https://orcid.org/0000-0001-9021-3197 https://orcid.org/0000-0003-1476-2121 DataPLANT Biology Ontology DPBO 1.2 muehlhaus MIAPPE NCBITaxon NCIT NFDI4PSO coverage: Missing Terms for the DataPLANT end-point repository templates creator: Dominik Brilhaus <dominik.brilhaus<-at->hhu.de> creator: Hajira Jabeen <hajira.jabeen<-at->uni-koeln.de> curator: Kathryn Dumschott <k.dumschott@fz-juelich.de> curator: Stella Eggels <s.eggels@fz-juelich.de> definition created by creation date has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_synonym_type id in_subset treat-xrefs-as-equivalent Imaging is a process that produces an image of something. DPBO AFP:0003774 imaging The date/time of the measurement. DPBO AFR:0000952 measurement time The date/time of the measurement. Allotrope 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. DPBO AFR:0001255 temperature setting 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 The injection volume setting is an injection setting that specifies the volume of the fluid to be injected. DPBO AFR:0001577 injection volume setting A sample temperature result is a quality quantification facet that quantifies the temperature of the sample. DPBO AFR:0002149 sample temperature A planned process in which water is artificially supplied to plant or soil to sustain plants. DPBO AGRO:00000006 irrigation process A pruning process in which one or more suckers are removed. desuckering process DPBO AGRO:00000007 Which suckers are removed depends on the criteria set by the agent of the desuckering process. desuckering 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. https://orcid.org/0000-0001-6284-4821 pruning thinning process DPBO AGRO:00000027 thinning 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 Location where the experiment is implemented. DPBO AGRO:00000360 experimental site Experimental site in which the experiment is implemented on the field of a farmer. DPBO AGRO:00000361 farmer field Experimental site in which the experiment is done in a the field of a research station. experimental station field DPBO AGRO:00000362 research station field 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. hothouse screenhouse glasshouse DPBO AGRO:00000363 greenhouse 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 Experimental site where the experiment is done in a forest owned by a government. DPBO AGRO:00000364 governmental forest Experimental site where the experiment is done in a private forest. DPBO AGRO:00000365 private forest A person engaged in agriculture, raising living organisms for food or raw materials. DPBO AGRO:00000372 farmer A person who conducts research. scientist DPBO AGRO:00000373 researcher A person that is enrolled or attends classes at a school, college, or university. DPBO intern AGRO:00000374 student A person that works in a research station. DPBO AGRO:00000375 research station employee A person that is employed by the government to assist people in rural areas with methods of farming and home economics. DPBO AGRO:00000376 extension agent A person that is an educator who works at a college or university. DPBO AGRO:00000377 faculty member Roled performed by a person during an experiment. DPBO AGRO:00000378 person role within the experiment A person that has a role of collecting data related to the experiment. DPBO AGRO:00000379 data collector A person that is the holder of an independent grant and the lead researcher for the grant project. DPBO AGRO:00000380 principal investigator A person that has a role of managing the experiment. DPBO AGRO:00000381 experiment manager A person that has a role of performing the operations required to run the experiment in the field. DPBO AGRO:00000382 field laborer Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots. pruning pruning method DPBO AGRO:00000566 pruning process 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 A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters geographic coordinate system GPS coordinates measurement datum geo-location geolocation DPBO AGRO:00000572 GPS coordinates 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 A person that own an agricultural field. DPBO AGRO:00000659 field owner A planned process which occurs in an agricultural field. DPBO AGRO:00002071 agricultural process 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. DPBO BAO:0000269 DNA 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. DPBO BAO:0000316 genomic DNA This microplate contains 96 wells. It is suitable for a low throughput assay. DPBO BAO:0000513 96 well plate The role of a company as a creator of detection instrumentation. DPBO BAO:0002628 instrumentation manufacturer DPBO BAO:0010013 6 well plate Protein profiling assays can be used to identify and quantify proteins together with their post-translational modifications protein profiling protein quantification assay protein quantification assay DPBO BAO:0010026 protein profiling assay 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) DPBO BAO:0010027 shotgun MS protein profiling assay 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 DPBO BAO:0010028 SWATH MS protein profiling assay A targeted phosphoproteomic assay that uses a data-driven approach to identify and quantify a set of 96 phosphopeptide probes DPBO BAO:0010029 P100 protein profiling assay 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 DPBO BAO:0010030 RPPA protein profiling assay DPBO BAO:0010049 Microwestern DPBO BAO:0010052 ELISA protein state assay DPBO BAO:0010070 Tandem Mass Tag (TMT) MS Protein Quantification DPBO BAO:0010071 Liquid Chromatography/Mass Spectroscopy (LC/MS) protein quantification 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. BrendaTissueOBO BTO:0001899 stationary phase culture 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 The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time. BrendaTissueOBO BTO:0001900 growth phase culture 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 A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases. BrendaTissueOBO BTO:0001901 death phase culture 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 The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth. BrendaTissueOBO BTO:0001902 lag phase culture 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 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. BrendaTissueOBO exponential growth phase culture log phase culture BTO:0001903 logarithmic phase culture 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 biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. DPBO CHEBI:36080 protein A fluid that percolates through or along the stationary bed in chromatography. DPBO CHMO:0000995 mobile phase 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. derivatization DPBO CHMO:0001485 derivatisation 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 The process of removing a solvent from a substance. DPBO drying CHMO:0001549 sample drying The process of removing a solvent from a substance. https://orcid.org/0000-0002-0640-0422 drying 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. DPBO CHMO:0001557 vacuum drying 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 The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it. DPBO CHMO:0001577 extraction 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). liquid-solid extraction solid phase extraction solid-phase extraction sorbent extraction sorptive extraction DPBO LSE SPE CHMO:0001583 liquid-solid extraction 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 LSE SPE 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. normal phase SPE normal phase solid-phase extraction normal-phase SPE DPBO CHMO:0001584 normal-phase solid-phase extraction 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 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. reverse phase SPE reverse phase solid-phase extraction reverse-phase SPE reverse-phase solid-phase extraction reversed phase SPE reversed-phase SPE DPBO CHMO:0001585 reversed-phase solid-phase extraction 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 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). SPME solid phase microextraction solid-phase microextraction DPBO CHMO:0001586 solid-phase micro-extraction 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 The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary. CME capillary microextraction DPBO CHMO:0001587 capillary micro-extraction 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 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. sgCME sol-gel CME sol-gel capillary micro-extraction sol-gel capillary microextraction solgel CME solgel capillary microextraction DPBO CHMO:0001588 sol–gel capillary micro-extraction 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 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. HSPME HSSE hSPME headspace solid-phase micro-extraction headspace solid-phase microextraction headspace sorptive extraction DPBO CHMO:0001589 headspace solid-phase micro-extraction 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 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. MEPS micro extraction by packed sorbent micro-extraction in packed syringe microextraction in a packed syringe microextraction in packed syringe packed syringe micro-extraction packed syringe microextraction packed-syringe micro-extraction packed-syringe microextraction DPBO CHMO:0001590 micro-extraction in a packed syringe 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 The process of transferring a substance from any matrix to an appropriate liquid phase. DPBO CHMO:0001598 solvent extraction The process of transferring a substance from any matrix to an appropriate liquid phase. OrangeBook:9.4.1 The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting. dry grinding milling solid-state grinding solvent-free grinding DPBO CHMO:0001652 grinding The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting. https://doi.org/10.1351/goldbook.M03928 Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties. methoxyamination derivatization DPBO CHMO:0002757 this typically happens prior to GC-MS, but not LC-MS methoxyamination derivatisation 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 Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups. TMS derivatisation trimethylsilyl derivatization DPBO CHMO:0002758 this typically happens prior to GC-MS, but not LC-MS trimethylsilyl derivatisation 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 dispersive solid-phase extraction DPBO CHMO:0002863 dispersive solid phase extraction DPBO CHMO:0002887 dispersive solid-phase microextraction 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 DPBO Experimental Randomisation DPBO:0000001 growth plot design The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478 DPBO DPBO:0000002 “We might need to add the relationship with the class referenced above” read alignment software The version of the read alignment software (DPBO:0000002). DPBO DPBO:0000003 read alignment software version The parameters of the read alignment software (DPBO:0000002). DPBO DPBO:0000004 read alignment software parameters 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) DPBO DPBO:0000005 "is_a: http://purl.obolibrary.org/obo/PECO_0007197" humidity day 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) DPBO DPBO:0000006 "is_a: http://purl.obolibrary.org/obo/PECO_0007197" humidity night This term defines the air temperature at daytime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) DPBO DPBO:0000007 “is_a: http://purl.obolibrary.org/obo/ENVO_09200001” temperature day This term defines the air temperature at nighttime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) DPBO DPBO:0000008 “is_a: http://purl.obolibrary.org/obo/ENVO_09200001” temperature night Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ” DPBO DPBO:0000009 sample collection method Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.” DPBO DPBO:0000010 “” metabolism quenching method 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” DPBO DPBO:0000011 “” sample storage The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.” DPBO DPBO:0000012 “” bio entity The amount (typically in milligram) of material from which a bio entity (DPBO:0000012) is extracted.” DPBO DPBO:0000013 “” biosource amount The name of the commercial kit used for extraction of a bio entity (DPBO:0000012). Should include the company name.” DPBO DPBO:0000014 “” extraction kit 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” DPBO DPBO:0000015 “Adapted from http://purl.obolibrary.org/obo/NCIT_C150423" library layout Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)” DPBO DPBO:0000016 “” library RNA amount The name of the software used for base-calling. DPBO DPBO:0000017 term description for base-calling http://edamontology.org/operation_3185 base-calling software The version of the base-calling software (DPBO:0000017).” DPBO DPBO:0000018 “” base-calling software version The parameters of the base-calling software (DPBO:0000017).” DPBO DPBO:0000019 “” base-calling software parameters Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (DPBO:0000015)” DPBO DPBO:0000020 “” library strand File format of the raw data file” DPBO DPBO:0000021 “This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915" raw data file format Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum DPBO DPBO:0000022 raw data file checksum Name of the software applied for data filtering DPBO DPBO:0000023 “For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)” data filtering software The version of the data filtering software (DPBO:0000023).” DPBO DPBO:0000024 “” data filtering software version The parameters of the data filtering software (DPBO:0000023).” DPBO DPBO:0000025 “” data filtering software parameters Name and version of the genome reference.” MS:1002644 NCIT:C16438 DPBO DPBO:0000026 “See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644” genome reference sequence File format of the processed data file” DPBO DPBO:0000027 “” processed data file format Name of the processed data file” DPBO DPBO:0000028 “” processed data file name Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum DPBO DPBO:0000029 processed data file checksum Publication reference for isolation and growth condition specifications of the organism/material DPBO DPBO:0000030 for submission to ENA isolation and growth condition The haploid chromosome count of a eukaryote DPBO DPBO:0000031 number of chromosomes The estimated size of the genome prior to sequencing DPBO DPBO:0000032 adapted from MIXS:0000024 estimated genome size 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). DPBO DPBO:0000033 “This is a specialization of age (http://www.ebi.ac.uk/efo/EFO_0000246)" plant age Health status of the plant at the time of sample collection DPBO DPBO:0000034 plant health state 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. DPBO DPBO:0000035 Seurat true The method used to select for or against, enrich, or screen the material being sequenced. GENEPIO:0001940 DPBO DPBO:0000036 term is redundant, please use GENEPIO:0001940 obsolete_library selection true Determination of the taxonomic ranking that is below species level i.e. variety, cultivar, ecotype, inbred line DPBO DPBO:0000037 subspecific taxonomic rank pH measurement of the culture rooting medium DPBO DPBO:0000038 adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist rooting medium pH Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L) DPBO DPBO:0000039 adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist rooting medium macronutrients Model name or number of next generation sequencing instrument EFO:0003739 DPBO DPBO:0000040 next generation sequencing instrument model 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) PECO:0007078 ZECO:0000147 light duration DPBO DPBO:0000041 “Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078" growth day length Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2') MS:1001809 DPBO DPBO:0000042 biological replicate Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection) DPBO DPBO:0000043 MS sample post-extraction Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile) DPBO DPBO:0000044 MS sample resuspension Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control) DPBO DPBO:0000045 MS sample type Company name, and instrument name or serial number of the chromatography instrument DPBO DPBO:0000046 chromatography instrument model Company name, and name or serial number of the chromatography autosampler model DPBO DPBO:0000047 chromatography autosampler model Company name, and name or serial number of the chromatography column DPBO DPBO:0000048 chromatography column model Company name, and name or serial number of the chromatography guard column DPBO DPBO:0000049 chromatography guard column model Chemical buffer, solvent or solution used to extract a component from a biological sample. DPBO DPBO:0000050 “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884). DB" extraction buffer Volume of the buffer (DPBO:0000050) used during extraction. DPBO DPBO:0000051 “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884)" extraction buffer volume Derivatization for metabolomics mass spectrometry. CHMO:0001485 DPBO DPBO:0000052 MS derivatization Type of chromatography column (DPBO:0000048) CHMO:0001000 DPBO DPBO:0000053 chromatography column type Method or kit that was used to extract DNA or RNA DPBO DPBO:0000054 “More general than DPBO:0000014, because not everyone uses a kit for RNA/DNA extraction" extraction method Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L) DPBO DPBO:0000055 adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist rooting medium micronutrients Amount of DNA (microgram) used as starting material for library construction DPBO DPBO:0000056 “" library DNA amount Name of the company that produces next generation sequencing instruments GENEPIO:0000071 DPBO DPBO:0000057 next generation sequencing platform Organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L) DPBO DPBO:0000058 adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist rooting medium organic supplements Strategy that was used to assemble reads into contigs GENEPIO:0000090 DPBO DPBO:0000059 “Just two options should be possible: de-novo assembly or mapping" sequence assembly method The version of the sequence assembly algorithm (OBI_0001522) DPBO DPBO:0000060 “" sequence assembly algorithm version Status of the genome sequence that is uploaded DPBO DPBO:0000061 “Just two options should be possible: full or partial" genome status Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis. DPBO DPBO:0000062 RNA quality check 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. NCIT:C175890 DPBO DPBO:0000063 “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" BioProject accession number Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly NCIT:C70713 DPBO DPBO:0000064 “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" sample type Source of organic carbon in the culture rooting medium; e.g. sucrose DPBO DPBO:0000065 adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist rooting medium carbon source Growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA DPBO DPBO:0000066 adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist rooting medium growth regulators Specification of the solidifying agent in the culture rooting medium; e.g. agar DPBO DPBO:0000067 adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist rooting medium solidifier A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [ NCI On-line Medical Dictionary ] NCIT:C16403 DPBO DPBO:0000068 “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]" obsolete_cell line true 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] DPBO DPBO:0000069 term is redundant, please use NCIT:C12508 obsolete_cell type true Incomplete CDS (coding sequence) with the start codon upstream of the submitted sequence. DPBO DPBO:0000070 adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences. 5' partial CDS Incomplete CDS (coding sequence) with the stop codon downstream of the submitted sequence. DPBO DPBO:0000071 adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences. 3' partial CDS Stage of plant disease at the time of sampling. DPBO DPBO:0000072 plant disease stage Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601 NCIT:C16977 DPBO DPBO:0000073 “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" phenotype 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' NCIT:C16632 DPBO DPBO:0000074 “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" geographic area Incomplete promoter with its 5' end upstream of the submitted sequence. DPBO DPBO:0000075 adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. 5' partial promoter Incomplete promoter with its 3' end downstream of the submitted sequence. DPBO DPBO:0000076 adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. 3' partial promoter 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 DPBO DPBO:0000077 “[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title" metabolite assignment file BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]! NCIT:C175889 DPBO DPBO:0000078 “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" BioSample accession number Coordinate of the 5' end of the promoter within the submitted sequence. DPBO DPBO:0000079 adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. promoter 5' end coordinate Coordinate of the 3' end of the promoter within the submitted sequence. DPBO DPBO:0000080 adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. promoter 3' end coordinate Settings of the gradient used during (e.g. liquid, gas or ion) chromatography DPBO DPBO:0000081 chromatography gradient Method used for rRNA depletion during construction of the sequencing library. DPBO DPBO:0000082 "see also http://purl.obolibrary.org/obo/NCIT_C18685" rRNA depletion Relative centrifugal force (RCF) is the amount of force applied to a sample when using a centrifuge. It is dependant on the speed of the centrifuge rotation as well as the distance of the sample from the center of rotation. RCF DPBO DPBO:0000083 relative centrifugal force G-force is the force acting on an object as a result of acceleration or gravity. DPBO DPBO:0000084 g-force The standard acceleration of an object in free fall at or near sea level equivalent to 9.807 m/s2. g0 standard acceleration due to gravity standard acceleration of free fall DPBO DPBO:0000085 standard gravity A library layout which describes that only one end of the library fragment is sequenced GEO_RNASEQ RAW FILES_single or paired-end DPBO DPBO:0000086 "Adapted from http://purl.obolibrary.org/obo/FBcv_0003220" single-end Short unique identifier for the sequencing library Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:0000087 "Required for upload of next-generation sequencing data to SRA." library ID A climatic chamber used for growing plants under controlled environmental conditions. DPBO DPBO:0000088 growth chamber 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. DPBO DPBO:0000089 SingleCellExperiment 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. DPBO DPBO:0000090 tidyverse 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. DPBO DPBO:0000091 Matrix Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. DPBO DPBO:0000092 scales 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. DPBO DPBO:0000093 cowplot A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc. DPBO DPBO:0000094 RCurl Packages are collections of R functions, data, and compiled code in a well-defined format, created to add specific functionality. DPBO DPBO:0000095 R package The version of the software package or library that was used in the analysis. DPBO DPBO:0000096 package version Targeted proteomics method that combines parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF). DPBO DPBO:0000097 Bruker Corporation term. Definition from https://www.bruker.com/ prm-PASEF Data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF) technology for proteomics analysis. DPBO DPBO:0000098 Bruker Corporation term. Definition from https://www.bruker.com/ dda-PASEF Concentration of an antibiotic that was added to a growth medium. DPBO DPBO:0000099 antibiotic concentration Duration of a bacterial cultivation. DPBO DPBO:0000100 growth time The OD600 that was used to inoculate a bacterial culture. DPBO DPBO:0000101 start OD600 Method that was used to harvest bacterial cells. DPBO DPBO:0000102 harvesting method Constant percentage of dissolved oxygen in a culture medium. DPBO DPBO:0000103 dissolved oxygen (DO) An experiment that is used to grow bacterial cells under oxygen limitation conditions. DPBO DPBO:0000104 oxygen limitation experiment Percent of oxygen that is added to a culture medium via gassing. DPBO DPBO:0000105 oxygen concentration Percent of nitrogen that is added to a culture medium via gassing. DPBO DPBO:0000106 nitrogen concentration An experiment that is used to grow bacterial cells under oxygen excess conditions. DPBO DPBO:0000107 oxygen excess experiment A measurement that is used to identify transcriptional binding sites in a genome. DPBO DPBO:0000108 transcriptional binding site identification Exchange of carbon dioxide, oxygen and water vapor between the plant leaf and the ambient air through stomata. Stella Eggels DPBO DPBO:0000109 leaf gas exchange Analyzer that measures the concentration of gases in air based on their absorption of infrared radiation. Stella Eggels DPBO DPBO:0000110 infrared gas analyzer Unique identificator for a study. This is used to link experiments to the study. DPBO DPBO:0002000 alias Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication. DPBO DPBO:0002001 study abstract Title of the study as would be used in a publication. DPBO DPBO:0002002 title Name of the project within which the experiment was organized. DPBO DPBO:0002005 project name Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid. DPBO DPBO:0002006 sequencing method Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium DPBO DPBO:0002007 investigation type 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. ENVO:01000813 DPBO DPBO:0002008 EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" [] environment (feature) 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. ENVO:00010483 DPBO DPBO:0002009 EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" [] environment (material) 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 DPBO DPBO:0002010 plant-associated environmental package The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data. 2022-02-02T08:33:08Z Dominik Brilhaus ENSGLOSSARY:0000217 DPBO DPBO:0010000 https://www.ebi.ac.uk/ena/ ENA The BioSample database contains descriptions of biological source materials used in experimental assays. 2022-02-02T08:33:08Z Dominik Brilhaus DPBO DPBO:0010002 https://www.ncbi.nlm.nih.gov/biosample/ BioSample 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. 2022-02-02T08:58:37Z Dominik Brilhaus GENEPIO:0001836 DPBO DPBO:0010004 https://www.ncbi.nlm.nih.gov/bioproject/ BioProject 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. 2022-02-02T08:59:49Z Dominik Brilhaus NCIT:C43818 DPBO DPBO:0010005 https://www.ncbi.nlm.nih.gov/genbank/ GenBank 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. 2022-02-02T09:02:27Z Dominik Brilhaus DPBO DPBO:0010006 https://www.ncbi.nlm.nih.gov/sra/ SRA Plant Genomics & Phenomics Research Data Repository 2022-02-02T09:03:35Z Dominik Brilhaus DPBO DPBO:0010007 https://edal-pgp.ipk-gatersleben.de PGP 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. 2022-02-02T09:04:46Z Dominik Brilhaus DPBO DPBO:0010008 https://www.ebi.ac.uk/bioimage-archive/ BIA The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay. Dominik Brilhaus DPBO DPBO:0010009 "Relates to DPBO:0000013" biosource material state Fresh (non-dry) biosource material Dominik Brilhaus DPBO DPBO:0010010 "Relates to https://cropontology.org/rdf/CO_347:0000193 fresh material Dry biosource material Dominik Brilhaus DPBO DPBO:0010011 "Relates to https://cropontology.org/rdf/CO_347:0000196 dry material Internal standard added in known amount to an analytical sample Dominik Brilhaus DPBO DPBO:0010012 "Similar to http://purl.obolibrary.org/obo/MSIO_0000005 internal standard Volume taken from the sample to be assayed (measured). Dominik Brilhaus DPBO DPBO:0010013 sample volume Volume of the sample injected during chromatography Dominik Brilhaus DPBO DPBO:0010014 "Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577 chromatography injection volume This is to specify split / splitless runs during e.g. gas-chromatography. Dominik Brilhaus DPBO DPBO:0010015 "Compare to http://purl.obolibrary.org/obo/OBI_0000525 chromatography injection mode placeholder def of RNA-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000003 To be transformed to an instance. DB obsolete_RNA-seq true A library strategy that can identify and quantify the microRNA sequences present in a biological sample. GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000004 "Adapted from http://purl.obolibrary.org/obo/NCIT_C156057" miRNA-seq A next-generation sequencing library strategy that can determine the small and large non-protein coding RNA transcripts in a sample. GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000005 "Adapted from http://purl.obolibrary.org/obo/NCIT_C172858" ncRNA-seq A library strategy with an additional size fractionation step after RNA-seq library preparation GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000006 RNA-seq (size fractionation) A library strategy that is used to sequence the 5' capped transcripts, using CAGE to biotinylate and isolate the 7-methylguanosine cap. GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000007 "Adapted from http://purl.obolibrary.org/obo/FBcv_0003051" RNA-seq (CAGE) 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. GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000008 "Adapted from http://www.ebi.ac.uk/efo/EFO_0004182." RNA-seq (RACE) placeholder def of ssRNA-seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000009 To be transformed to an instance. DB obsolete_ssRNA-seq true placeholder def of ChIP-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000010 To be transformed to an instance. DB obsolete_ChIP-seq true placeholder def of MNase-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000011 To be transformed to an instance. DB obsolete_MNase-seq true placeholder def of MBD-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000012 To be transformed to an instance. DB obsolete_MBD-seq true placeholder def of MRE-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000013 To be transformed to an instance. DB obsolete_MRE-seq true placeholder def of Bisulfite-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000014 Replaced by EFO term Bisulfite-seq (id:0003753) obsolete_Bisulfite-seq true A library strategy that uses one or more restriction enzymes on a genomic DNA sample prior to sequencing to produce sequence-specific fragmentation GEO_RNASEQ PROTOCOLS_library strategy RRBS-Seq reduced-representation bisulfite sequencing DPBO DPBO:1000015 To be transformed to an instance. DB Bisulfite-seq (reduced representation) placeholder def of MeDIP-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000016 To be transformed to an instance. DB obsolete_MeDIP-seq true A library strategy that is used to characterize the DNase hypersensitivity of a genome by treatment with DNase before library preparation. GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000017 "Adapted from FBcv:0003058." DNase hypersensitivity A library strategy that is used to sequence transposons. GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000018 "Adapted from http://www.ebi.ac.uk/efo/EFO_0008973." Tn-seq placeholder def of FAIRE-seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000019 To be transformed to an instance. DB obsolete_FAIRE-seq true A library strategy for high-througput sequencing that is based on Systematic evolution of ligands by exponential enrichment. GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000020 "Adapted from http://www.ebi.ac.uk/efo/EFO_0008918." SELEX placeholder def of RIP-Seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000021 To be transformed to an instance. DB obsolete_RIP-seq true placeholder def of ATAC-seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000022 To be transformed to an instance. DB obsolete_ATAC-seq true placeholder def of ChIA-PET GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000023 To be transformed to an instance. DB obsolete_ChIA-PET true placeholder def of Hi-C GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000024 To be transformed to an instance. DB obsolete_Hi-C true Any other possible library strategy that can be used for RNA-seq GEO_RNASEQ PROTOCOLS_library strategy DPBO DPBO:1000025 "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." OTHER: specify placeholder def of fastq GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000026 To be transformed to an instance. DB obsolete_fastq true Binary format for storing of sequencing data GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000027 Adapted from http://purl.obolibrary.org/obo/NGBO_6000021. bam Illumina´s native QSEQ format GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000028 Illumina_native_qseq Illumina´s native sequencing format GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000029 Illumina_native SOLID´s native csfasta sequencing format GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000030 SOLiD_native_csfasta SOLI´s native quality sequencing format GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000031 SOLiD_native_qual 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. GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000032 http://edamontology.org/format_3284 sff 454 pyrosequencing native sequencing file format GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000033 454_native_seq 454 pyrosequencing native quality sequencing file format GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000034 454_native_qual Helicos native file format GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000035 Helicos_native Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000036 http://edamontology.org/format_3017 srf 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. GEO_RNASEQ RAW FILES_file type DPBO DPBO:1000037 Adapted from http://purl.obolibrary.org/obo/NCIT_C184763 PacBio_HDF5 GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000038 term is redundant, use EFO:0004202 or OBI:0002000 instead obsolete_Illumina Genome Analyzer IIx true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000039 term is redundant, use EFO:0004204 or OBI:0002022 instead obsolete_Illumina HiSeq 1000 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000040 term is redundant, use GENEPIO:0100115, OBI:0003386 or EFO:0011027 obsolete_Illumina HiSeq 1500 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000041 Term is redundant, please use OBI:0002001 or EFO:0004203 obsolete_Illumina HiSeq 2000 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000042 Term is redundant, please use OBI:0002002 or EFO:0008565 obsolete_Illumina HiSeq 2500 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000043 Term is redundant, please use OBI:0002048 or EFO:0008564 obsolete_Illumina HiSeq 3000 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000044 Term is redundant, please use OBI:0002049 or EFO:0008563 obsolete_Illumina HiSeq 4000 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000045 Term is redundant, please use EFO:0009173 obsolete_Illumina NextSeq 500 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000046 Term is redundant, please use GENEPIO:0100128 or EFO:0008566 obsolete_Illumina NextSeq 550 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000047 Term is redundant, please use GENEPIO:0100113 or OBI:0002129 obsolete_Illumina HiSeq X Ten true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000048 Term is redundant, please use GENEPIO:0100112 obsolete_Illumina HiSeq X Five true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000049 Term is redundant, please use GENEPIO:0100123, OBI:0002630 or EFO:0008637 obsolete_Illumina NovaSeq 6000 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000050 Redundant term, please use EFO:0004205 instead obsolete_Illumina MiSeq true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000051 Redundant term, please use GENEPIO:0100109 instead obsolete_Illumina HiScanSQ true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000052 Term is redundant, please use GENEPIO:0100124, OBI:0003114 or EFO:0008636 instead. obsolete_Illumina MiniSeq true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000053 Term is redundant, please use GENEPIO:0100121 or EFO:0008635 instead obsolete_Illumina iSeq 100 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000054 Term is redundant, please use NCIT:C146812 or GENEPIO:0100145 instead obsolete_BGISEQ-500 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000055 Term is redundant, please use GENEPIO:0100148 obsolete_DNBSEQ-G400 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000056 Term is redundant, please use GENEPIO:0100147 obsolete_DNBSEQ-T7 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000057 Term is redundant, please use GENEPIO:0100150 obsolete_DNBSEQ-G50 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000058 Term is redundant, please use GENEPIO:0100136 obsolete_Ion Torrent PGM true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000059 Term is redundant, please use GENEPIO:0100137 obsolete_Ion Torrent Proton true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000060 Term is redundant, please use GENEPIO:0100139 obsolete_Ion Torrent S5 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000061 Term is redundant, please use GENEPIO:0100138 obsolete_Ion Torrent S5 XL true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000062 Term is redundant, please use GENEPIO:0100131 obsolete_PacBio RS true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000063 Term is redundant, please use OBI:0002012 or EFO:0008631 obsolete_PacBio RS II true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000064 Term is redundant, please use GENEPIO:0100133 or OBI:0002632 obsolete_Sequel true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000065 Term is redundant, please use GENEPIO:0100134 or OBI:0002633 obsolete_Sequel II true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000066 Term is redundant, please use GENEPIO:0001932 or EFO:0004442 obsolete_AB SOLiD System 2.0 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000067 Term is redundant, please use EFO:0004439 or GENEPIO:0001933 obsolete_AB SOLiD System 3.0 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000068 Term is redundant, please use OBI:0002007. obsolete_AB SOLiD 3 Plus System true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000069 Term is redundant, please use EFO:0004438 obsolete_AB SOLiD 4 System true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000070 Term is redundant, please use GENEPIO:0001928 or EFO:0004441 obsolete_AB SOLiD 4hq System true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000071 Term is redundant, please use EFO:0004437 or GENEPIO:0001931 obsolete_AB SOLiD PI System true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000072 AB 5500 Genetic Analyzer GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000073 AB 5500xl Genetic Analyzer GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000074 AB 5500xl-W Genetic Analysis System GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000075 Term is redundant, please use EFO:0004431 obsolete_454 GS true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000076 Term is redundant, please use EFO:0004206 obsolete_454 GS 20 true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000077 Term is redundant, please use EFO:0004432 or OBI:0000702 obsolete_454 GS FLX true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000078 454 GS FLX+ GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000079 Term is redundant, please use EFO:0004434 or GENEPIO:0001938 obsolete_454 GS Junior true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000080 Term is redundant, please use EFO:0004433 or GENEPIO:0001936 obsolete_454 GS FLX Titanium true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000081 Term is redundant, please use NCIT:C146815 or GENEPIO:0001924 obsolete_Complete Genomics true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000082 Term is redundant, please use OBI:0000717 obsolete_Helicos HeliScope true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000083 Term is redundant, please use GENEPIO:0100141 obsolete_GridION true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000084 Term is redundant, please use OBI:0002750, EFO:0008632 or GENEPIO:0100142 obsolete_MinION true GEO_RNASEQ RAW FILES_instrument model DPBO DPBO:1000085 Term is redundant, please use OBI:0002752 or GENEPIO:0100143 obsolete_PromethION true placeholder def of single GEO_RNASEQ RAW FILES_single or paired-end DPBO DPBO:1000086 Deprecated, please use DPBO:0000086 "single-end" instead obsolete_single true A library layout which describes that both ends of the library fragment are sequenced GEO_RNASEQ RAW FILES_single or paired-end DPBO DPBO:1000087 Adapted from http://purl.obolibrary.org/obo/FBcv_0003221 paired-end placeholder def of total RNA GEO_RNASEQ SAMPLES_molecule DPBO DPBO:1000088 term is redundant, please use EFO:0004964 obsolete_total RNA true placeholder def of polyA RNA GEO_RNASEQ SAMPLES_molecule DPBO DPBO:1000089 Term is redundant, please use OBI_0000869 obsolete_polyA RNA placeholder def of cytoplasmic RNA GEO_RNASEQ SAMPLES_molecule DPBO DPBO:1000090 Term is redundant, please use NCIT:C84512 obsolete_cytoplasmic RNA true placeholder def of nuclear RNA GEO_RNASEQ SAMPLES_molecule DPBO DPBO:1000091 Term is redundant. Please use EFO:0030052 obsolete_nuclear RNA true placeholder def of genomic DNA GEO_RNASEQ SAMPLES_molecule DPBO DPBO:1000092 Term is redundant, please use BAO:0000316 obsolete_genomic DNA true placeholder def of protein GEO_RNASEQ SAMPLES_molecule DPBO DPBO:1000093 Term is redundant, please use CHEBI:36080 obsolete_protein true Any other bio entity that can be characterized by high-throuput sequencing. GEO_RNASEQ SAMPLES_molecule DPBO DPBO:1000094 other Parent term to collect endpoint repositories (ER). DPBO DPBO:1000095 "For an overview of relevant repositories, check https://www.re3data.org or https://fairsharing.org" endpoint repository 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. DPBO DPBO:1000096 https://www.ncbi.nlm.nih.gov/geo/ GEO 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. DPBO DPBO:1000097 https://www.ebi.ac.uk/metabolights/ MetaboLights 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. DPBO DPBO:1000098 https://www.ebi.ac.uk/pride/ PRIDE Parent term to collect terms required for RNASeq submission to GEO DPBO DPBO:1000099 GEO_RNAseq Parent term to collect terms required for microarray submission to GEO DPBO DPBO:1000100 GEO_microarray 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. OME:Well DPBO DPBO:1000101 term is redundant, please use REPR:Well obsolete_well true The number of a well in a well plate. DPBO DPBO:1000102 well Number The identifier of a siRNA from a reagent library. DPBO DPBO:1000103 siRNA identifier Unique name of a chemical compound. EDAM:data_0990 DPBO DPBO:1000104 term is redundant, please use data:0990 obsolete_compound name true Identifier of an entry from a database of chemicals. data:1086 DPBO DPBO:1000105 term is redundant, please use data:1086 obsolete_compound identifier true The class a compound belongs to, defined by its biological function or the chemical property. DPBO DPBO:1000106 "Needed for imaging templates" compound class A unique gene name within a specific repository, database, or collection. NCIT:C48664 DPBO DPBO:1000108 obsolete_gene identifier true The sequence of the sense strand. DPBO DPBO:1000109 "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" sense sequence The sequence of the antisense strand. DPBO DPBO:1000110 "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" antisense sequence A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated. NCIT:C49647 DPBO DPBO:1000111 term is redundant, please use NCIT:C49647 obsolete_control type true Result of quality control. This can be: pass/fail, or other information such as: no cells DPBO DPBO:1000112 "Definition according to IDR" quality control 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. DPBO DPBO:1000113 "Needed for imaging templates. Definition form IDR" channel The type of a high content screening experiment like RNAi screen or antibody screen. DPBO DPBO:1000114 "Needed for imaging templates" screen technology type Version of a reagent library used e.g. in high content screening. DPBO DPBO:1000116 "Needed for imaging templates" library version 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. NCIT:C16295 DPBO DPBO:1000117 term is redundant, please use NCIT:C16295 obsolete_antibody true A thin flat piece of transparent material that is placed over a specimen for viewing with a microscope. NCIT:C126370 DPBO DPBO:1000118 use NCIT:C126370 obsolete_cover slip true DPBO DPBO:1000120 "Needed for imaging templates" image file path Compartment of interest in the prepared sample DPBO DPBO:1000121 "Needed for imaging templates" target compartment The name of the software program to capture and/or process imaging data. NCIT:C175898 DPBO DPBO:1000122 false obsolete_imaging software name true The version of the software program to capture and/or process imaging data. DPBO DPBO:1000123 "Needed for imaging templates" imaging software version The used settings in the software program to capture and/or process imaging data. DPBO DPBO:1000124 "Needed for imaging templates" imaging software settings Channel the image was taken with. DPBO DPBO:1000125 "Needed for imaging templates" microscope filter dwc:datasetName DPBO DPBO:1000126 "Needed for imaging templates" dataset name The name of the assay. NCIT:C178857 DPBO DPBO:1000127 obsolete_assay name true Software used for the processing of microscopy images like for adaption of contrast or stacking. DPBO DPBO:1000128 "Needed for imaging templates" image processing software Software used to analyze data extracted from microscopy images. DPBO DPBO:1000129 "Needed for imaging templates" image data analysis software Applied settings of the software used for the processing of microscopy images DPBO DPBO:1000130 "Needed for imaging templates" image processing software parameters Software used for the extraction of features from microscopy images. DPBO DPBO:1000131 "Needed for imaging templates" feature extraction software Description of the approach to extract features from microscopy images. DPBO DPBO:1000133 "Needed for imaging templates" feature extraction strategy Whether a microscopy image is intended to be used illustrational or analytically by deriving values from it. DPBO DPBO:1000135 "Needed for imaging templates" use of image The gene annotation build the siRNAs for a high content screen library were mapped to. DPBO DPBO:1000136 "Needed for imaging templates" reagent design genome reference version additional information about the quality control in high content screening studies e.g. 'checks for transfection', 'gives strong phenotype' DPBO DPBO:1000137 "Needed for imaging templates. Definition from IDR." control specification additional information why a quality control passed or failed' DPBO DPBO:1000138 "Needed for imaging templates. Definition from IDR." quality control comments Type of an imaging study. DPBO DPBO:1000139 "Needed for imaging templates" microscopy study type The magnification of a microscopy image DPBO DPBO:1000140 "Needed for imaging templates" magnification The sizes along the axis of the XYZCT dimensions in a microscopy image. DPBO DPBO:1000141 "Needed for imaging templates" image dimensionality The microscope's objective lens. OME:Objective DPBO DPBO:1000142 use OME:objective obsolete_objective true How a sample was further prepared for microscopy. MS:1000831 DPBO DPBO:1000143 microscopy sample preparation Plant material fixation on a microscopy slide. DPBO DPBO:1000144 "Needed for imaging templates" material fixation The part of an organism that has been prepared for an experiment DPBO DPBO:1000145 "Needed for imaging templates" prepared organism part A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics. "Fabian Haas | ORCID:0000-0002-7711-5282" EFO:0005135 DPBO DPBO:1000146 use EFO:0005135 obsolete_strain true A device that can be used to restrict the location of material entities over time "Fabian Haas | ORCID:0000-0002-7711-5282" OBI:0000967 DPBO DPBO:1000147 term is redundant, please use OBI:0000967 obsolete_container true A wide-mouthed cylindrical container made of glass or pottery and typically having a lid "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000148 jar A flat dish, typically circular "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000149 plate 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] "Fabian Haas | ORCID:0000-0002-7711-5282" PATO:0015031 DPBO DPBO:1000150 obsolete_contamination true Free from other living organisms "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000151 axenic Latest laboratory cultivated the strain. Who sent the strain to your laboratory "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000152 laboratory strain 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. "Fabian Haas | ORCID:0000-0002-7711-5282" dc:date DPBO DPBO:1000153 date 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] "Fabian Haas | ORCID:0000-0002-7711-5282" PATO:0000918 DPBO DPBO:1000154 term is redundant, please use PATO:0000918 obsolete_volume true Volume of culture medium used to grow the organism "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000155 culture medium volume The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. "Fabian Haas | ORCID:0000-0002-7711-5282" EFO:0000568 DPBO DPBO:1000156 term is redundant, please use EFO:0000568 obsolete_light true The spectral distribution of light (blue, green, red, far red and other light spectrums emitted from a light source) "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000157 "close to the term http://purl.obolibrary.org/obo/PECO_0007154" light quality 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. "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000158 term is redundant, please use UO:0010006 obsolete_ratio true 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 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. "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000159 "Thermofisher NanoDrop https://tools.thermofisher.com/content/sfs/brochures/T123-NanoDrop-Lite-Interpretation-of-Nucleic-Acid-260-280-Ratios.pdf" 260/280 ratio 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 "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO DPBO:1000160 "Thermofisher NanoDrop https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf" 260/230 ratio 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. Dominik Brilhaus DPBO DPBO:1000161 "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)." protocol type 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. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0003789 DPBO DPBO:1000162 replaced term with EFO:0003789 obsolete_growth protocol true A protocol that provides instructions for growing algae. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000163 algae growth protocol A protocol that provides instructions for growing a plant cultivar. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000164 plant growth protocol A protocol that provides instructions for growing a microbial sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000165 microbe growth protocol A protocol that provides instructions for growing a bacterial sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000166 bacteria growth protocol A protocol that provides instructions for growing yeast. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000167 yeast growth protocol A protocol that aims to treat sample or collection of samples, organism or group of organisms, for some experimental purpose. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0003969 DPBO DPBO:1000168 definition from http://www.ebi.ac.uk/efo/EFO_0003969. Term is redundant, please use EFO:0003969 obsolete_treatment protocol true A protocol that provides instructions on how a biological sample for an experiment was collected. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0005518 DPBO DPBO:1000169 definition from http://www.ebi.ac.uk/efo/EFO_0005518. Term is redundant, please use EFO:0005518 obsolete_sample collection protocol true A protocol that details how a sample is processed or changed to prepare it for analysis. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000170 sample processing protocol 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 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0000490 DPBO DPBO:1000171 definition taken heavily from http://www.ebi.ac.uk/efo/EFO_0000490. Term is redundant, please use EFO:0000490 obsolete_extraction protocol true 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. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000172 definition taken from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425773/. Term is redundant, please use EFO:0022384. obsolete_DNA extraction protocol true A protocol that describes the steps for removing and purifying DNA from a biological sample Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0010959 DPBO DPBO:1000173 term is redundant, please use EFO:0010959 obsolete_RNA extraction protocol true A protocol that describes how to isolate protein from a tissue, cell culture or other biological sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000174 term is redundant, please use EFO:0022383 obsolete_protein extraction protocol true A protocol that describes the step by step process for removing metabolites from a biological sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000175 metabolite extraction protocol A protocol that describes the steps to be taken to transform a sample before an assay can be performed Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO DPBO:1000176 assay pre-processing protocol A protocol that describes how to perform an assay. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO DPBO:1000177 assay protocol A protocol that describes the operations performed on data by a computer in order to retrieve, transform, or classify information. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO DPBO:1000178 definition heavily based on http://purl.obolibrary.org/obo/NCIT_C47925 data processing protocol 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 Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO DPBO:1000179 data filtering protocol A protocol that describes the operations performed to convert data from one format, structure, or value into another. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO DPBO:1000180 data transformation protocol 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. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO DPBO:1000181 data extraction protocol 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. Kevin Schneider | ORCID: 0000-0002-2198-5262 DPBO DPBO:1000182 replicate group 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. Kevin Schneider | ORCID: 0000-0002-2198-5262 DPBO DPBO:1000183 biological replicate group 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. Kevin Schneider | ORCID: 0000-0002-2198-526 DPBO DPBO:1000184 technical replicate group 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. Kathryn Dumschott | ORCID: 0000-0002-9905-401 BAO:0002833 DPBO DPBO:1000185 incubation time Axiovert series, inverse microscope Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000186 Zeiss Axiovert binocular, stereo microscope Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000187 Olympus SZX7 (Bino) camera Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000188 Zeiss AxioCam MRc5 white Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000189 01 white Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000190 01 differential interference contrast Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000191 DIC yellow Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000192 09 green Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000193 10 red Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000194 15 software controlling imaging systems from ZEISS. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000195 Zeiss ZEN 3.5 (blue edition) microscope slide Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000196 Thermo Scientific Menzel slides, 76 x 26 mm, 1,0 mm microscope slide Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000197 VWR frosted edges, ground edges 90°, 76 x 26 mm, 0,8 - 1,0 mm microscope slide Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000198 Roth SuperFrost® white, cut edges, 76 x 26 mm, 1,0 mm cover slip Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000199 Menzel, 24 x 50 mm, selected 0,17 +/- 0,01, strength 1,5 cover slip Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000200 Roth, 24 x 50 mm, strength 1 cover slip Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000201 VWR, 18 x 18 mm, 0,13 - 0,16 mm, strength 1,5 magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000202 0.8x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000203 1x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000204 1.25x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000205 1.6x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000206 2x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000207 2.5x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000208 3.2x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000209 4x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000210 5x magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000211 5.6x objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000212 Plan-Neofluar 5x/0.15 objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000213 Plan-Neofluar 10x/0.3 objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000214 Plan-Neofluar 20x/0.50 Ph2 objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000215 Plan-Neofluar 40x/0.75 objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000216 Plan-Neofluar 63x/1.25 Oil objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000217 Plan-Neofluar 100x/1.30 Oil objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000218 Achroplan 5x/012 objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000219 Achroplan 10x/0.25 Ph1 objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000220 Achroplan 20x/0.40 objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000221 Achroplan 40x/0.60 korr Ph2 objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000222 Achroplan 63x/0.75 korr Ph2 A solution designed for the growth of plant cell, tissue and organ culture. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO Knop ME Knop solution DPBO:1000223 Knop medium The activity or process of determining, analyzing, or predicting all or part of an organism's phenotype. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000224 Definition from https://www.merriam-webster.com/dictionary/phenotyping phenotyping Axioplan series, imaging fluorescence microscope Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO DPBO:1000225 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) Zeiss Axioplan 2 A role of a student in a research project which is acknowledged in papers. Andrea Schrader | 0000-0002-3879-7057 DPBO DPBO:1000226 student helper 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. DPBO DPBO:1000227 Suggested by Andrea Schrader | 0000-0002-3879-7057 plant work helper 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. particle bombardment DPBO DPBO:1000228 Suggested by Andrea Schrader | 0000-0002-3879-7057 biolistic transformation 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/) DPBO DPBO:1000229 Suggested by Andrea Schrader | 0000-0002-3879-7057 bioimaging protocol A protocol describing a transformation method of cell, tissues or organisms. DPBO DPBO:1000230 Suggested by Andrea Schrader | 0000-0002-3879-7057 transformation protocol Inverted fluorescence microscope suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 DPBO DPBO:1000231 https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research.html Zeiss Axio Observer Z1 Upright fluorescence microscope suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 DPBO DPBO:1000232 https://microscopy.ucsf.edu/instruments/zeiss-axioimager-m1, https://profcontrol.de/Zeiss-Axio-Imager-M1m-Fluorescence-DIC-Microscope-Fluoreszenz-Mikroskop Zeiss Imager M1 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. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000233 https://www.mg-rast.org/mgmain.html?mgpage=analysis MG-RAST accession number field Tool/Software used for assembly. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000234 https://genomicsstandardsconsortium.github.io/mixs/0000058/ assembly software Parameters used for assembly. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000235 https://genomicsstandardsconsortium.github.io/mixs/0000058/ assembly parameters 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. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000236 https://genomicsstandardsconsortium.github.io/mixs/0000056/ MISAG/MIMAG assembly quality Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000237 https://genomicsstandardsconsortium.github.io/mixs/0000078/ binning software The parameters that have been applied during the extraction of genomes from metagenomic datasets. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000238 https://genomicsstandardsconsortium.github.io/mixs/0000077/ binning parameters The phylogenetic marker(s) used to assign an organism name to the SAG or MAG. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000239 https://genomicsstandardsconsortium.github.io/mixs/0000053/ taxonomic identity marker Tools used for completion estimate, i.e. checkm, anvi'o, busco. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000240 https://genomicsstandardsconsortium.github.io/mixs/0000070/ completeness software 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. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000241 https://genomicsstandardsconsortium.github.io/mixs/0000069/ completeness score 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 Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO DPBO:1000242 https://genomicsstandardsconsortium.github.io/mixs/0000072/ contamination score 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. Spectroscopy NMR spectroscopy Nuclear magnetic resonance spectroscopy HOESY Heteronuclear Overhauser Effect Spectroscopy NOESY Nuclear Overhauser Effect Spectroscopy ROESY Rotational Frame Nuclear Overhauser Effect Spectroscopy DPBO EDAM:0593 NMR FASTQ short read format ignoring quality scores. DPBO EDAM:1930 FASTQ DPBO EFO:0000490 extraction protocol DPBO EFO:0000568 light ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins. NCIt:C106049 DPBO EFO:0002692 ChIP-seq 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 Methylation-Sensitive Restriction Enzyme sequencing DPBO EFO:0003748 MRE-seq 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. Methylated DNA Immunoprecipitation sequencing DPBO EFO:0003749 MeDIP-seq 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. methyl binding domain sequencing DPBO EFO:0003750 MBD-seq 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. DPBO EFO:0003751 MNase-seq 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. DPBO EFO:0003753 Bisulfite-seq DPBO EFO:0003789 growth protocol DPBO EFO:0003969 treatment protocol A DNA sequencer developed by Illumina. DPBO EFO:0004202 Illumina Genome Analyzer IIx The Illumina HiSeq 2000 is a sequencing machine developed by Illumina. DPBO EFO:0004203 Illumina HiSeq 2000 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. DPBO EFO:0004205 Illumina MiSeq The 454 GS 20 is a GS20 high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004206 454 GS 20 sequencer 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. NCIt:C106051 DPBO EFO:0004428 FAIRE-seq The 454 GS is a GS high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004431 454 GS sequencer DPBO EFO:0004432 454 GS FLX sequencer The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004433 454 GS FLX Titanium sequencer The 454 GS Junior is a GS high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004434 454 GS Junior sequencer DPBO EFO:0004437 AB SOLiD PI System DPBO EFO:0004438 AB SOLiD 4 System DPBO EFO:0004439 AB SOLiD System 3.0 DPBO EFO:0004441 AB SOLiD 4hq System DPBO EFO:0004442 AB SOLiD System 2.0 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. DPBO EFO:0004964 total RNA A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics. DPBO EFO:0005135 strain 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. DPBO EFO:0005310 RIP-seq DPBO EFO:0005518 sample collection protocol 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. http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html DPBO EFO:0007045 ATAC-seq 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. DPBO EFO:0007693 Hi-C The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina. DPBO EFO:0008563 Illumina HiSeq 4000 The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina. DPBO EFO:0008564 Illumina HiSeq 3000 The Illumina HiSeq 2500 is a sequencing machine developed by Illumina. DPBO EFO:0008565 Illumina HiSeq 2500 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. DPBO EFO:0008566 Illumina NextSeq 550 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. DPBO EFO:0008631 PacBio RS II The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies. DPBO EFO:0008632 ONT MinION 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. DPBO EFO:0008635 Illumina iSeq 100 The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina. DPBO EFO:0008636 Illumina MiniSeq The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina. DPBO EFO:0008637 Illumina NovaSeq 6000 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. PMID:20181287 chromatin interaction analysis by paired-end tag sequencing DPBO EFO:0008684 Chia-PET RNA-seq is a method that involves purifying RNA and making cDNA, followed by high-throughput sequencing. Dani Welter PMID:18516045 DPBO EFO:0008896 RNA-Seq Strand-specific RNA-seq (ssRNA-seq) Dani Welter PMID:19609351 DPBO EFO:0008950 ssRNA-seq Transposon sequencing (TN-Seq) Dani Welter PMID:23712350 DPBO EFO:0008973 TN-Seq The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina. DPBO EFO:0009173 Illumina NextSeq 500 DPBO EFO:0010959 RNA extraction protocol The Illumina HiSeq 1500 is a sequencing machine developed by Illumina. DPBO EFO:0011027 Illumina HiSeq 1500 DPBO EFO:0022383 protein extraction protocol DPBO EFO:0022384 DNA extraction protocol DPBO EFO:0030052 nuclear RNA 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. DPBO ERO:0001788 image processing technique Anatomical or other piece(s) or substance derived from one or more plants. DPBO FOODON:00004331 plant material Numbers of base pairs per read DPBO GENEPIO:0000076 read length Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters. DPBO GENEPIO:0000083 adapter sequence 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. DPBO GENEPIO:0000085 library preparation kit The version identifier of a packaged kit tailored for specific sequencing workflows. DPBO GENEPIO:0000149 library preparation kit version SRR11177792 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). SRA accession SRA_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z SRA accession slot Sequence Read Archive accession field Sequence Read Archive accession slot DPBO GENEPIO:0001142 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. SRA accession field The name of the agency that collected the original sample. NCIT:C45262 DPBO GENEPIO:0001153 sample collected by The date on which the sample was collected NCIT:C81286 DPBO GENEPIO:0001174 sample collection date DPBO GENEPIO:0001681 laboratory sequencing datum 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).' DPBO GENEPIO:0001924 Complete Genomics platform DPBO GENEPIO:0001928 SOLiD 4hq System DPBO GENEPIO:0001931 SOLiD PI System DPBO GENEPIO:0001932 SOLiD System 2.0 DPBO GENEPIO:0001933 SOLiD System 3.0 DPBO GENEPIO:0001936 454 Genome Sequencer FLX Titanium DPBO GENEPIO:0001938 454 Genome Sequencer Junior https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly Whether any method was used to select for or against, enrich, or screen the material being sequenced. Damion Dooley NCBI SRA: LIBRARY_SELECTION DPBO GENEPIO:0001940 library selection The library source specifies the type of source material that is being sequenced. DPBO GENEPIO:0001965 library source Sequencing technique intended for this library. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly DPBO GENEPIO:0001973 library strategy 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. DPBO GENEPIO:0100109 Illumina HiScanSQ A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. DPBO GENEPIO:0100112 Illumina HiSeq X Five A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. DPBO GENEPIO:0100113 Illumina HiSeq X Ten 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. DPBO GENEPIO:0100115 Illumina HiSeq 1500 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. DPBO GENEPIO:0100121 Illumina iSeq 100 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. DPBO GENEPIO:0100123 Illumina NovaSeq 6000 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. DPBO GENEPIO:0100124 Illumina MiniSeq 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. DPBO GENEPIO:0100128 Illumina NextSeq 550 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. DPBO GENEPIO:0100131 PacBio RS 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 DPBO GENEPIO:0100133 PacBio Sequel 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. DPBO GENEPIO:0100134 PacBio Sequel II A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. DPBO GENEPIO:0100136 Ion Torrent PGM A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. DPBO GENEPIO:0100137 Ion Torrent Proton 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. DPBO GENEPIO:0100138 Ion Torrent S5 XL A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. DPBO GENEPIO:0100139 Ion Torrent S5 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 DPBO GENEPIO:0100141 Oxford Nanopore GridION 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. DPBO GENEPIO:0100142 Oxford Nanopore MinION 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. DPBO GENEPIO:0100143 Oxford Nanopore PromethION A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and 'DNA Nanoballs'. DPBO GENEPIO:0100145 BGI Genomics BGISEQ-500 A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. DPBO GENEPIO:0100147 MGI DNBSEQ-T7 A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. DPBO GENEPIO:0100148 MGI DNBSEQ-G400 A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. DPBO GENEPIO:0100150 MGI DNBSEQ-G50 A sequence data which is the short name of a gene typically derived from the gene name. DPBO GENEPIO:0100598 gene symbol DPBO GEO:000000370 geographical entity 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. François Modave Mathias Brochhausen Matt Diller William R. Hogan DPBO GEO:000000372 geographical region DPBO MIAPPE:0095 Growth facility Reference of a protein object pointing to its genomic or nucleic acid sequence. DPBO MI:0251 gene product 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. DPBO MI:0507 tag 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 DPBO NCIT:C126370 Cover Slip 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. DPBO NCIT:C146812 BGISEQ-500 Sequencing 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. DPBO NCIT:C146815 Complete Genomics Sequencing The name of the software program capture and/or process imaging data. DPBO NCIT:C175898 Imaging Software Name The name of the software program capture and/or process imaging data. NCI DPBO NCIT:C181919 Objective Lens MIAPPE:0043 NCBITaxon:species DPBO NCIT:C45293 Species RNA present in the cytoplasm. It is involved in the protein export process from the cells. DPBO NCIT:C84512 Cytoplasmic RNA DPBO NMR:1000019 sample pH Parameters used in the NMR spectrometry acquisition. DPBO NMR:1001954 NMR acquisition parameter DPBO NMR:1002011 pH The intensity of an electric, magnetic, or other field. DPBO NMR:1400027 field strength The number of repeat scans performed and summed to create the data set for an NMR sample. DPBO NMR:1400087 number of scans DPBO NMR:1400253 defneed magnetic field strength a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. DPBO OBI:0000079 culture medium A planned process which results in physical changes in a specified input material DPBO OBI:0000094 material processing 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. DPBO OBI:0000702 454 Genome Sequencer FLX Is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry DPBO OBI:0000717 HeliScope Single Molecule Sequencer DPBO OBI:0000967 container An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. DPBO OBI:0001048 digital camera 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. DPBO OBI:0002000 Genome Analyzer IIx 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. DPBO OBI:0002001 Illumina HiSeq 2000 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. DPBO OBI:0002002 Illumina HiSeq 2500 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. DPBO OBI:0002007 SOLiD 3 Plus System 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. DPBO OBI:0002012 PacBio RS II 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. DPBO OBI:0002022 Illumina HiSeq 1000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. DPBO OBI:0002048 Illumina HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. DPBO OBI:0002049 Illumina HiSeq 4000 A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. DPBO OBI:0002129 Illumina HiSeq X Ten 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. DPBO OBI:0002630 Illumina NovaSeq 6000 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 DPBO OBI:0002632 PacBio Sequel 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. DPBO OBI:0002633 PacBio Sequel II 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. DPBO OBI:0002750 Oxford Nanopore MinION 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. DPBO OBI:0002752 Oxford Nanopore PromethION 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. DPBO OBI:0003114 Illumina MiniSeq 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. DPBO OBI:0003386 Illumina HiSeq 1500 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. MIAPPE:0041 NCIT:C14250 NFDI4PSO:0000030 DPBO OBI:0100026 organism 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) DPBO OBI:0400169 microscope 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 DPBO OBI:0400170 microscope slide DPBO OME:Objective Class "Objective" is microscopes' objective lens. 19.02.2024: term has been deprecated, please use REPR:Objective obsolete_Objective true DPBO PATO:0000918 volume 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. DPBO PATO:0015031 contamination 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 jg 2011-07-22T09:15:33Z PRIDE PRIDE:0000307 Defines various quantification methods Quantification method jg 2011-07-22T09:16:24Z PRIDE PRIDE:0000308 Describes gel-based quantification methods Gel-based quantification method jg 2011-07-22T09:17:03Z PRIDE PRIDE:0000309 Describes gel-free quantification methods Gel-free quantification method jg 2011-07-22T09:17:34Z PRIDE PRIDE:0000310 Describes quantification techniques using isotope labeling Isotope labeling jg 2011-07-22T09:18:39Z PRIDE PRIDE:0000311 Describes quantification techniques based on selected / multiple reaction monitoring Selected Reaction Monitoring jg 2011-07-22T09:19:54Z PRIDE PRIDE:0000312 Describes label free quantification techniques. Label free jg 2011-07-22T09:20:23Z PRIDE PRIDE:0000313 Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level iTRAQ jg 2011-07-22T09:23:12Z Tandem Mass Tag PRIDE PRIDE:0000314 Tandem Mass Tag is a MS2 based isotope labeling quantification technique TMT jg 2011-07-22T09:25:50Z Stable isotope labeling with amino acids in cell culture PRIDE PRIDE:0000315 Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification SILAC jg 2011-07-22T09:28:05Z PRIDE PRIDE:0000316 Describes isotope labeling quantification techniques detectable at MS1 level. MS1 based isotope labeling jg 2011-07-22T09:29:15Z PRIDE PRIDE:0000317 Describes isotope labeling quantification techniques detectable at MS1 level. MS2 based isotope labeling jg 2011-07-22T09:30:12Z PRIDE PRIDE:0000318 The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen. 18O jg 2011-07-22T09:31:24Z Isotope-Coded Affinity Tags PRIDE PRIDE:0000319 Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements. ICAT jg 2011-07-22T09:32:46Z PRIDE PRIDE:0000320 AQUA is an isotope labeling based quantification technique that uses known peptides. AQUA jg 2011-07-22T09:34:37Z Isotope-coded protein label PRIDE PRIDE:0000321 Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses. ICPL jg 2011-07-22T09:36:57Z Exponentially Modified Protein Abundance Index PRIDE PRIDE:0000322 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. emPAI jg 2011-07-22T09:38:17Z Total Ion Current PRIDE PRIDE:0000323 The Total Ion Current (TIC) can be measured or calculated in order to target specific ions. TIC rw PRIDE PRIDE:0000425 MS1 intensity based label-free quantification method acsordas PRIDE PRIDE:0000435 Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140. Peptide counting acsordas PRIDE PRIDE:0000436 Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 Spectrum counting acsordas PRIDE PRIDE:0000437 Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140 Protein Abundance Index - PAI acsordas PRIDE PRIDE:0000438 Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 Spectrum count/molecular weight acsordas PRIDE PRIDE:0000439 The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 Spectral Abundance Factor - SAF acsordas PRIDE PRIDE:0000440 Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 Normalized Spectral Abundance Factor - NSAF acsordas PRIDE PRIDE:0000441 Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140 APEX - Absolute Protein Expression Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method. DPBO PRIDE:0000457 Experiment Type Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. PRIDE PRIDE:0000463 Parallel Reaction Monitoring (PRM) Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. PRIDE:PRIDE Dimethyl Labeling (DML) yperez 2019-08-07T15:21:19Z PRIDE PRIDE:0000513 Dimethyl Labeling Dimethyl Labeling (DML) PRIDE:PRIDE Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 yperez DPBO PRIDE:0000650 diaPASEF Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 PRIDE:PRIDE A biotic plant stress caused by exposure to an environment containing a biological stress agent. DPBO PSO:0000013 plant disease The microscope's objective lens. DPBO REPR:Objective Objective 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. DPBO REPR:Well Well DPBO SCTID:71661000 cover slip preparation (procedure) 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. DPBO SIO:000318 longitude Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane DPBO SIO:000319 latitude 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 DPBO SIO:001051 data analysis A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid. DPBO SIO:010016 nucleic acid sequence The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. INSDC_feature:regulatory http://en.wikipedia.org/wiki/Terminator_(genetics) INSDC_qualifier:terminator terminator sequence DPBO SO:0000141 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. terminator 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 http://en.wikipedia.org/wiki/Terminator_(genetics) wiki 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. DPBO SO:0000167 promoter The first base to be translated into protein. coding start translation initiation site sequence translation start SO:0000323 coding_start The first base to be translated into protein. SO:ke The last base to be translated into protein. It does not include the stop codon. coding end translation termination site translation_end sequence SO:0000327 coding_end The last base to be translated into protein. It does not include the stop codon. SO:ke A promoter that can allow for transcription in both directions. bidirectional promoter sequence SO:0000568 Definition updated in Aug 2020 by Dave Sant. bidirectional_promoter A promoter that can allow for transcription in both directions. PMID:21601935 SO:ke A region of a CDS. DPBO SO:0000851 CDS_region 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. DPBO:0000035 DPBO SWO:1100130 Seurat DPBO UO:0000000 unit A unit which is a standard measure of the rate of change of velocity in either speed or direction. george gkoutos unit.ontology UO:0000048 acceleration unit A unit which is a standard measure of the rate of change of velocity in either speed or direction. Wikipedia:Wikipedia DPBO UO:0010006 ratio DPBO data:0962 Small molecule report DPBO data:0982 Molecule identifier DPBO data:0984 Molecule name Unique name of a chemical compound. beta12orEarlier Chemical name DPBO data:0990 Compound name true Identifier of an entry from a database of chemicals. beta12orEarlier Chemical compound identifier Compound ID Small molecule identifier DPBO data:1086 Compound identifier An identifier of an open reading frame. DPBO data:2795 ORF identifier Sequencing technique intended for a next generation sequencing library. GENEPIO:0001973 DPBO obsolete_DPBO:0000035 term is redundant, please use GENEPIO:0001973 library strategy true 1.1 Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. Oligonucleotide alignment Oligonucleotide alignment construction Oligonucleotide alignment generation Oligonucleotide mapping Read alignment Short oligonucleotide alignment Short read alignment Short read mapping Short sequence read mapping DPBO operation:3198 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. Read mapping DPBO topic:0077 Nucleic acids RNA sequences and structures. beta12orEarlier RNA Small RNA DPBO topic:0099 RNA A mutant in which a gene ore genes are expressed at higher levels than the wild type. DPBO MCO_0000041 overexpression mutant A mutant genotype in which one or more genes can have modifications (subtitutions, indels, partial truncations, etc), but they conserve functionality. DPBO MCO_0000042 gene variant mutant 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. DPBO MCO_0000051 knockout mutant a mutant in which a foreign DNA sequence is introduced to cell in an extrachromosomal unit of replication. DPBO MCO_0000052 plasmid mutant An optical density that specifies the amount of light of 600 nm of wavelenght the bearer is able to transmit. DPBO MCO_0000059 OD600 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. DPBO MCO_0000077 optical density DPBO MCO_0000173 nutrient availability stress treatment DPBO MCO_0000174 nutrient depletion treatment DPBO MCO_0000177 iron depletion DPBO MCO_0000178 carbon starvation DPBO MCO_0000179 nitrogen starvation DPBO MCO_0000180 phosphate starvation A biological quality that inheres in specific organisms and that describes its total genetic content DPBO MCO_0000851 genotype A process in which the act is intended to modify or alter some other material entity. DPBO MCO_0000866 treatment 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. DPBO NCIT_C146817 Illumina Sequencing 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. DPBO NCIT_C146818 Nanopore Sequencing 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). DPBO NCIT_C25360 mutant The naturally-occurring, normal, non-mutated version of a gene or genome. DPBO NCIT_C62195 wild type 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. DPBO OBI_0000869 polyA RNA DPBO ObsoleteClass Obsolete Class