500xl-W Genetic Analysis System is_a: DPBO:0000040 ! next generation sequencing instrument model property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string [Term] id: DPBO:1000075 name: obsolete_454 GS comment: Term is redundant, please use EFO:0004431 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000076 name: obsolete_454 GS 20 comment: Term is redundant, please use EFO:0004206 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000077 name: obsolete_454 GS FLX comment: Term is redundant, please use EFO:0004432 or OBI:0000702 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000078 name: 454 GS FLX+ is_a: DPBO:0000040 ! next generation sequencing instrument model property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string [Term] id: DPBO:1000079 name: obsolete_454 GS Junior comment: Term is redundant, please use EFO:0004434 or GENEPIO:0001938 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000080 name: obsolete_454 GS FLX Titanium comment: Term is redundant, please use EFO:0004433 or GENEPIO:0001936 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000081 name: obsolete_Complete Genomics comment: Term is redundant, please use NCIT:C146815 or GENEPIO:0001924 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000082 name: obsolete_Helicos HeliScope comment: Term is redundant, please use OBI:0000717 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000083 name: obsolete_GridION comment: Term is redundant, please use GENEPIO:0100141 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000084 name: obsolete_MinION comment: Term is redundant, please use OBI:0002750, EFO:0008632 or GENEPIO:0100142 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000085 name: obsolete_PromethION comment: Term is redundant, please use OBI:0002752 or GENEPIO:0100143 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_instrument model" xsd:string is_obsolete: true [Term] id: DPBO:1000086 name: obsolete_single def: "placeholder def of single" [] comment: Deprecated, please use DPBO:0000086 "single-end" instead is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "RAW FILES_single or paired-end" xsd:string is_obsolete: true [Term] id: DPBO:1000087 name: paired-end def: "A library layout which describes that both ends of the library fragment are sequenced" [] comment: Adapted from http://purl.obolibrary.org/obo/FBcv_0003221 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:1000088 name: obsolete_total RNA def: "placeholder def of total RNA" [] comment: term is redundant, please use EFO:0004964 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "SAMPLES_molecule" xsd:string is_obsolete: true [Term] id: DPBO:1000089 name: obsolete_polyA RNA def: "placeholder def of polyA RNA" [] comment: Term is redundant, please use OBI_0000869 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "SAMPLES_molecule" xsd:string [Term] id: DPBO:1000090 name: obsolete_cytoplasmic RNA def: "placeholder def of cytoplasmic RNA" [] comment: Term is redundant, please use NCIT:C84512 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "SAMPLES_molecule" xsd:string is_obsolete: true [Term] id: DPBO:1000091 name: obsolete_nuclear RNA def: "placeholder def of nuclear RNA" [] comment: Term is redundant. Please use EFO:0030052 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "SAMPLES_molecule" xsd:string is_obsolete: true [Term] id: DPBO:1000092 name: obsolete_genomic DNA def: "placeholder def of genomic DNA" [] comment: Term is redundant, please use BAO:0000316 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "SAMPLES_molecule" xsd:string is_obsolete: true [Term] id: DPBO:1000093 name: obsolete_protein def: "placeholder def of protein" [] comment: Term is redundant, please use CHEBI:36080 is_a: ObsoleteClass ! Obsolete Class property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "SAMPLES_molecule" xsd:string is_obsolete: true [Term] id: DPBO:1000094 name: other def: "Any other bio entity that can be characterized by high-throuput sequencing." [] is_a: DPBO:0000012 ! bio entity is_a: NCIT:C63816 property_value: ER_target "GEO_RNASEQ" xsd:string property_value: ER_target_term "SAMPLES_molecule" xsd:string [Term] id: DPBO:1000095 name: endpoint repository def: "Parent term to collect endpoint repositories (ER)." [] comment: "For an overview of relevant repositories, check https://www.re3data.org or https://fairsharing.org" [Term] id: DPBO:1000096 name: GEO def: "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." [] comment: https://www.ncbi.nlm.nih.gov/geo/ is_a: DPBO:1000095 ! endpoint repository disjoint_from: DPBO:1000097 ! MetaboLights [Term] id: DPBO:1000097 name: MetaboLights def: "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." [] comment: https://www.ebi.ac.uk/metabolights/ is_a: DPBO:1000095 ! endpoint repository [Term] id: DPBO:1000098 name: PRIDE def: "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." [] comment: https://www.ebi.ac.uk/pride/ is_a: DPBO:1000095 ! endpoint repository [Term] id: DPBO:1000099 name: GEO_RNAseq def: "Parent term to collect terms required for RNASeq submission to GEO" [] is_a: DPBO:1000096 ! GEO disjoint_from: DPBO:1000100 ! GEO_microarray [Term] id: DPBO:1000100 name: GEO_microarray def: "Parent term to collect terms required for microarray submission to GEO" [] is_a: DPBO:1000096 ! GEO [Term] id: DPBO:1000101 name: obsolete_well def: "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." [] comment: term is redundant, please use REPR:Well xref: OME:Well is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000102 name: well Number def: "The number of a well in a well plate." [] [Term] id: DPBO:1000103 name: siRNA identifier def: "The identifier of a siRNA from a reagent library." [] [Term] id: DPBO:1000104 name: obsolete_compound name def: "Unique name of a chemical compound." [] comment: term is redundant, please use data:0990 xref: EDAM:data_0990 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000105 name: obsolete_compound identifier def: "Identifier of an entry from a database of chemicals." [] comment: term is redundant, please use data:1086 xref: data:1086 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000106 name: compound class def: "The class a compound belongs to, defined by its biological function or the chemical property." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000108 name: obsolete_gene identifier def: "A unique gene name within a specific repository, database, or collection." [] xref: NCIT:C48664 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000109 name: sense sequence def: "The sequence of the sense strand." [] comment: "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" [Term] id: DPBO:1000110 name: antisense sequence def: "The sequence of the antisense strand." [] comment: "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" [Term] id: DPBO:1000111 name: obsolete_control type def: "A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated." [] comment: term is redundant, please use NCIT:C49647 xref: NCIT:C49647 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000112 name: quality control def: "Result of quality control. This can be: pass/fail, or other information such as: no cells" [] comment: "Definition according to IDR" [Term] id: DPBO:1000113 name: channel def: "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." [] comment: "Needed for imaging templates. Definition form IDR" [Term] id: DPBO:1000114 name: screen technology type def: "The type of a high content screening experiment like RNAi screen or antibody screen." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000116 name: library version def: "Version of a reagent library used e.g. in high content screening." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000117 name: obsolete_antibody def: "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." [] comment: term is redundant, please use NCIT:C16295 xref: NCIT:C16295 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000118 name: obsolete_cover slip def: "A thin flat piece of transparent material that is placed over a specimen for viewing with a microscope." [] comment: use NCIT:C126370 xref: NCIT:C126370 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000120 name: image file path comment: "Needed for imaging templates" [Term] id: DPBO:1000121 name: target compartment def: "Compartment of interest in the prepared sample" [] comment: "Needed for imaging templates" [Term] id: DPBO:1000122 name: obsolete_imaging software name def: "The name of the software program to capture and/or process imaging data." [] comment: false xref: NCIT:C175898 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000123 name: imaging software version def: "The version of the software program to capture and/or process imaging data." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000124 name: imaging software settings def: "The used settings in the software program to capture and/or process imaging data." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000125 name: microscope filter def: "Channel the image was taken with." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000126 name: dataset name comment: "Needed for imaging templates" xref: dwc:datasetName [Term] id: DPBO:1000127 name: obsolete_assay name def: "The name of the assay." [] xref: NCIT:C178857 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000128 name: image processing software def: "Software used for the processing of microscopy images like for adaption of contrast or stacking." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000129 name: image data analysis software def: "Software used to analyze data extracted from microscopy images." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000130 name: image processing software parameters def: "Applied settings of the software used for the processing of microscopy images" [] comment: "Needed for imaging templates" [Term] id: DPBO:1000131 name: feature extraction software def: "Software used for the extraction of features from microscopy images." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000133 name: feature extraction strategy def: "Description of the approach to extract features from microscopy images." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000135 name: use of image def: "Whether a microscopy image is intended to be used illustrational or analytically by deriving values from it." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000136 name: reagent design genome reference version def: "The gene annotation build the siRNAs for a high content screen library were mapped to." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000137 name: control specification def: "additional information about the quality control in high content screening studies e.g. 'checks for transfection', 'gives strong phenotype'" [] comment: "Needed for imaging templates. Definition from IDR." [Term] id: DPBO:1000138 name: quality control comments def: "additional information why a quality control passed or failed'" [] comment: "Needed for imaging templates. Definition from IDR." [Term] id: DPBO:1000139 name: microscopy study type def: "Type of an imaging study." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000140 name: magnification def: "The magnification of a microscopy image" [] comment: "Needed for imaging templates" [Term] id: DPBO:1000141 name: image dimensionality def: "The sizes along the axis of the XYZCT dimensions in a microscopy image." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000142 name: obsolete_objective def: "The microscope's objective lens." [] comment: use OME:objective xref: OME:Objective is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: DPBO:1000143 name: microscopy sample preparation def: "How a sample was further prepared for microscopy." [] xref: MS:1000831 [Term] id: DPBO:1000144 name: material fixation def: "Plant material fixation on a microscopy slide." [] comment: "Needed for imaging templates" [Term] id: DPBO:1000145 name: prepared organism part def: "The part of an organism that has been prepared for an experiment" [] comment: "Needed for imaging templates" [Term] id: DPBO:1000146 name: obsolete_strain def: "A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics." [] comment: use EFO:0005135 xref: EFO:0005135 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000147 name: obsolete_container def: "A device that can be used to restrict the location of material entities over time" [] comment: term is redundant, please use OBI:0000967 xref: OBI:0000967 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000148 name: jar def: "A wide-mouthed cylindrical container made of glass or pottery and typically having a lid" [] is_a: OBI:0000967 ! container created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000149 name: plate def: "A flat dish, typically circular" [] is_a: OBI:0000967 ! container created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000150 name: obsolete_contamination def: "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]" [] xref: PATO:0015031 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000151 name: axenic def: "Free from other living organisms" [] is_a: PATO:0015031 ! contamination created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000152 name: laboratory strain def: "Latest laboratory cultivated the strain. Who sent the strain to your laboratory" [] is_a: EFO:0005135 ! strain created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000153 name: date def: "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." [] xref: dc:date created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000154 name: obsolete_volume def: "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]" [] comment: term is redundant, please use PATO:0000918 xref: PATO:0000918 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000155 name: culture medium volume def: "Volume of culture medium used to grow the organism" [] is_a: PATO:0000918 ! volume created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000156 name: obsolete_light def: "The photoperiod and type (e.g., natural, restricted wavelength) of light exposure." [] comment: term is redundant, please use EFO:0000568 xref: EFO:0000568 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000157 name: light quality def: "The spectral distribution of light (blue, green, red, far red and other light spectrums emitted from a light source)" [] comment: "close to the term http://purl.obolibrary.org/obo/PECO_0007154" is_a: EFO:0000568 ! light created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000158 name: obsolete_ratio def: "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." [UOB:LKSR] comment: term is redundant, please use UO:0010006 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000159 name: 260/280 ratio def: "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." [] comment: "Thermofisher NanoDrop https://tools.thermofisher.com/content/sfs/brochures/T123-NanoDrop-Lite-Interpretation-of-Nucleic-Acid-260-280-Ratios.pdf" is_a: UO:0010006 ! ratio created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000160 name: 260/230 ratio def: "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" [] comment: "Thermofisher NanoDrop https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf" is_a: UO:0010006 ! ratio created_by: \"Fabian Haas | ORCID:0000-0002-7711-5282\" [Term] id: DPBO:1000161 name: protocol type def: "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." [] 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)." created_by: Dominik Brilhaus [Term] id: DPBO:1000162 name: obsolete_growth protocol def: "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." [] comment: replaced term with EFO:0003789 xref: EFO:0003789 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000163 name: algae growth protocol def: "A protocol that provides instructions for growing algae." [] is_a: EFO:0003789 ! growth protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000164 name: plant growth protocol def: "A protocol that provides instructions for growing a plant cultivar." [] is_a: EFO:0003789 ! growth protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000165 name: microbe growth protocol def: "A protocol that provides instructions for growing a microbial sample." [] is_a: EFO:0003789 ! growth protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000166 name: bacteria growth protocol def: "A protocol that provides instructions for growing a bacterial sample." [] is_a: DPBO:1000165 ! microbe growth protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000167 name: yeast growth protocol def: "A protocol that provides instructions for growing yeast." [] is_a: DPBO:1000165 ! microbe growth protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000168 name: obsolete_treatment protocol def: "A protocol that aims to treat sample or collection of samples, organism or group of organisms, for some experimental purpose." [] comment: definition from http://www.ebi.ac.uk/efo/EFO_0003969. Term is redundant, please use EFO:0003969 xref: EFO:0003969 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000169 name: obsolete_sample collection protocol def: "A protocol that provides instructions on how a biological sample for an experiment was collected." [] comment: definition from http://www.ebi.ac.uk/efo/EFO_0005518. Term is redundant, please use EFO:0005518 xref: EFO:0005518 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000170 name: sample processing protocol def: "A protocol that details how a sample is processed or changed to prepare it for analysis." [] is_a: DPBO:1000161 ! protocol type created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000171 name: obsolete_extraction protocol def: "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" [] comment: definition taken heavily from http://www.ebi.ac.uk/efo/EFO_0000490. Term is redundant, please use EFO:0000490 xref: EFO:0000490 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000172 name: obsolete_DNA extraction protocol def: "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." [] comment: definition taken from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425773/. Term is redundant, please use EFO:0022384. is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000173 name: obsolete_RNA extraction protocol def: "A protocol that describes the steps for removing and purifying DNA from a biological sample" [] comment: term is redundant, please use EFO:0010959 xref: EFO:0010959 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000174 name: obsolete_protein extraction protocol def: "A protocol that describes how to isolate protein from a tissue, cell culture or other biological sample." [] comment: term is redundant, please use EFO:0022383 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000175 name: obsolete_metabolite extraction protocol def: "A protocol that describes the step by step process for removing metabolites from a biological sample." [] is_a: ObsoleteClass ! Obsolete Class created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 xref: EFO:0022981 comment: term is redundant, please use EFO:0022981 is_obsolete: true [Term] id: DPBO:1000176 name: assay pre-processing protocol def: "A protocol that describes the steps to be taken to transform a sample before an assay can be performed" [] is_a: DPBO:1000161 ! protocol type created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-401 [Term] id: DPBO:1000177 name: assay protocol def: "A protocol that describes how to perform an assay." [] is_a: DPBO:1000161 ! protocol type created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-401 [Term] id: DPBO:1000178 name: data processing protocol def: "A protocol that describes the operations performed on data by a computer in order to retrieve, transform, or classify information." [] comment: definition heavily based on http://purl.obolibrary.org/obo/NCIT_C47925 is_a: DPBO:1000161 ! protocol type created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-401 [Term] id: DPBO:1000179 name: data filtering protocol def: "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" [] is_a: DPBO:1000178 ! data processing protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-401 [Term] id: DPBO:1000180 name: data transformation protocol def: "A protocol that describes the operations performed to convert data from one format, structure, or value into another." [] is_a: DPBO:1000178 ! data processing protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-401 [Term] id: DPBO:1000181 name: data extraction protocol def: "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." [] is_a: DPBO:1000178 ! data processing protocol created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-401 [Term] id: DPBO:1000182 name: replicate group def: "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 [Term] id: DPBO:1000183 name: biological replicate group def: "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." [] is_a: DPBO:1000182 ! replicate group created_by: Kevin Schneider | ORCID: 0000-0002-2198-5262 [Term] id: DPBO:1000184 name: technical replicate group def: "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." [] is_a: DPBO:1000182 ! replicate group created_by: Kevin Schneider | ORCID: 0000-0002-2198-526 [Term] id: DPBO:1000185 name: incubation time def: "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. " [] xref: BAO:0002833 created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-401 [Term] id: DPBO:1000186 name: Zeiss Axiovert def: "Axiovert series, inverse microscope" [] is_a: OBI:0400169 ! microscope created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000187 name: Olympus SZX7 (Bino) def: "binocular, stereo microscope" [] is_a: OBI:0400169 ! microscope created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000188 name: Zeiss AxioCam MRc5 def: "camera" [] is_a: OBI:0001048 ! digital camera created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000189 name: 01 def: "white" [] is_a: DPBO:1000125 ! microscope filter created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000190 name: 01 def: "white" [] is_a: DPBO:1000125 ! microscope filter created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000191 name: DIC def: "differential interference contrast" [] is_a: DPBO:1000125 ! microscope filter created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000192 name: 09 def: "yellow" [] is_a: DPBO:1000125 ! microscope filter created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000193 name: 10 def: "green" [] is_a: DPBO:1000125 ! microscope filter created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000194 name: 15 def: "red" [] is_a: DPBO:1000125 ! microscope filter created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000195 name: Zeiss ZEN 3.5 (blue edition) def: "software controlling imaging systems from ZEISS." [] is_a: NCIT:C175898 ! Imaging Software Name created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000196 name: Thermo Scientific Menzel slides, 76 x 26 mm, 1,0 mm def: "microscope slide" [] is_a: OBI:0400170 ! microscope slide created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000197 name: VWR frosted edges, ground edges 90°, 76 x 26 mm, 0,8 - 1,0 mm def: "microscope slide" [] is_a: OBI:0400170 ! microscope slide created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000198 name: Roth SuperFrost® white, cut edges, 76 x 26 mm, 1,0 mm def: "microscope slide" [] is_a: OBI:0400170 ! microscope slide created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000199 name: Menzel, 24 x 50 mm, selected 0,17 +/- 0,01, strength 1,5 def: "cover slip" [] is_a: NCIT:C126370 ! Cover Slip created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000200 name: Roth, 24 x 50 mm, strength 1 def: "cover slip" [] is_a: NCIT:C126370 ! Cover Slip created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000201 name: VWR, 18 x 18 mm, 0,13 - 0,16 mm, strength 1,5 def: "cover slip" [] is_a: NCIT:C126370 ! Cover Slip created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000202 name: 0.8x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000203 name: 1x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000204 name: 1.25x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000205 name: 1.6x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000206 name: 2x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000207 name: 2.5x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000208 name: 3.2x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000209 name: 4x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000210 name: 5x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000211 name: 5.6x def: "magnification of Olympus SZX7 (Bino)" [] is_a: DPBO:1000140 ! magnification created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000212 name: Plan-Neofluar 5x/0.15 def: "objective lens of Zeiss Axioplan 2" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000213 name: Plan-Neofluar 10x/0.3 def: "objective lens of Zeiss Axioplan 2" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000214 name: Plan-Neofluar 20x/0.50 Ph2 def: "objective lens of Zeiss Axioplan 2" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000215 name: Plan-Neofluar 40x/0.75 def: "objective lens of Zeiss Axioplan 2" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000216 name: Plan-Neofluar 63x/1.25 Oil def: "objective lens of Zeiss Axioplan 2" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000217 name: Plan-Neofluar 100x/1.30 Oil def: "objective lens of Zeiss Axioplan 2" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000218 name: Achroplan 5x/012 def: "objective lens of Zeiss Axiovert" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000219 name: Achroplan 10x/0.25 Ph1 def: "objective lens of Zeiss Axiovert" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000220 name: Achroplan 20x/0.40 def: "objective lens of Zeiss Axiovert" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000221 name: Achroplan 40x/0.60 korr Ph2 def: "objective lens of Zeiss Axiovert" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000222 name: Achroplan 63x/0.75 korr Ph2 def: "objective lens of Zeiss Axiovert" [] is_a: NCIT:C181919 ! Objective Lens created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000223 name: Knop medium def: "A solution designed for the growth of plant cell, tissue and organ culture. " [] synonym: "Knop ME" RELATED [] synonym: "Knop solution" RELATED [] xref: PECO:0001074 is_a: OBI:0000079 ! culture medium created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000224 name: phenotyping def: "The activity or process of determining, analyzing, or predicting all or part of an organism's phenotype." [] comment: Definition from https://www.merriam-webster.com/dictionary/phenotyping created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000225 name: Zeiss Axioplan 2 def: "Axioplan series, imaging fluorescence microscope" [] 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) is_a: OBI:0400169 ! microscope created_by: Kathryn Dumschott | ORCID: 0000-0002-9905-4011 [Term] id: DPBO:1000226 name: student helper def: "A role of a student in a research project which is acknowledged in papers." [] xref: AGRO:00000374 created_by: Andrea Schrader | 0000-0002-3879-7057 [Term] id: DPBO:1000227 name: plant work helper def: "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." [] comment: Suggested by Andrea Schrader | 0000-0002-3879-7057 [Term] id: DPBO:1000228 name: biolistic transformation def: "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." [] comment: Suggested by Andrea Schrader | 0000-0002-3879-7057 synonym: "particle bombardment" EXACT [] [Term] id: DPBO:1000229 name: bioimaging protocol def: "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/)" [] comment: Suggested by Andrea Schrader | 0000-0002-3879-7057 [Term] id: DPBO:1000230 name: transformation protocol def: "A protocol describing a transformation method of cell, tissues or organisms." [] comment: Suggested by Andrea Schrader | 0000-0002-3879-7057 [Term] id: DPBO:1000231 name: Zeiss Axio Observer Z1 def: "Inverted fluorescence microscope" [] comment: https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research.html is_a: OBI:0400169 ! microscope created_by: suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 [Term] id: DPBO:1000232 name: Zeiss Imager M1 def: "Upright fluorescence microscope" [] comment: https://microscopy.ucsf.edu/instruments/zeiss-axioimager-m1, https://profcontrol.de/Zeiss-Axio-Imager-M1m-Fluorescence-DIC-Microscope-Fluoreszenz-Mikroskop is_a: OBI:0400169 ! microscope created_by: suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 [Term] id: DPBO:1000233 name: MG-RAST accession number field def: "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." [] comment: https://www.mg-rast.org/mgmain.html?mgpage=analysis created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000234 name: assembly software def: "Tool/Software used for assembly." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000058/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000235 name: assembly parameters def: "Parameters used for assembly." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000058/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000236 name: genome assembly quality def: "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." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000056/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000237 name: binning software def: "Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000078/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000238 name: binning parameters def: "The parameters that have been applied during the extraction of genomes from metagenomic datasets." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000077/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000239 name: taxonomic identity marker def: "The phylogenetic marker(s) used to assign an organism name to the SAG or MAG." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000053/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000240 name: completeness software def: "Tools used for completion estimate, i.e. checkm, anvi'o, busco." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000070/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000241 name: completeness score def: "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." [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000069/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000242 name: contamination score def: "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" [] comment: https://genomicsstandardsconsortium.github.io/mixs/0000072/ created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000243 name: ENA accession field def: "A data field which describes the ENA experiment accession assigned to the sequencing data." [] created_by: Angela Kranz | ORCID: 0000-0002-8000-0400 [Term] id: DPBO:1000244 name: IonQuant def: "IonQuant is a software tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as a stand-alone tool or it can be run within [FragPipe] (http://fragpipe.nesvilab.org/) computational platform." [] is_a: MS:1003429 ! FragPipe is_a: MS:1001139 ! quantitation software name [Term] id: DPBO:1000245 name: MSBooster def: "MSBooster is a tool for incorporating spectral libary predictions into peptide-spectrum match (PSM) rescoring in bottom-up tandem liquid chromatography mass spectrometry proteomics data. It is incorporated into [FragPipe] (https://fragpipe.nesvilab.org/)" [] is_a: MS:1003429 ! FragPipe [Term] id: DPBO:1000246 name: infection def: "To implant pathogenic microbes or infective materials. Special case of NCIT_C68774" [] is_a: NCIT:C68774 ! inoculation created_by: Ursula Eberhardt | ORCID: 0000-0003-1221-7074 [Term] id: DPBO:1000247 name: days post infection def: "Abbreviated dpi or DPI. Unit to describe the length of the period after an infection or inoculation treatment." [] synonym: "days post-infection" EXACT [] synonym: "days post inoculation" NARROW [] synonym: "days post-inoculation" NARROW [] created_by: Ursula Eberhardt | ORCID: 0000-0003-1221-7074 [Term] id: DPBO:1000248 name: apoplast extraction def: "Extraction of the soluble apoplast constituents, in particular, apoplastic proteins." [] is_a: OBI:0302884 ! extraction created_by: Ursula Eberhardt | ORCID: 0000-0003-1221-7074 [Term] id: DPBO:1000249 name: apoplast extraction solution def: "Solution used to extract apoplast proteins. Examples are ultra pure water, sorbitol or NaCl solutions." [] synonym: "apoplast infiltration solution" EXACT [] comment: see https://doi.org/10.1186/1746-4811-7-48 created_by: Ursula Eberhardt | ORCID: 0000-0003-1221-7074 [Term] id: DPBO:1000250 name: plant phenotyping protocol def: "A protocol that provides instructions for phenotyping a plant sample." is_a: DPBO:1000161 ! protocol type created_by: Manuel Feser | ORCID: 0000-0001-6546-1818 [Term] id: MS:1003429 name: FragPipe [Term] id: MS:1001139 name: quantitation software name [Term] id: ECSO:00000517 name: Soil Moisture Percentage def: "wetness caused by water" [] [Term] id: EDAM:0593 name: NMR def: "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." [] synonym: "Heteronuclear Overhauser Effect Spectroscopy" NARROW [] synonym: "HOESY" NARROW [] synonym: "NMR spectroscopy" EXACT [] synonym: "NOESY" NARROW [] synonym: "Nuclear magnetic resonance spectroscopy" EXACT [] synonym: "Nuclear Overhauser Effect Spectroscopy" NARROW [] synonym: "ROESY" NARROW [] synonym: "Rotational Frame Nuclear Overhauser Effect Spectroscopy" NARROW [] synonym: "Spectroscopy" BROAD [] [Term] id: EDAM:1930 name: FASTQ def: "FASTQ short read format ignoring quality scores." [] is_a: DPBO:0000021 ! raw data file format [Term] id: EFO:0000434 name: ecotype def: "A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler" [] is_a: DPBO:0000037 ! subspecific taxonomic rank [Term] id: EFO:0000490 name: extraction protocol is_a: DPBO:1000170 ! sample processing protocol [Term] id: EFO:0000568 name: light [Term] id: EFO:0001032 name: transcription profiling is_a: AFR:0002229 ! experiment type [Term] id: EFO:0002692 name: ChIP-seq def: "ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0002694 name: experimental process def: "A process performed as part of an experiment or wider study, i.e. intentionally designed." [] [Term] id: EFO:0003741 name: pooled clone sequencing def: "An assay in which DNA is the input molecule derived from pooled clones (for example BACs and Fosmids) is sequenced using high throughput technology using shotgun methodology." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003748 name: MRE-seq def: "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" [] synonym: "Methylation-Sensitive Restriction Enzyme sequencing" EXACT [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003749 name: MeDIP-seq def: "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." [] synonym: "Methylated DNA Immunoprecipitation sequencing" EXACT [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003750 name: MBD-seq def: "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." [] synonym: "methyl binding domain sequencing" EXACT [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003751 name: MNase-seq def: "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." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003753 name: Bisulfite-seq def: "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." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003754 name: EST sequencing def: "An assay in which RNA derived from an EST is sequenced." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003755 name: FL-cDNA def: "An assay in which RNA derived from a full length cDNA template is sequenced." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0003789 name: growth protocol is_a: DPBO:1000161 ! protocol type [Term] id: EFO:0003969 name: treatment protocol is_a: DPBO:1000161 ! protocol type [Term] id: EFO:0004160 name: whole chromosome random sequencing is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0004161 name: finishing sequencing assay is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0004202 name: Illumina Genome Analyzer IIx def: "A DNA sequencer developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004203 name: Illumina HiSeq 2000 def: "The Illumina HiSeq 2000 is a sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004205 name: Illumina MiSeq def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004206 name: 454 GS 20 sequencer def: "The 454 GS 20 is a GS20 high-throughput sequencing machine developed by 454 Life Sciences." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004428 name: FAIRE-seq def: "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." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0004431 name: 454 GS sequencer def: "The 454 GS is a GS high-throughput sequencing machine developed by 454 Life Sciences." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004432 name: 454 GS FLX sequencer is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004433 name: 454 GS FLX Titanium sequencer def: "The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004434 name: 454 GS Junior sequencer def: "The 454 GS Junior is a GS high-throughput sequencing machine developed by 454 Life Sciences." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004437 name: AB SOLiD PI System is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004438 name: AB SOLiD 4 System is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004439 name: AB SOLiD System 3.0 is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004441 name: AB SOLiD 4hq System is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004442 name: AB SOLiD System 2.0 is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0004964 name: total RNA def: "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." [] is_a: DPBO:0000012 ! bio entity is_a: NCIT:C63816 [Term] id: EFO:0004998 name: carbohydrate measurement def: "The quantification of some carbohydrate, typically obtained from an individual with the intention of using the measurement in some diagnostic process." [] [Term] id: EFO:0005135 name: strain def: "A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics." [] [Term] id: EFO:0005136 name: cultivar def: "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." [] is_a: DPBO:0000037 ! subspecific taxonomic rank [Term] id: EFO:0005310 name: RIP-seq def: "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." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0005518 name: sample collection protocol is_a: DPBO:1000161 ! protocol type [Term] id: EFO:0007045 name: ATAC-seq def: "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." [] is_a: GENEPIO:0001973 ! library strategy property_value: definition:citation "http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html" xsd:string [Term] id: EFO:0007693 name: Hi-C def: "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." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0008563 name: Illumina HiSeq 4000 def: "The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008564 name: Illumina HiSeq 3000 def: "The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008565 name: Illumina HiSeq 2500 def: "The Illumina HiSeq 2500 is a sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008566 name: Illumina NextSeq 550 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008631 name: PacBio RS II def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008632 name: ONT MinION def: "The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008635 name: Illumina iSeq 100 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008636 name: Illumina MiniSeq def: "The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008637 name: Illumina NovaSeq 6000 def: "The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0008684 name: Chia-PET def: "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." [] synonym: "chromatin interaction analysis by paired-end tag sequencing" EXACT [] xref: PMID:20181287 is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0008686 name: ChIPmentation is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0008800 name: MDA def: "Multiple displacement amplification (MDA)." [] is_a: GENEPIO:0001940 ! library selection [Term] id: EFO:0008891 name: Ribo-seq def: "Ribosome profiling (also named ribosome footprinting) that uses specialized messenger RNA (mRNA) sequencing to determine which mRNAs are being actively translated. It produces a “global snapshot” of all the ribosomes active in a cell at a particular moment, known as a translatome." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0008896 name: RNA-Seq def: "RNA-seq is a method that involves purifying RNA and making cDNA, followed by high-throughput sequencing." [] xref: PMID:18516045 is_a: GENEPIO:0001973 ! library strategy property_value: IAO:0000117 "Dani Welter" xsd:string [Term] id: EFO:0008950 name: ssRNA-seq def: "Strand-specific RNA-seq (ssRNA-seq)" [] xref: PMID:19609351 is_a: GENEPIO:0001973 ! library strategy property_value: IAO:0000117 "Dani Welter" xsd:string [Term] id: EFO:0008973 name: TN-Seq def: "Transposon sequencing (TN-Seq)" [] xref: PMID:23712350 is_a: GENEPIO:0001973 ! library strategy property_value: IAO:0000117 "Dani Welter" xsd:string [Term] id: EFO:0009173 name: Illumina NextSeq 500 def: "The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0009809 name: single nucleus RNA sequencing is_a: GENEPIO:0001973 ! library strategy [Term] id: EFO:0010959 name: RNA extraction protocol is_a: EFO:0000490 ! extraction protocol [Term] id: EFO:0011027 name: Illumina HiSeq 1500 def: "The Illumina HiSeq 1500 is a sequencing machine developed by Illumina." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: EFO:0022383 name: protein extraction protocol is_a: EFO:0000490 ! extraction protocol [Term] id: EFO:0022384 name: DNA extraction protocol is_a: EFO:0000490 ! extraction protocol [Term] id: EFO:0022981 name: metabolite extraction protocol def: "A protocol that describes the step by step process for isolating metabolites from a biological sample." [] is_a: EFO:0000490 ! extraction protocol [Term] id: EFO:0030052 name: nuclear RNA is_a: DPBO:0000012 ! bio entity is_a: NCIT:C63816 [Term] id: EFO:0920055 name: sample volume def: "The volume of a specimen that is taken or allocated for the purpose of conducting one or more assays or measurements." [] [Term] id: EFO:0920056 name: buffer volume def: "The volume of a buffer." [] [Term] id: ENVO:00000050 name: geyser def: "A hot spring that erupts periodically, ejecting a column of hot water and steam into the air." [] is_a: DPBO:0002008 ! environment (feature) [Term] id: ENVO:01000263 name: cold seep def: "A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor." [] is_a: DPBO:0002008 ! environment (feature) [Term] id: ENVO:01000403 name: tropical mangrove def: "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." [] is_a: DPBO:0002008 ! environment (feature) [Term] id: ERO:0001788 name: image processing technique def: "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." [] [Term] id: FOODON:00004331 name: plant material def: "Anatomical or other piece(s) or substance derived from one or more plants." [] [Term] id: GENEPIO:0000076 name: read length def: "Numbers of base pairs per read" [] [Term] id: GENEPIO:0000083 name: adapter sequence def: "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters." [] [Term] id: GENEPIO:0000085 name: library preparation kit def: "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." [] [Term] id: GENEPIO:0000093 name: contig count def: "A contig count is the count of contigs that belong to a sequence assembly." [] [Term] id: GENEPIO:0000149 name: library preparation kit version def: "The version identifier of a packaged kit tailored for specific sequencing workflows." [] [Term] id: GENEPIO:0001142 name: SRA accession field def: "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)." [] 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. synonym: "Sequence Read Archive accession field" EXACT [] synonym: "Sequence Read Archive accession slot" EXACT [] synonym: "SRA accession slot" EXACT [] property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-1107-9135 " xsd:string property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-8844-9165 " xsd:string property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-9578-0788 " xsd:string property_value: http://purl.org/dc/terms/date "2021-04-24T00:42:14Z" xsd:dateTime property_value: IAO:0000112 "SRR11177792" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000118 "SRA accession" xsd:string property_value: IAO:0000118 "SRA_accession" xsd:string [Term] id: GENEPIO:0001153 name: sample collected by def: "The name of the agency that collected the original sample." [] xref: NCIT:C45262 [Term] id: GENEPIO:0001174 name: sample collection date def: "The date on which the sample was collected" [] xref: NCIT:C81286 [Term] id: GENEPIO:0001561 name: assembly genome size def: "The assembly genome size is the sum of all lengths of a sequence assembly's contigs." [] comment: As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. " [Term] id: GENEPIO:0001681 name: laboratory sequencing datum [Term] id: GENEPIO:0001924 name: Complete Genomics platform def: "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).'" [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0001928 name: SOLiD 4hq System is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0001931 name: SOLiD PI System is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0001932 name: SOLiD System 2.0 is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0001933 name: SOLiD System 3.0 is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0001936 name: 454 Genome Sequencer FLX Titanium is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0001938 name: 454 Genome Sequencer Junior is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0001940 name: library selection def: "Whether any method was used to select for or against, enrich, or screen the material being sequenced." [] xref: NCBI SRA: LIBRARY_SELECTION is_a: GENEPIO:0001681 ! laboratory sequencing datum property_value: GENEPIO:0000005 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001941 name: 5-methylcytidine antibody method def: "Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C)." [] xref: NCBI SRA: 5-methylcytidine antibody is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001942 name: CAGE method def: "Cap-analysis gene expression." [] xref: NCBI SRA: CAGE is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001943 name: CF-H method def: "Cot-filtered highly repetitive genomic DNA" [] xref: NCBI SRA: CF-H is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001944 name: CF-M method def: "Cot-filtered moderately repetitive genomic DNA" [] xref: NCBI SRA: CF-M is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001945 name: CF-S method def: "Cot-filtered single/low-copy genomic DNA" [] xref: NCBI SRA: CF-S is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001946 name: CF-T method def: "Cot-filtered theoretical single-copy genomic DNA" [] xref: NCBI SRA: CF-T is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001947 name: ChIP method def: "Chromatin immunoprecipitation" [] xref: NCBI SRA: ChIP is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001948 name: DNAse method def: "Deoxyribonuclease (MNase) digestion" [] xref: NCBI SRA: DNAse is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001949 name: HMPR method def: "Hypo-methylated partial restriction digest" [] xref: NCBI SRA: HMPR is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001950 name: Hybrid Selection method def: "Selection by hybridization in array or solution." [] xref: NCBI SRA: Hybrid Selection is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001951 name: MBD2 protein methyl-CpG binding domain method def: "Enrichment by methyl-CpG binding domain." [] xref: NCBI SRA: MBD2 protein methyl-CpG binding domain is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001952 name: MF method def: "Methyl Filtrated" [] xref: NCBI SRA: MF is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001953 name: MNase method def: "Micrococcal Nuclease (MNase) digestion" [] xref: NCBI SRA: MNase is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001954 name: MSLL method def: "Methylation Spanning Linking Library" [] xref: NCBI SRA: MSLL is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001955 name: PCR method def: "Source material was selected by designed primers." [] xref: NCBI SRA: PCR is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001956 name: RACE method def: "Rapid Amplification of cDNA Ends." [] xref: NCBI SRA: RACE is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001957 name: RANDOM PCR method def: "Source material was selected by randomly generated primers." [] xref: NCBI SRA: RANDOM PCR is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001958 name: RANDOM method def: "Random selection by shearing or other method." [] xref: NCBI SRA: RANDOM is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001959 name: RT-PCR method def: "Source material was selected by reverse transcription PCR" [] xref: NCBI SRA: RT-PCR is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001960 name: Reduced Representation method def: "Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling." [] xref: NCBI SRA: Reduced Representation is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001961 name: Restriction Digest method def: "DNA fractionation using restriction enzymes." [] xref: NCBI SRA: Restriction Digest is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001962 name: cDNA method def: "PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA." [] xref: NCBI SRA: cDNA is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001963 name: size fractionation method def: "Physical selection of size appropriate targets." [] xref: NCBI SRA: size fractionation is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001964 name: other library method def: "Other library enrichment, screening, or selection process." [] xref: NCBI SRA: other is_a: GENEPIO:0001940 ! library selection [Term] id: GENEPIO:0001965 name: library source def: "The library source specifies the type of source material that is being sequenced." [] is_a: GENEPIO:0001681 ! laboratory sequencing datum [Term] id: GENEPIO:0001966 name: genomic source def: "Genomic DNA (includes PCR products from genomic DNA)." [] xref: NCBI SRA: GENOMIC is_a: GENEPIO:0001965 ! library source property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001967 name: metagenomic source def: "Mixed material from metagenome." [] xref: NCBI SRA: METAGENOMIC is_a: GENEPIO:0001965 ! library source property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001968 name: metatranscriptomic source def: "Transcription products from community targets" [] xref: NCBI SRA: METATRANSCRIPTOMIC is_a: GENEPIO:0001965 ! library source property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001969 name: other library source def: "Other, unspecified, or unknown library source material." [] xref: NCBI SRA: OTHER is_a: GENEPIO:0001965 ! library source property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001970 name: synthetic source def: "Synthetic DNA." [] xref: NCBI SRA: SYNTHETIC is_a: GENEPIO:0001965 ! library source property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001971 name: transcriptomic source def: "Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries)." [] xref: NCBI SRA: TRANSCRIPTOMIC is_a: GENEPIO:0001965 ! library source property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001972 name: viral RNA source def: "Viral RNA." [] xref: NCBI SRA: VIRAL RNA is_a: GENEPIO:0001965 ! library source property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001973 name: library strategy def: "Sequencing technique intended for this library." [] is_a: GENEPIO:0001681 ! laboratory sequencing datum property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 "https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly" xsd:string [Term] id: GENEPIO:0100109 name: Illumina HiScanSQ def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100112 name: Illumina HiSeq X Five def: "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100113 name: Illumina HiSeq X Ten def: "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100115 name: Illumina HiSeq 1500 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100121 name: Illumina iSeq 100 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100123 name: Illumina NovaSeq 6000 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100124 name: Illumina MiniSeq def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100128 name: Illumina NextSeq 550 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100131 name: PacBio RS def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100133 name: PacBio Sequel def: "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" [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100134 name: PacBio Sequel II def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100136 name: Ion Torrent PGM def: "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100137 name: Ion Torrent Proton def: "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100138 name: Ion Torrent S5 XL def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100139 name: Ion Torrent S5 def: "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100141 name: Oxford Nanopore GridION def: "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" [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100142 name: Oxford Nanopore MinION def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100143 name: Oxford Nanopore PromethION def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100145 name: BGI Genomics BGISEQ-500 def: "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and 'DNA Nanoballs'." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100147 name: MGI DNBSEQ-T7 def: "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100148 name: MGI DNBSEQ-G400 def: "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100150 name: MGI DNBSEQ-G50 def: "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: GENEPIO:0100598 name: gene symbol def: "A sequence data which is the short name of a gene typically derived from the gene name." [] [Term] id: GEO:000000370 name: geographical entity [Term] id: GEO:000000372 name: geographical region def: "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." [] is_a: GEO:000000370 ! geographical entity property_value: IAO:0000117 "François Modave" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Matt Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] id: MCO:0000041 name: overexpression mutant def: "A mutant in which a gene ore genes are expressed at higher levels than the wild type." [] is_a: NCIT:C25360 ! mutant [Term] id: MCO:0000042 name: gene variant mutant def: "A mutant genotype in which one or more genes can have modifications (subtitutions, indels, partial truncations, etc), but they conserve functionality." [] is_a: NCIT:C25360 ! mutant [Term] id: MCO:0000051 name: knockout mutant def: "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." [] is_a: NCIT:C25360 ! mutant [Term] id: MCO:0000052 name: plasmid mutant def: "a mutant in which a foreign DNA sequence is introduced to cell in an extrachromosomal unit of replication." [] is_a: NCIT:C25360 ! mutant [Term] id: MCO:0000059 name: OD600 def: "An optical density that specifies the amount of light of 600 nm of wavelenght the bearer is able to transmit." [] is_a: MCO:0000077 ! optical density [Term] id: MCO:0000077 name: optical density def: "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." [] [Term] id: MCO:0000173 name: nutrient availability stress treatment is_a: MCO:0000866 ! treatment [Term] id: MCO:0000174 name: nutrient depletion treatment is_a: MCO:0000173 ! nutrient availability stress treatment [Term] id: MCO:0000177 name: iron depletion is_a: MCO:0000173 ! nutrient availability stress treatment [Term] id: MCO:0000178 name: carbon starvation is_a: MCO:0000173 ! nutrient availability stress treatment [Term] id: MCO:0000179 name: nitrogen starvation is_a: MCO:0000173 ! nutrient availability stress treatment [Term] id: MCO:0000180 name: phosphate starvation is_a: MCO:0000173 ! nutrient availability stress treatment [Term] id: MCO:0000851 name: genotype def: "A biological quality that inheres in specific organisms and that describes its total genetic content" [] [Term] id: MCO:0000866 name: treatment def: "A process in which the act is intended to modify or alter some other material entity." [] [Term] id: MI:0251 name: gene product def: "Reference of a protein object pointing to its genomic or nucleic acid sequence." [] [Term] id: MI:0507 name: tag def: "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." [PMID:14755292] [Term] id: MIAPPE:0049 name: Biological material preprocessing [Term] id: MIAPPE:0095 name: Growth facility [Term] id: MICRO:0001593 name: culture tube def: "A test tube used to culture a microorganism." is_a: DPBO:0002011 ! cultivation container [Term] id: MICRO:000052 name: LB medium def: "An organic-rich, liquid microbiological culture medium containing tryptone, yeast extract, and sodium chloride." is_a: OBI:0000079 ! culture medium [Term] id: MICRO:000067 name: microbiological culture medium def: "A culture medium used to select for, grow, and maintain prokaryotic microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) forms." is_a: OBI:0000079 ! culture medium [Term] id: MICRO:0000569 name: brain heart infusion medium def: "An organic-rich, liquid microbiological culture medium containing water infusions of calf brains and beef hearts, proteose peptone, and dextrose (i.e. D-glucose)." is_a: OBI:0000079 ! culture medium [Term] id: NCIT:C101294 name: Whole Genome Sequencing def: "A procedure that can determine the DNA sequence for nearly the entire genome of an individual." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C101295 name: Whole Exome Sequencing def: "A procedure that can determine the DNA sequence for all of the exons in an individual." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C103199 name: Organism Part is_a: DPBO:0000177 ! plant material type [Term] id: NCIT:C106053 name: NOMe-Seq is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C115935 name: Healthy def: "Having no significant health-related issues." [] is_a: DPBO:0000034 ! plant health state [Term] id: NCIT:C126370 name: Cover Slip [Term] id: NCIT:C13413 name: Whole Organism is_a: DPBO:0000177 ! plant material type [Term] id: NCIT:C146812 name: BGISEQ-500 Sequencing def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: NCIT:C146815 name: Complete Genomics Sequencing def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: NCIT:C146817 name: Illumina Sequencing def: "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." [] is_a: DPBO:0002006 ! sequencing method [Term] id: NCIT:C146818 name: Nanopore Sequencing def: "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." [] is_a: DPBO:0002006 ! sequencing method [Term] id: NCIT:C169106 name: Environmental DNA def: "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." [] [Term] id: NCIT:C175249 name: Diseased def: "An indication that an anatomic structure has detectable aberrations." [] is_a: DPBO:0000034 ! plant health state [Term] id: NCIT:C175898 name: Imaging Software Name def: "The name of the software program capture and/or process imaging data." [] {P378="NCI"} [Term] id: NCIT:C181919 name: Objective Lens [Term] id: NCIT:C204813 name: Amplicon Sequencing def: "A method for targeted DNA sequencing that uses oligonucleotide primers to amplify regions of interest, followed by next-generation sequencing (NGS) for deep coverage of the region." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C204814 name: Clone-Based Sequencing def: "DNA sequencing where a target is cloned into a vector, physically mapped, and then shotgun sequenced." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C204815 name: Clone End Sequencing def: "A DNA sequencing strategy where a single read is initiated from one or both ends of a cloned DNA fragment." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C204816 name: Concatenated Tag Sequencing def: "A DNA sequencing strategy where a sequencing primer is chosen from a sequenced region in order to extend the sequenced region." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C204824 name: Restriction-site Associated DNA Sequencing def: "A type of genome-wide sampling sequencing that reduces the complexity of the genome by subsampling only at specific sites defined by restriction enzymes. It is able to identify, verify, and score markers simultaneously and to identify which markers derive from each site." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C204827 name: Synthetic Long-Read Sequencing def: "A sequence analysis method that uses sample processing and conventional sequencing to computationally reconstruct long reads from shorter sequencing reads." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C204828 name: Targeted Capture Sequencing def: "A method to enrich and sequence genomic regions of interest. Sequences are selected by oligonucleotides that are used to pull-down complementary DNA through hybridization." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C204829 name: Tethered Chromatin Conformation Capture Sequencing def: "A method for genome-wide mapping of chromatin interactions. It is similar to Hi-C sequencing except that the ligations are performed on a solid substrate rather than in solution. This enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes." [] is_a: GENEPIO:0001973 ! library strategy [Term] id: NCIT:C25360 name: mutant def: "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)." [] is_a: MCO:0000851 ! genotype [Term] id: NCIT:C449 name: DNA is_a: DPBO:0000177 ! plant material type [Term] id: NCIT:C68774 name: Inoculation [Term] id: NCIT:C45293 name: Species xref: MIAPPE:0043 xref: NCBITaxon:species [Term] id: NCIT:C49487 name: No def: "The non-affirmative response to a question." [] is_a: DPBO:0000070 ! 5' partial CDS is_a: DPBO:0000071 ! 3' partial CDS is_a: DPBO:0000075 ! 5' partial promoter is_a: DPBO:0000076 ! 3' partial promoter is_a: NCIT:C169106 ! Environmental DNA is_a: SO:0000568 ! bidirectional_promoter [Term] id: NCIT:C49488 name: Yes def: "The affirmative response to a question." [] is_a: DPBO:0000070 ! 5' partial CDS is_a: DPBO:0000071 ! 3' partial CDS is_a: DPBO:0000075 ! 5' partial promoter is_a: DPBO:0000076 ! 3' partial promoter is_a: NCIT:C169106 ! Environmental DNA is_a: SO:0000568 ! bidirectional_promoter [Term] id: NCIT:C62195 name: wild type def: "The naturally-occurring, normal, non-mutated version of a gene or genome." [] is_a: MCO:0000851 ! genotype [Term] id: NCIT:C62709 name: Variety def: "In botanical nomenclature, a rank below subspecies but above forma." [] is_a: DPBO:0000037 ! subspecific taxonomic rank [Term] id: NCIT:C63816 name: Molecule [Term] id: NCIT:C84512 name: Cytoplasmic RNA def: "RNA present in the cytoplasm. It is involved in the protein export process from the cells." [] is_a: DPBO:0000012 ! bio entity is_a: NCIT:C63816 [Term] id: NMR:1000019 name: sample pH is_a: NMR:1002011 ! pH [Term] id: NMR:1001954 name: NMR acquisition parameter def: "Parameters used in the NMR spectrometry acquisition." [] [Term] id: NMR:1002011 name: pH [Term] id: NMR:1400027 name: field strength def: "The intensity of an electric, magnetic, or other field." [] [Term] id: NMR:1400087 name: number of scans def: "The number of repeat scans performed and summed to create the data set for an NMR sample." [] is_a: NMR:1001954 ! NMR acquisition parameter [Term] id: NMR:1400253 name: magnetic field strength comment: defneed is_a: NMR:1400027 ! field strength [Term] id: OBI:0000079 name: culture medium def: "a processed material that provides the needed nourishment for microorganisms or cells grown in vitro." [] [Term] id: OBI:0000094 name: material processing def: "A planned process which results in physical changes in a specified input material" [] [Term] id: OBI:0000702 name: 454 Genome Sequencer FLX def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0000717 name: HeliScope Single Molecule Sequencer def: "Is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry" [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0000967 name: container [Term] id: OBI:0001048 name: digital camera def: "An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor." [] [Term] id: OBI:0001058 name: microplate reader def: "A measurement device that detects biological, chemical or physical events of samples in microtiter plates." [] [Term] id: OBI:0001076 name: incubator shaker is_a: DPBO:0000176 ! shaker type [Term] id: OBI:0001094 name: plate shaker is_a: DPBO:0000176 ! shaker type [Term] id: OBI:0002000 name: Genome Analyzer IIx def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002001 name: Illumina HiSeq 2000 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002002 name: Illumina HiSeq 2500 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002007 name: SOLiD 3 Plus System def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002012 name: PacBio RS II def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002022 name: Illumina HiSeq 1000 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002048 name: Illumina HiSeq 3000 def: "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002049 name: Illumina HiSeq 4000 def: "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002129 name: Illumina HiSeq X Ten def: "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002630 name: Illumina NovaSeq 6000 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002632 name: PacBio Sequel def: " 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" [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002633 name: PacBio Sequel II def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002750 name: Oxford Nanopore MinION def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0002752 name: Oxford Nanopore PromethION def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0003114 name: Illumina MiniSeq def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0003386 name: Illumina HiSeq 1500 def: "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." [] is_a: DPBO:0000040 ! next generation sequencing instrument model [Term] id: OBI:0100026 name: organism def: "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." [] xref: MIAPPE:0041 xref: NCIT:C14250 xref: NFDI4PSO:0000030 [Term] id: OBI:0302911 name: validation def: "A planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results" [] is_a: GENEPIO:0001973 ! library strategy [Term] id: OBI:0400169 name: microscope def: "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)" [] [Term] id: OBI:0400170 name: microscope slide def: "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" [] [Term] id: OBI_0000869 name: polyA RNA def: "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." [] is_a: DPBO:0000012 ! bio entity is_a: NCIT:C63816 [Term] id: OME:Objective name: obsolete_Objective comment: Class "Objective" is microscopes' objective lens. 19.02.2024: term has been deprecated, please use REPR:Objective is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: ObsoleteClass name: Obsolete Class [Term] id: PATO:0000918 name: volume [Term] id: PATO:0015031 name: contamination def: "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." [https://en.wikipedia.org/wiki/Contamination, https://github.com/pato-ontology/pato/issues/420] [Term] id: PECO:0001001 name: plant exposure def: "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." [] is_a: MIAPPE:0049 ! Biological material preprocessing [Term] id: PO:0009001 name: fruit is_a: DPBO:0000112 ! tissue [Term] id: PO:0009008 name: plant organ is_a: DPBO:0000112 ! tissue [Term] id: PO:0009010 name: seed is_a: DPBO:0000112 ! tissue [Term] id: PO:0025498 name: cardinal part of multi-tissue plant structure is_a: DPBO:0000112 ! tissue [Term] id: PRIDE:0000307 name: Quantification method namespace: PRIDE comment: Defines various quantification methods created_by: jg creation_date: 2011-07-22T09:15:33Z [Term] id: PRIDE:0000308 name: Gel-based quantification method namespace: PRIDE comment: Describes gel-based quantification methods is_a: PRIDE:0000307 ! Quantification method created_by: jg creation_date: 2011-07-22T09:16:24Z [Term] id: PRIDE:0000309 name: Gel-free quantification method namespace: PRIDE comment: Describes gel-free quantification methods is_a: PRIDE:0000307 ! Quantification method created_by: jg creation_date: 2011-07-22T09:17:03Z [Term] id: PRIDE:0000310 name: Isotope labeling namespace: PRIDE comment: Describes quantification techniques using isotope labeling is_a: PRIDE:0000309 ! Gel-free quantification method created_by: jg creation_date: 2011-07-22T09:17:34Z [Term] id: PRIDE:0000311 name: Selected Reaction Monitoring namespace: PRIDE comment: Describes quantification techniques based on selected / multiple reaction monitoring is_a: PRIDE:0000309 ! Gel-free quantification method created_by: jg creation_date: 2011-07-22T09:18:39Z [Term] id: PRIDE:0000312 name: Label free namespace: PRIDE comment: Describes label free quantification techniques. is_a: PRIDE:0000309 ! Gel-free quantification method created_by: jg creation_date: 2011-07-22T09:19:54Z [Term] id: PRIDE:0000313 name: iTRAQ namespace: PRIDE comment: Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level is_a: PRIDE:0000317 ! MS2 based isotope labeling created_by: jg creation_date: 2011-07-22T09:20:23Z [Term] id: PRIDE:0000314 name: TMT namespace: PRIDE comment: Tandem Mass Tag is a MS2 based isotope labeling quantification technique synonym: "Tandem Mass Tag" EXACT [] is_a: PRIDE:0000317 ! MS2 based isotope labeling created_by: jg creation_date: 2011-07-22T09:23:12Z [Term] id: PRIDE:0000315 name: SILAC namespace: PRIDE comment: Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification synonym: "Stable isotope labeling with amino acids in cell culture" EXACT [] is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:25:50Z [Term] id: PRIDE:0000316 name: MS1 based isotope labeling namespace: PRIDE comment: Describes isotope labeling quantification techniques detectable at MS1 level. is_a: PRIDE:0000310 ! Isotope labeling created_by: jg creation_date: 2011-07-22T09:28:05Z [Term] id: PRIDE:0000317 name: MS2 based isotope labeling namespace: PRIDE comment: Describes isotope labeling quantification techniques detectable at MS1 level. is_a: PRIDE:0000310 ! Isotope labeling created_by: jg creation_date: 2011-07-22T09:29:15Z [Term] id: PRIDE:0000318 name: 18O namespace: PRIDE comment: The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen. is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:30:12Z [Term] id: PRIDE:0000319 name: ICAT namespace: PRIDE comment: Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements. synonym: "Isotope-Coded Affinity Tags" EXACT [] is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:31:24Z [Term] id: PRIDE:0000320 name: AQUA namespace: PRIDE comment: AQUA is an isotope labeling based quantification technique that uses known peptides. is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:32:46Z [Term] id: PRIDE:0000321 name: ICPL namespace: PRIDE comment: Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses. synonym: "Isotope-coded protein label" EXACT [] is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:34:37Z [Term] id: PRIDE:0000322 name: emPAI namespace: PRIDE 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. synonym: "Exponentially Modified Protein Abundance Index" EXACT [] is_a: PRIDE:0000312 ! Label free created_by: jg creation_date: 2011-07-22T09:36:57Z [Term] id: PRIDE:0000323 name: TIC namespace: PRIDE comment: The Total Ion Current (TIC) can be measured or calculated in order to target specific ions. synonym: "Total Ion Current" EXACT [] is_a: PRIDE:0000312 ! Label free created_by: jg creation_date: 2011-07-22T09:38:17Z [Term] id: PRIDE:0000425 name: MS1 intensity based label-free quantification method namespace: PRIDE is_a: PRIDE:0000309 ! Gel-free quantification method created_by: rw [Term] id: PRIDE:0000427 name: Top-down proteomics namespace: PRIDE def: "A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics)" [PRIDE:PRIDE] is_a: PRIDE:0000426 is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000428 name: Bottom-up proteomics namespace: PRIDE def: "Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer" [PRIDE:PRIDE] is_a: PRIDE:0000426 is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000435 name: Peptide counting namespace: PRIDE comment: Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140. is_a: PRIDE:0000312 ! Label free created_by: acsordas [Term] id: PRIDE:0000436 name: Spectrum counting namespace: PRIDE comment: Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 is_a: PRIDE:0000312 ! Label free created_by: acsordas [Term] id: PRIDE:0000437 name: Protein Abundance Index - PAI namespace: PRIDE comment: Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140 is_a: PRIDE:0000312 ! Label free created_by: acsordas [Term] id: PRIDE:0000438 name: Spectrum count/molecular weight namespace: PRIDE comment: Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 is_a: PRIDE:0000312 ! Label free created_by: acsordas [Term] id: PRIDE:0000439 name: Spectral Abundance Factor - SAF namespace: PRIDE comment: The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 is_a: PRIDE:0000312 ! Label free created_by: acsordas [Term] id: PRIDE:0000440 name: Normalized Spectral Abundance Factor - NSAF namespace: PRIDE comment: Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 is_a: PRIDE:0000312 ! Label free created_by: acsordas [Term] id: PRIDE:0000441 name: APEX - Absolute Protein Expression namespace: PRIDE 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 is_a: PRIDE:0000312 ! Label free created_by: acsordas [Term] id: PRIDE:0000457 name: Experiment Type def: "Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method." [] [Term] id: PRIDE:0000458 name: Metaproteomics namespace: PRIDE def: "Studying all protein samples of diverse host environments like the human body, soil or sea water" [PRIDE:PRIDE] synonym: "Community Proteomics" EXACT [PRIDE] synonym: "Environmental Proteomics" RELATED [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000460 name: Proteogenomics namespace: PRIDE def: "Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000461 name: Multi-omics study namespace: PRIDE def: "Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000463 name: Parallel Reaction Monitoring (PRM) namespace: PRIDE def: "Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis." [PRIDE:PRIDE] is_a: PRIDE:0000311 ! Selected Reaction Monitoring [Term] id: PRIDE:0000513 name: Dimethyl Labeling namespace: PRIDE def: "Dimethyl Labeling (DML)" [PRIDE:PRIDE] is_a: PRIDE:0000310 ! Isotope labeling created_by: yperez creation_date: 2019-08-07T15:21:19Z [Term] id: PRIDE:0000543 name: Quality Control namespace: PRIDE def: "MS experiments conducted to control the quality of measurements" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000635 name: Affinity proteomics namespace: PRIDE def: "The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000649 name: Immunopeptidomics namespace: PRIDE def: "Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome" [PRIDE:PRIDE] is_a: PRIDE:0000426 is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000650 name: diaPASEF def: "Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825" [PRIDE:PRIDE] created_by: yperez [Term] id: PRIDE:0000665 name: Glycoproteomics namespace: PRIDE def: "Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PSO:0000013 name: plant disease def: "A biotic plant stress caused by exposure to an environment containing a biological stress agent." [] [Term] id: REPR:Objective name: Objective def: "The microscope's objective lens." [] [Term] id: REPR:Well name: Well def: "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." [] [Term] id: SCTID:71661000 name: cover slip preparation (procedure) [Term] id: SHARELOC:000006 name: target molecule [Term] id: SIO:000318 name: longitude def: "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." [] [Term] id: SIO:000319 name: latitude def: "Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane" [] [Term] id: SIO:001051 name: data analysis def: "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" [] [Term] id: SIO:010016 name: nucleic acid sequence def: "A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid." [] [Term] id: SNOMED:260707002 name: Method of extraction (attribute) [Term] id: SNOMED:260757005 name: Species of origin (attribute) [Term] id: SNOMED:430862008 name: Microscope slide mounting medium (substance) [Term] id: SNOMED:81547007 name: Vacuum (physical force) [Term] id: SO:0000141 name: terminator def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.insdc.org/files/feature_table.html] 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. synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:terminator" EXACT [] synonym: "terminator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" [Term] id: SO:0000167 name: promoter def: "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." [] [Term] id: SO:0000323 name: coding_start namespace: sequence def: "The first base to be translated into protein." [SO:ke] synonym: "coding start" EXACT [] synonym: "translation initiation site" EXACT [] synonym: "translation start" RELATED [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000327 name: coding_end namespace: sequence def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke] synonym: "coding end" EXACT [] synonym: "translation termination site" EXACT [] synonym: "translation_end" EXACT [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000568 name: bidirectional_promoter namespace: sequence def: "A promoter that can allow for transcription in both directions." [PMID:21601935, SO:ke] comment: Definition updated in Aug 2020 by Dave Sant. synonym: "bidirectional promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0000851 name: CDS_region def: "A region of a CDS." [] [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." [] xref: DPBO:0000035 is_a: DPBO:0000095 ! R package [Term] id: UO:0000000 name: unit [Term] id: UO:0000048 name: acceleration unit namespace: unit.ontology def: "A unit which is a standard measure of the rate of change of velocity in either speed or direction." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 ! unit created_by: george gkoutos [Term] id: UO:0010006 name: ratio [Term] id: XCO:0000058 name: room temperature def: "The temperature of the air surrounding an organism which is considered the most common level for the facility. For humans the temperature considered most comfortable for a room is between 18 and 27 degrees celsius." [Dorland:Dorlands_Illustrated_Medical_Dictionary--31st_Ed, ISBN:978-1416049982] [Term] id: data:0962 name: Small molecule report [Term] id: data:0982 name: Molecule identifier [Term] id: data:0984 name: Molecule name [Term] id: data:0990 name: Compound name def: "Unique name of a chemical compound." [] subset: data subset: edam subset: identifiers synonym: "Chemical name" EXACT [] is_a: data:0984 ! Molecule name is_a: data:1086 ! Compound identifier property_value: created:in "beta12orEarlier" xsd:string [Term] id: data:1086 name: Compound identifier def: "Identifier of an entry from a database of chemicals." [] subset: data subset: edam subset: identifiers synonym: "Chemical compound identifier" EXACT [] synonym: "Compound ID" EXACT [] synonym: "Small molecule identifier" EXACT [] is_a: data:0982 ! Molecule identifier relationship: http://edamontology.org/is_identifier_of data:0962 ! Small molecule report property_value: created:in "beta12orEarlier" xsd:string property_value: http://edamontology.org/notRecommendedForAnnotation "true" xsd:string [Term] id: data:2795 name: ORF identifier def: "An identifier of an open reading frame." [] [Term] id: obsolete_DPBO:0000035 name: library strategy def: "Sequencing technique intended for a next generation sequencing library." [] comment: term is redundant, please use GENEPIO:0001973 xref: GENEPIO:0001973 is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: operation:3198 name: Read mapping 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. subset: edam subset: operations synonym: "Oligonucleotide alignment" EXACT [] synonym: "Oligonucleotide alignment construction" EXACT [] synonym: "Oligonucleotide alignment generation" EXACT [] synonym: "Oligonucleotide mapping" EXACT [] synonym: "Read alignment" EXACT [] synonym: "Short oligonucleotide alignment" EXACT [] synonym: "Short read alignment" EXACT [] synonym: "Short read mapping" EXACT [] synonym: "Short sequence read mapping" EXACT [] property_value: created:in "1.1" xsd:string property_value: hasDefinition "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence." xsd:string [Term] id: topic:0077 name: Nucleic acids [Term] id: topic:0099 name: RNA def: "RNA sequences and structures." [] subset: edam subset: topics synonym: "Small RNA" NARROW [] is_a: DPBO:0000177 ! plant material type is_a: topic:0077 ! Nucleic acids property_value: created:in "beta12orEarlier" xsd:string property_value: hasHumanReadableId "RNA" xsd:string property_value: seeAlso https://en.wikipedia.org/wiki/RNA