ORNASEQ: Ontology for RNA sequencing
June 2018
Copyright © 2018 Stephen Fisher and Junhyong Kim, All rights reserved.
This work is licensed under the Creative Commons Attribution 4.0 International License.
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Thing
entity
continuant
Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. 8216;My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant. (BFO)
independent continuant
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. (BFO)
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. (CHEBI)
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. (CHEBI)
multiplexing sequence identifier
A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library (OBI)
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. (CL)
astrocyte
A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury. (CL)
brown adipose cell
A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation. (CL)
neuron
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. (CL)
central nervous system neuron
Any neuron that is part of a central nervous system. (CL)
cardiac muscle cell
Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. (CL)
cellular_component
The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. (GO)
cell part
Any constituent part of a cell, the basic structural and functional unit of all organisms. (GO)
mitochondria
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. (GO)
dendrite
A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. (GO)
cell body
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. (GO)
processed material
Is a material entity that is created or changed during material processing. (OBI)
sequencing kit
Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. (GENEPIO)
Illumina TruSeq Rapid SBS Kit v2
A processed material that is a sequencing kit used with Illumina HiSeq 2500 and 1500 sequencers allowing for single-end or paired-end sequencing. (ORNASEQ)
library preparation kit
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. (GENEPIO)
Illumina TruSeq Stranded
A processed material that is used to create a sequencing library that retains mRNA strand orientation. (ORNASEQ)
paired-end library
Is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs (OBI)
device
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. (OBI)
measurement device
A device in which a measure function inheres. (OBI)
DNA sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. (OBI)
material separation device
A device with a separation function realized in a planed process (OBI)
flow cytometer sorter
A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. (OBI)
microraft
A material separation device also commerically known as Isoraft, that is used to isolate single cells. (OBI)
pipette
A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. (OBI)
ERCC RNA spike-in
A processed material developed by External RNA Controls Consortium (ERCC) that is consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids. (OBI)
SIRV RNA spike-in
A processed material that is consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes. (OBI)
single-end library
A processed material that is a collection of short tags from only one end of DNA fragments. (OBI)
population
A population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area (OBI)
organization
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. (OBI)
sequencing facility organization
An organization that provides sequence determination service (OBI)
manufacturer
A person or organization that has a manufacturer role (OBI)
organism
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. (OBI)
Homo sapiens
specimen collector
A person who collects the specimen (OBI)
study principle investigator or responsible
The principle investigtor or responsible person for a study or a sample collection. (OMIABIS)
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms (OBI)
specimen
A material entity that has the specimen role. (OBI)
material anatomical entity
Anatomical entity that has mass. (UBERON)
region of material anatomical entity
An area within a material anatomical entity that is distinct from the other areas of that entity such as the parietal cortex, hippocampus CA1 and amygdala. (ORNASEQ)
genome
A genome is the full genetic content of an organism, contained in either DNA or RNA (such as for viruses). (EFO)
reference genome
A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. (SO)
transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. (EFO)
specimen harvest source type
A material entity that contained the specimen during harvesting such as a primary culture, tissue, or fixed section. (ORNASEQ)
specimen harvest source unit
A material entity that represents the number of number of material entities used during harvesting; for example, a single cell, pooled single cells, tissue, a culture dish, or a coverslip. (ORNASEQ)
specifically dependent continuant
realizable entity
role
reference substance role
A role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. (OBI)
spike-in quality control role
A reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes (OBI)
reference genome role
A reference substance role that is played by a reference genome when used during sequence alignment. (OBI)
detector reagent role
A role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. (OBI)
participant under investigation
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. (OBI)
reference subject role
A reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference (OBI)
biological replicate role
A reference participant role realized by equivalent treatment of participants (OBI)
technical replicate role
Technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay (OBI)
investigation agent role
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. (OBI)
responsible party role
A study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study (OBI)
principal investigator role
A responsible party role played by a person responsible for the overall conduct of a study (OBI)
worker role
A personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline (OBI)
material amplification role
A worker role played by the person who runs the enzymatic amplifying process. (OBI)
material sequencing library preparation role
A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced. (OBI)
service provider role
Is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person (OBI)
material supplier role
A role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. (OBI)
replicate
A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured. (EFO)
generically dependent continuant
information content entity
A generically dependent continuant that is about some thing. (IAO)
data item
A data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. (IAO)
sequencing run date
Date the sequencing run was performed (GENEPIO)
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process. (IAO)
data format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file (IAO)
sequence data format specification
A data format specification for molecular sequence feature information. (OBIws)
FASTQ format
FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. (EFO)
BAM format
BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format (EFO)
CEL data file format
CEL data file format describes the format used in a CEL file for storing the results of the intensity calculations on the pixel values of a DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. (EFO)
BCL format
A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell. (OBI)
plan specification
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. (IAO)
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. (IAO)
software application
A software application is software that can be directly executed by some processing unit. (IAO)
alignment counting application
A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes. (OBI)
verse
An alignment counting application that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. (ORNASEQ)
base calling application
A software application that implements a base calling algorithm (OBI)
bcl2fastq software application
A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. (OBI)
pairwise sequence alignment application
A software application that implements a pairwise sequence alignment algorithm to attempt to align two molecular sequences (nucleic acid or protein sequences). (ORNASEQ)
star
A software application that implements a RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference. (ORNASEQ)
algorithm
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. (IAO)
pairwise sequence alignment algorithm
An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences). (OBIws)
blast algorithm
BLAST (Basic Local Alignment Search Tool), a pairwise sequence alignment algorithm is a heuristic search algorithm for comparing primary biological sequence information, such as the amino-acid or nucleotides sequences with a database of sequences, and identify sequences that resemble the query sequence above a certain threshold. (OBIws)
blastn
A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level. (OBIws)
alignment counting algorithm
An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts). (OBI)
verse algorithm
An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. (OBI)
base calling algorithm
An algorithm that assigns nucleotides to temporal or spacial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer (OBI)
reference genome-transcriptome alignment algorithm
An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome. (OBI)
star algorithm
A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference. (OBI)
protocol
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. (OBI)
enzymatic amplification protocol (aka amplification protocol)
A protocol document that contains detailed instructions on how to perform an enzymatic amplification planned process. (ORNASEQ)
library preparation protocol
A protocol document that contains detailed instructions on how to perform a library preparation planned process. (ORNASEQ)
measurement datum
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. (IAO)
organism datum
scalar measurement datum
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. (IAO)
time measurement datum
A scalar measurement datum that is the result of measuring a temporal interval (IAO)
age measurement datum
A time measurement datum that is the result of measurement of age of an organism (OBI)
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. (OBI)
age since culture seeding measurement datum (aka age of culture)
An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). (OBI)
sequencing library input quantity measurement datum (aka library input amount)
A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. (OBI)
specimen harvest quantity (aka harvest quantity)
A scalar measurement datum that indicates the amount of specimen collected. (OBI)
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. (OBI)
RNA sequence data
A sequence data that is about the primary structure of RNA. (OBIws)
sequence read length measurement datum (aka read length, read length measurement datum)
A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. (OBI)
date of specimen collection
A data item that indicates the time when the collection of a specimen occurred. (OMIABIS)
date process started
A data item that is the date when a process was initiated. (OBI)
date of specimen amplification (aka amplified date)
A date process started item that indicates when a specimen was run through the amplification protocol prior to library preparation and sequencing. (ORNASEQ)
date of specimen library preparation (aka library preparation date)
A date process started item that indicates when a specimen was run through the library preparation protocol prior to sequencing. (ORNASEQ)
number of PCR cycles during library construction (aka library construction PCR cycles)
A data item that is the number of PCR cycles used during the construction of a sequencing library. (OBI)
number of rounds of amplification
A data item that is the number of times an amplification reaction happened. (OBI)
spike-in dilution factor
A data item that indicates the dilution of spike-in added to a specimen. (OBI)
number of flow cell lanes
A data item that indicates the number of lanes in a flow cell that were used to sequence a specimen (ORNASEQ)
number of flow cells
A data item that indicates the number of flow cells used to sequence a specimen. (ORNASEQ)
symbol
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. (IAO)
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. (IAO)
centrally registered identifier symbol
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. (IAO)
dbGaP identifier symbol (aka dbGaP accession number, dbGaP study identifier, dbGaP release)
A central registered identifier symbol that denotes a specific study in dbGaP. (OBI)
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. (OBI)
experiment name
The name for identifying an experiment. (ORNASEQ)
value specification
An information content entity that specifies a value within a classification scheme or on a quantitative scale. (OBI)
occurrent
process
planned process
A processual entity that realizes a plan which is the concretization of a plan specification. (OBI)
assay
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. (OBI)
sequencing assay
The use of a chemical or biochemical means to infer the sequence of a biomaterial (OBI)
DNA sequencing
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. (OBI)
RNA-seq assay
An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance (OBI)
transcript analysis by paired-end tag sequencing
An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions. (OBI)
transcript analysis by single-end sequencing
A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. (OBI)
material processing
A planned process which results in physical changes in a specified input material (OBI)
library preparation
Is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. (OBI)
paired-end library preparation
A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. (OBI)
sequencing library multiplexing
A planned process which consists in running a set of samples as a pool in one single instrument run of data acquisition process while retaining the ability to associate individual results to each of the individual input samples thanks to the use of a multiplex identifier, introduced during the ligation step of the individual library preparation and specific to a given sample. (OBI)
enzymatic amplification
The use of enzymes to increase the number of molecules of a biomaterial (OBI)
polymerase chain reaction
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. (OBI)
linear amplification
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. (OBI)
specimen collection process
A planned process with the objective of collecting a specimen. (OBI)
treatment
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder (OGMS)
conceptual entity
An organizational header for concepts representing mostly abstract entities. (NCIT)
record
Anything (e.g., a document) providing permanent evidence of or information about past events. (NCIT)
document
A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable. (NCIT)
identifier
One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing. (NCIT)
unique identifier
A set of characters used as a code that is unique in the context or the system for which it is created. It serves as a means of identification and reference (often instead of a name) for an entity, person, thing, function, procedure, activity, variable, or body of data. (NCIT)
accession number
A control number unique to an object. It is used to identify the object among other objects in a collection. (NCIT)
SRS identifier (aka SRA sample accession number)
An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database. (OBI)