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>
Imaging is a process that produces an image of something.
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.
The injection volume setting is an injection setting that specifies the volume of the fluid to be injected.
A sample temperature result is a quality quantification facet that quantifies the temperature of the sample.
A cycle count is a count of the number of iterations of a repeated process.
A planned process in which water is artificially supplied to plant or soil to sustain plants.
A pruning process in which one or more suckers are removed.
Which suckers are removed depends on the criteria set by the agent of the desuckering process.
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.
Location where the experiment is implemented.
Experimental site in which the experiment is implemented on the field of a farmer.
Experimental site in which the experiment is done in a the field of a research station.
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.
Experimental site where the experiment is done in a forest owned by a government.
Experimental site where the experiment is done in a private forest.
A person engaged in agriculture, raising living organisms for food or raw materials.
A person that is enrolled or attends classes at a school, college, or university.
A person that works in a research station.
A person that is employed by the government to assist people in rural areas with methods of farming and home economics.
A person that is an educator who works at a college or university.
Roled performed by a person during an experiment.
A person that has a role of collecting data related to the experiment.
A person that is the holder of an independent grant and the lead researcher for the grant project.
A person that has a role of managing the experiment.
A person that has a role of performing the operations required to run the experiment in the field.
Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots.
A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters
A person that own an agricultural field.
A planned process which occurs in an agricultural field.
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.
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.
This microplate contains 96 wells. It is suitable for a low throughput assay.
The role of a company as a creator of detection instrumentation.
Protein profiling assays can be used to identify and quantify proteins together with their post-translational modifications
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)
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
A targeted phosphoproteomic assay that uses a data-driven approach to identify and quantify a set of 96 phosphopeptide probes
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
Tandem Mass Tag (TMT) MS Protein Quantification
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.
The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time.
A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases.
The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth.
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.
A complex mixture of polysaccharides extracted from species of red algae. Its two main components are agarose and agaropectin. Agarose is the component responsible for the high-strength gelling properties of agar, while agaropectin provides the viscous properties.
biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
A fluid that percolates through or along the stationary bed in chromatography.
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.
The process of removing a solvent from a substance.
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.
The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it.
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).
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.
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.
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).
The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary.
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.
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.
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.
The process of transferring a substance from any matrix to an appropriate liquid phase.
The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting.
Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties.
this typically happens prior to GC-MS, but not LC-MS
Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups.
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
The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478
“We might need to add the relationship with the class referenced above”
The version of the read alignment software (DPBO:0000002).
The parameters of the read alignment software (DPBO:0000002).
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)
"is_a: http://purl.obolibrary.org/obo/PECO_0007197"
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)
This term defines the air temperature at daytime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001)
“is_a: http://purl.obolibrary.org/obo/ENVO_09200001”
This term defines the air temperature at nighttime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001)
Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ”
Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.”
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”
The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.”
The amount (typically in milligram) of material from which a bio entity (DPBO:0000012) is extracted.”
The name of the commercial kit used for extraction of a bio entity (DPBO:0000012). Should include the company name.”
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”
“Adapted from http://purl.obolibrary.org/obo/NCIT_C150423"
Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)”
The name of the software used for base-calling.
term description for base-calling http://edamontology.org/operation_3185
The version of the base-calling software (DPBO:0000017).”
The parameters of the base-calling software (DPBO:0000017).”
Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (DPBO:0000015)”
“This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915"
Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum
Name of the software applied for data filtering
“For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)”
The version of the data filtering software (DPBO:0000023).”
The parameters of the data filtering software (DPBO:0000023).”
Name and version of the genome reference.”
“See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644”
Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum
Publication reference for isolation and growth condition specifications of the organism/material
The haploid chromosome count of a eukaryote
The estimated size of the genome prior to sequencing
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).
“This is a specialization of age (http://www.ebi.ac.uk/efo/EFO_0000246)"
Health status of the plant at the time of sample collection
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.
The method used to select for or against, enrich, or screen the material being sequenced.
term is redundant, please use GENEPIO:0001940
Determination of the taxonomic ranking that is below species level i.e. variety, cultivar, ecotype, inbred line
pH measurement of the culture rooting medium
adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist
Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)
Model name or number of next generation sequencing instrument
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)
“Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078"
Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2')
Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection)
Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile)
Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control)
Company name, and instrument name or serial number of the chromatography instrument
Company name, and name or serial number of the chromatography autosampler model
Company name, and name or serial number of the chromatography column
Company name, and name or serial number of the chromatography guard column
Chemical buffer, solvent or solution used to extract a component from a biological sample.
“related to extraction (http://purl.obolibrary.org/obo/OBI_0302884). DB"
Volume of the buffer (DPBO:0000050) used during extraction.
“related to extraction (http://purl.obolibrary.org/obo/OBI_0302884)"
Derivatization for metabolomics mass spectrometry.
Type of chromatography column (DPBO:0000048)
Method or kit that was used to extract DNA or RNA
“More general than DPBO:0000014, because not everyone uses a kit for RNA/DNA extraction"
Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)
Amount of DNA (microgram) used as starting material for library construction
Name of the company that produces next generation sequencing instruments
Organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L)
Strategy that was used to assemble reads into contigs
“Just two options should be possible: de-novo assembly or mapping"
The version of the sequence assembly algorithm (OBI_0001522)
Status of the genome sequence that is uploaded
“Just two options should be possible: full or partial"
Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis.
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.
“[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly
Source of organic carbon in the culture rooting medium; e.g. sucrose
Growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA
Specification of the solidifying agent in the culture rooting medium; e.g. agar
A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [ NCI On-line Medical Dictionary ]
“[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]"
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]
term is redundant, please use NCIT:C12508
Incomplete CDS (coding sequence) with the start codon upstream of the submitted sequence.
adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences.
Incomplete CDS (coding sequence) with the stop codon downstream of the submitted sequence.
Stage of plant disease at the time of sampling.
Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601
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'
Incomplete promoter with its 5' end upstream of the submitted sequence.
adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences.
Incomplete promoter with its 3' end downstream of the submitted sequence.
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
“[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title"
BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]!
Coordinate of the 5' end of the promoter within the submitted sequence.
Coordinate of the 3' end of the promoter within the submitted sequence.
Settings of the gradient used during (e.g. liquid, gas or ion) chromatography
Method used for rRNA depletion during construction of the sequencing library.
"see also http://purl.obolibrary.org/obo/NCIT_C18685"
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.
G-force is the force acting on an object as a result of acceleration or gravity.
The standard acceleration of an object in free fall at or near sea level equivalent to 9.807 m/s2.
A library layout which describes that only one end of the library fragment is sequenced
"Adapted from http://purl.obolibrary.org/obo/FBcv_0003220"
Short unique identifier for the sequencing library
"Required for upload of next-generation sequencing data to SRA."
A climatic chamber used for growing plants under controlled environmental conditions.
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.
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.
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.
Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.
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.
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.
Packages are collections of R functions, data, and compiled code in a well-defined format, created to add specific functionality.
The version of the software package or library that was used in the analysis.
Targeted proteomics method that combines parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF).
Bruker Corporation term. Definition from https://www.bruker.com/
Data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF) technology for proteomics analysis.
Concentration of an antibiotic that was added to a growth medium.
The OD600 that was used to inoculate a bacterial culture.
Method that was used to harvest bacterial cells.
Constant percentage of dissolved oxygen in a culture medium.
An experiment that is used to grow bacterial cells under oxygen limitation conditions.
Percent of oxygen that is added to a culture medium via gassing.
Percent of nitrogen that is added to a culture medium via gassing.
An experiment that is used to grow bacterial cells under oxygen excess conditions.
A measurement that is used to identify transcriptional binding sites in a genome.
transcriptional binding site identification
Exchange of carbon dioxide, oxygen and water vapor between the plant leaf and the ambient air through stomata.
Analyzer that measures the concentration of gases in air based on their absorption of infrared radiation.
A word, term or short statement that clarifies the cause, context and/or consequence of another entity.
Multicellular structure comprising similar cells with some specific function.
The vertical distance below local surface at which the sample was taken. For sediment or soil samples depth is measured from sediment or soil surface, respectively.
Number of injections of a sample into a mass spectrometer or chromatograph.
Nearly identical and homozygous genotypes, resulting from repeated selfing over several generations.
Volume of the buffer in which the sample is diluted.
Suggested by Lukas Weil | 0000-0003-1945-6342
Combination of two tools used for grinding or shearing substances to a fine paste or powder.
Device used for the mechanical reduction of the particle size of a solid sample.
Tris-Acetate-Phosphate medium for the growth of Chlamydomonas.
Medium composition can be found at doi.org/10.1101/pdb.rec560
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 (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []
Unique identificator for a study. This is used to link experiments to the study.
Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.
Title of the study as would be used in a publication.
Name of the project within which the experiment was organized.
Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid.
Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium
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.
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
The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data.
The BioSample database contains descriptions of biological source materials used in experimental assays.
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.
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.
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.
Plant Genomics & Phenomics Research Data Repository
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.
The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay.
"Relates to https://cropontology.org/rdf/CO_347:0000193
"Relates to https://cropontology.org/rdf/CO_347:0000196
Internal standard added in known amount to an analytical sample
"Similar to http://purl.obolibrary.org/obo/MSIO_0000005
Volume taken from the sample to be assayed (measured).
Volume of the sample injected during chromatography
"Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577
This is to specify split / splitless runs during e.g. gas-chromatography.
"Compare to http://purl.obolibrary.org/obo/OBI_0000525
A library strategy that can identify and quantify the microRNA sequences present in a biological sample.
"Adapted from http://purl.obolibrary.org/obo/NCIT_C156057"
A next-generation sequencing library strategy that can determine the small and large non-protein coding RNA transcripts in a sample.
"Adapted from http://purl.obolibrary.org/obo/NCIT_C172858"
A library strategy with an additional size fractionation step after RNA-seq library preparation
A library strategy that is used to sequence the 5' capped transcripts, using CAGE to biotinylate and isolate the 7-methylguanosine cap.
"Adapted from http://purl.obolibrary.org/obo/FBcv_0003051"
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.
"Adapted from http://www.ebi.ac.uk/efo/EFO_0004182."
Replaced by EFO term Bisulfite-seq (id:0003753)
A library strategy that uses one or more restriction enzymes on a genomic DNA sample prior to sequencing to produce sequence-specific fragmentation
reduced-representation bisulfite sequencing
A library strategy that is used to characterize the DNase hypersensitivity of a genome by treatment with DNase before library preparation.
A library strategy that is used to sequence transposons.
"Adapted from http://www.ebi.ac.uk/efo/EFO_0008973."
A library strategy for high-througput sequencing that is based on Systematic evolution of ligands by exponential enrichment.
"Adapted from http://www.ebi.ac.uk/efo/EFO_0008918."
Any other possible library strategy that can be used for RNA-seq
"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."
Binary format for storing of sequencing data
Adapted from http://purl.obolibrary.org/obo/NGBO_6000021.
SOLID´s native csfasta sequencing format
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.
454 pyrosequencing native sequencing file format
454 pyrosequencing native quality sequencing file format
Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.
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.
Adapted from http://purl.obolibrary.org/obo/NCIT_C184763
term is redundant, use EFO:0004202 or OBI:0002000 instead
term is redundant, use EFO:0004204 or OBI:0002022 instead
term is redundant, use GENEPIO:0100115, OBI:0003386 or EFO:0011027
Term is redundant, please use OBI:0002001 or EFO:0004203
Term is redundant, please use OBI:0002002 or EFO:0008565
Term is redundant, please use OBI:0002048 or EFO:0008564
Term is redundant, please use OBI:0002049 or EFO:0008563
Term is redundant, please use EFO:0009173
Term is redundant, please use GENEPIO:0100128 or EFO:0008566
Term is redundant, please use GENEPIO:0100113 or OBI:0002129
Term is redundant, please use GENEPIO:0100112
Term is redundant, please use GENEPIO:0100123, OBI:0002630 or EFO:0008637
Redundant term, please use EFO:0004205 instead
Redundant term, please use GENEPIO:0100109 instead
Term is redundant, please use GENEPIO:0100124, OBI:0003114 or EFO:0008636 instead.
Term is redundant, please use GENEPIO:0100121 or EFO:0008635 instead
Term is redundant, please use NCIT:C146812 or GENEPIO:0100145 instead
Term is redundant, please use GENEPIO:0100148
Term is redundant, please use GENEPIO:0100147
Term is redundant, please use GENEPIO:0100150
Term is redundant, please use GENEPIO:0100136
Term is redundant, please use GENEPIO:0100137
Term is redundant, please use GENEPIO:0100139
Term is redundant, please use GENEPIO:0100138
Term is redundant, please use GENEPIO:0100131
Term is redundant, please use OBI:0002012 or EFO:0008631
Term is redundant, please use GENEPIO:0100133 or OBI:0002632
Term is redundant, please use GENEPIO:0100134 or OBI:0002633
Term is redundant, please use GENEPIO:0001932 or EFO:0004442
Term is redundant, please use EFO:0004439 or GENEPIO:0001933
Term is redundant, please use OBI:0002007.
Term is redundant, please use EFO:0004438
Term is redundant, please use GENEPIO:0001928 or EFO:0004441
Term is redundant, please use EFO:0004437 or GENEPIO:0001931
Term is redundant, please use EFO:0004431
Term is redundant, please use EFO:0004206
Term is redundant, please use EFO:0004432 or OBI:0000702
Term is redundant, please use EFO:0004434 or GENEPIO:0001938
Term is redundant, please use EFO:0004433 or GENEPIO:0001936
Term is redundant, please use NCIT:C146815 or GENEPIO:0001924
Term is redundant, please use OBI:0000717
Term is redundant, please use GENEPIO:0100141
Term is redundant, please use OBI:0002750, EFO:0008632 or GENEPIO:0100142
Term is redundant, please use OBI:0002752 or GENEPIO:0100143
Deprecated, please use DPBO:0000086 "single-end" instead
A library layout which describes that both ends of the library fragment are sequenced
Adapted from http://purl.obolibrary.org/obo/FBcv_0003221
term is redundant, please use EFO:0004964
Term is redundant, please use OBI_0000869
Term is redundant, please use NCIT:C84512
Term is redundant. Please use EFO:0030052
Term is redundant, please use BAO:0000316
Term is redundant, please use CHEBI:36080
Any other bio entity that can be characterized by high-throuput sequencing.
Parent term to collect endpoint repositories (ER).
"For an overview of relevant repositories, check https://www.re3data.org or https://fairsharing.org"
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.
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.
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.
Parent term to collect terms required for RNASeq submission to GEO
Parent term to collect terms required for microarray submission to GEO
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.
The identifier of a siRNA from a reagent library.
Identifier of an entry from a database of chemicals.
The class a compound belongs to, defined by its biological function or the chemical property.
A unique gene name within a specific repository, database, or collection.
"definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html"
A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated.
term is redundant, please use NCIT:C49647
Result of quality control. This can be: pass/fail, or other information such as: no cells
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.
"Needed for imaging templates. Definition form IDR"
The type of a high content screening experiment like RNAi screen or antibody screen.
Version of a reagent library used e.g. in high content screening.
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.
term is redundant, please use NCIT:C16295
A thin flat piece of transparent material that is placed over a specimen for viewing with a microscope.
Compartment of interest in the prepared sample
The name of the software program to capture and/or process imaging data.
The version of the software program to capture and/or process imaging data.
The used settings in the software program to capture and/or process imaging data.
Software used for the processing of microscopy images like for adaption of contrast or stacking.
Software used to analyze data extracted from microscopy images.
Applied settings of the software used for the processing of microscopy images
Software used for the extraction of features from microscopy images.
Description of the approach to extract features from microscopy images.
Whether a microscopy image is intended to be used illustrational or analytically by deriving values from it.
The gene annotation build the siRNAs for a high content screen library were mapped to.
additional information about the quality control in high content screening studies e.g. 'checks for transfection', 'gives strong phenotype'
"Needed for imaging templates. Definition from IDR."
additional information why a quality control passed or failed'
The sizes along the axis of the XYZCT dimensions in a microscopy image.
How a sample was further prepared for microscopy.
Plant material fixation on a microscopy slide.
The part of an organism that has been prepared for an experiment
A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
A device that can be used to restrict the location of material entities over time
term is redundant, please use OBI:0000967
A wide-mouthed cylindrical container made of glass or pottery and typically having a lid
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]
Latest laboratory cultivated the strain. Who sent the strain to your laboratory
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.
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]
term is redundant, please use PATO:0000918
Volume of culture medium used to grow the organism
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
term is redundant, please use EFO:0000568
The spectral distribution of light (blue, green, red, far red and other light spectrums emitted from a light source)
"close to the term http://purl.obolibrary.org/obo/PECO_0007154"
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.
term is redundant, please use UO:0010006
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.
"Thermofisher NanoDrop https://tools.thermofisher.com/content/sfs/brochures/T123-NanoDrop-Lite-Interpretation-of-Nucleic-Acid-260-280-Ratios.pdf"
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
"Thermofisher NanoDrop https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf"
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.
"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)."
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
A protocol that provides instructions for growing algae.
A protocol that provides instructions for growing a plant cultivar.
A protocol that provides instructions for growing a microbial sample.
A protocol that provides instructions for growing a bacterial sample.
A protocol that provides instructions for growing yeast.
A protocol that aims to treat sample or collection of samples, organism or group of organisms, for some experimental purpose.
definition from http://www.ebi.ac.uk/efo/EFO_0003969. Term is redundant, please use EFO:0003969
A protocol that provides instructions on how a biological sample for an experiment was collected.
definition from http://www.ebi.ac.uk/efo/EFO_0005518. Term is redundant, please use EFO:0005518
A protocol that details how a sample is processed or changed to prepare it for analysis.
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
definition taken heavily from http://www.ebi.ac.uk/efo/EFO_0000490. Term is redundant, please use EFO:0000490
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.
definition taken from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425773/. Term is redundant, please use EFO:0022384.
A protocol that describes the steps for removing and purifying DNA from a biological sample
term is redundant, please use EFO:0010959
A protocol that describes how to isolate protein from a tissue, cell culture or other biological sample.
term is redundant, please use EFO:0022383
A protocol that describes the step by step process for removing metabolites from a biological sample.
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
A protocol that describes how to perform an assay.
A protocol that describes the operations performed on data by a computer in order to retrieve, transform, or classify information.
definition heavily based on http://purl.obolibrary.org/obo/NCIT_C47925
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
A protocol that describes the operations performed to convert data from one format, structure, or value into another.
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.
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.
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.
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.
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.
software controlling imaging systems from ZEISS.
Thermo Scientific Menzel slides, 76 x 26 mm, 1,0 mm
VWR frosted edges, ground edges 90°, 76 x 26 mm, 0,8 - 1,0 mm
Roth SuperFrost® white, cut edges, 76 x 26 mm, 1,0 mm
Menzel, 24 x 50 mm, selected 0,17 +/- 0,01, strength 1,5
A solution designed for the growth of plant cell, tissue and organ culture.
The activity or process of determining, analyzing, or predicting all or part of an organism's phenotype.
Definition from https://www.merriam-webster.com/dictionary/phenotyping
Axioplan series, imaging fluorescence microscope
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)
A role of a student in a research project which is acknowledged in papers.
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.
Suggested by Andrea Schrader | 0000-0002-3879-7057
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.
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/)
A protocol describing a transformation method of cell, tissues or organisms.
suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074
https://microscopy.ucsf.edu/instruments/zeiss-axioimager-m1, https://profcontrol.de/Zeiss-Axio-Imager-M1m-Fluorescence-DIC-Microscope-Fluoreszenz-Mikroskop
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.
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.
Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used.
The parameters that have been applied during the extraction of genomes from metagenomic datasets.
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG.
Tools used for completion estimate, i.e. checkm, anvi'o, busco.
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.
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
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.
Heteronuclear Overhauser Effect Spectroscopy
Rotational Frame Nuclear Overhauser Effect Spectroscopy
FASTQ short read format ignoring quality scores.
A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins.
A process performed as part of an experiment or wider study, i.e. intentionally designed.
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
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
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.
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.
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.
The Illumina HiSeq 2000 is a sequencing machine developed by Illumina.
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.
The 454 GS 20 is a GS20 high-throughput sequencing machine developed by 454 Life Sciences.
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.
The 454 GS is a GS high-throughput sequencing machine developed by 454 Life Sciences.
The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences.
The 454 GS Junior is a GS high-throughput sequencing machine developed by 454 Life Sciences.
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.
The quantification of some carbohydrate, typically obtained from an individual with the intention of using the measurement in some diagnostic process.
A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species.
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.
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.
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.
The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina.
The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina.
The Illumina HiSeq 2500 is a sequencing machine developed by Illumina.
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.
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.
The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies.
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.
The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina.
The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina.
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.
chromatin interaction analysis by paired-end tag sequencing
RNA-seq is a method that involves purifying RNA and making cDNA, followed by high-throughput sequencing.
The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina.
The Illumina HiSeq 1500 is a sequencing machine developed by Illumina.
A hot spring that erupts periodically, ejecting a column of hot water and steam into the air.
A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor.
This class corresponds to the 'Tropical Mixed needleleaf / broadleaf forest' category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the 'tropical mixed needleleaf forest' class can be made. The relationship between this 'forest' class and the mangrove swamp must be clarified.
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.
Anatomical or other piece(s) or substance derived from one or more plants.
Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters.
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.
The version identifier of a packaged kit tailored for specific sequencing workflows.
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).
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.
The name of the agency that collected the original sample.
The date on which the sample was collected
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).'
Whether any method was used to select for or against, enrich, or screen the material being sequenced.
Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
Cot-filtered highly repetitive genomic DNA
Cot-filtered moderately repetitive genomic DNA
Cot-filtered single/low-copy genomic DNA
Cot-filtered theoretical single-copy genomic DNA
Hypo-methylated partial restriction digest
Selection by hybridization in array or solution.
Enrichment by methyl-CpG binding domain.
NCBI SRA: MBD2 protein methyl-CpG binding domain
MBD2 protein methyl-CpG binding domain method
Source material was selected by designed primers.
Source material was selected by randomly generated primers.
Random selection by shearing or other method.
Source material was selected by reverse transcription PCR
Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.
DNA fractionation using restriction enzymes.
PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA.
Physical selection of size appropriate targets.
Other library enrichment, screening, or selection process.
The library source specifies the type of source material that is being sequenced.
Genomic DNA (includes PCR products from genomic DNA).
Transcription products from community targets
Other, unspecified, or unknown library source material.
Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
Sequencing technique intended for this library.
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.
A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.
A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.
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.
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.
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.
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.
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.
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.
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
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.
A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.
A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.
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.
A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.
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
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.
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.
A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and 'DNA Nanoballs'.
A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day.
A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run.
A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.
A sequence data which is the short name of a gene typically derived from the gene name.
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.
A mutant in which a gene ore genes are expressed at higher levels than the wild type.
A mutant genotype in which one or more genes can have modifications (subtitutions, indels, partial truncations, etc), but they conserve functionality.
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.
a mutant in which a foreign DNA sequence is introduced to cell in an extrachromosomal unit of replication.
An optical density that specifies the amount of light of 600 nm of wavelenght the bearer is able to transmit.
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.
A biological quality that inheres in specific organisms and that describes its total genetic content
A process in which the act is intended to modify or alter some other material entity.
Reference of a protein object pointing to its genomic or nucleic acid sequence.
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.
Having no significant health-related issues.
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.
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.
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.
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.
DNA obtained directly from environmental samples (soil, sediment, water, etc.) without any obvious signs of biological source material. It originates from cellular material shed by organisms (via skin, excrement, etc.) into aquatic or terrestrial environments.
An indication that an anatomic structure has detectable aberrations.
The name of the software program capture and/or process imaging data.
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).
The non-affirmative response to a question.
The naturally-occurring, normal, non-mutated version of a gene or genome.
In botanical nomenclature, a rank below subspecies but above forma.
RNA present in the cytoplasm. It is involved in the protein export process from the cells.
Parameters used in the NMR spectrometry acquisition.
The intensity of an electric, magnetic, or other field.
The number of repeat scans performed and summed to create the data set for an NMR sample.
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
A planned process which results in physical changes in a specified input material
Is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.
Is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
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.
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.
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.
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.
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.
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.
A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.
A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.
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.
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.
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.
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)
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
Class "Objective" is microscopes' objective lens. 19.02.2024: term has been deprecated, please use REPR:Objective
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.
A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (biotic plant exposurePECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357plant experimental condition) or set of conditions describing the application of an abiotic (abiotic plant exposure) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof.
cardinal part of multi-tissue plant structure
Describes gel-based quantification methods
Describes gel-free quantification methods
Describes quantification techniques using isotope labeling
Describes quantification techniques based on selected / multiple reaction monitoring
Describes label free quantification techniques.
Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level
Tandem Mass Tag is a MS2 based isotope labeling quantification technique
Stable isotope labeling with amino acids in cell culture
Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification
Describes isotope labeling quantification techniques detectable at MS1 level.
The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen.
Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements.
AQUA is an isotope labeling based quantification technique that uses known peptides.
Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses.
Exponentially Modified Protein Abundance Index
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.
The Total Ion Current (TIC) can be measured or calculated in order to target specific ions.
MS1 intensity based label-free quantification method
Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140.
Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140
Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140
Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140
The spectrum count is normalized for protein length. Method reviewed in PMID 22772140
Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140
Normalized Spectral Abundance Factor - NSAF
Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140
Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method.
Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis.
Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825
A biotic plant stress caused by exposure to an environment containing a biological stress agent.
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.
Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane
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
A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid.
Microscope slide mounting medium (substance)
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
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.
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.
The first base to be translated into protein.
The last base to be translated into protein. It does not include the stop codon.
A promoter that can allow for transcription in both directions.
Definition updated in Aug 2020 by Dave Sant.
A unit which is a standard measure of the rate of change of velocity in either speed or direction.
Sequencing technique intended for a next generation sequencing library.
term is redundant, please use GENEPIO:0001973
Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.
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.
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.