Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/OBI_0002465 age since culture seeding measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum 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). http://purl.obolibrary.org/obo/OBI_0002472 dbGaP study identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol dbGaP accession number A central registered identifier symbol that denotes a specific study in dbGaP. http://purl.obolibrary.org/obo/OBI_0002475 number of PCR cycles during library construction http://purl.obolibrary.org/obo/IAO_0000027 data item library construction PCR cycles A data item that is the number of PCR cycles used during the construction of a sequencing library. http://purl.obolibrary.org/obo/OBI_0002479 sequence read length measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum 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. http://purl.obolibrary.org/obo/OBI_0002480 sequencing library input quantity measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum library input amount A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. http://purl.obolibrary.org/obo/OBI_0002482 specimen harvest quantity http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum harvest quantity A scalar measurement datum that indicates the amount of specimen collected. http://purl.obolibrary.org/obo/OBI_0002464 SRS identifier http://purl.obolibrary.org/obo/NCIT_C25402 Accession Number 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. http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data 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. http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol http://purl.obolibrary.org/obo/IAO_0000028 symbol CRID symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/OBI_0000018 material supplier role http://purl.obolibrary.org/obo/OBI_0000947 service provider role supplier a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. http://purl.obolibrary.org/obo/OBI_0000025 reference substance role http://purl.obolibrary.org/obo/BFO_0000023 role reference substance a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/OBI_0000011 planned process scientific observation A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. http://purl.obolibrary.org/obo/OBI_0000094 material processing http://purl.obolibrary.org/obo/OBI_0000011 planned process material transformation A planned process which results in physical changes in a specified input material http://purl.obolibrary.org/obo/OBI_0000102 responsible party role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role responsible party 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 http://purl.obolibrary.org/obo/OBI_0000103 principal investigator role http://purl.obolibrary.org/obo/OBI_0000102 responsible party role principal investigator a responsible party role played by a person responsible for the overall conduct of a study http://purl.obolibrary.org/obo/OBI_0000116 worker role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role worker 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 http://purl.obolibrary.org/obo/OBI_0000198 biological replicate role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role biological replicate a reference participant role realized by equivalent treatment of participants http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role http://purl.obolibrary.org/obo/BFO_0000023 role investigator 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. http://purl.obolibrary.org/obo/OBI_0000220 reference subject role http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role reference participant 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 http://purl.obolibrary.org/obo/OBI_0000249 technical replicate role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role technical replicate technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification PCR 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. http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process http://purl.obolibrary.org/obo/OBI_0000011 planned process specimen collection A planned process with the objective of collecting a specimen. http://purl.obolibrary.org/obo/OBI_0000711 library preparation http://purl.obolibrary.org/obo/OBI_0000094 material processing library construction 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. http://purl.obolibrary.org/obo/OBI_0000722 paired-end library http://purl.obolibrary.org/obo/OBI_0000047 processed material paired-end tag (PET) library is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs http://purl.obolibrary.org/obo/OBI_0000968 device http://purl.obolibrary.org/obo/OBI_0000047 processed material instrument A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. http://purl.obolibrary.org/obo/OBI_0001185 selectively maintained organism http://purl.obolibrary.org/obo/OBI_0100026 organism strain An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay transcription profiling by high throughput sequencing 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 http://purl.obolibrary.org/obo/OBI_0001616 specimen identifier http://purl.obolibrary.org/obo/IAO_0000028 symbol specimen ID A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. http://purl.obolibrary.org/obo/OBI_0001850 transcript analysis by paired-end tag sequencing http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RNA-PET assay An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions. http://purl.obolibrary.org/obo/OMIABIS_0001039 date of specimen collection http://purl.obolibrary.org/obo/IAO_0000027 data item date of specimen preparation A data item that indicates the time when the collection of a specimen occurred. http://purl.obolibrary.org/obo/OBIws_0000106 sequence data format specification http://purl.obolibrary.org/obo/IAO_0000098 data format specification sequence data format A data format specification for molecular sequence feature information. http://purl.obolibrary.org/obo/OBI_0002466 alignment counting algorithm http://purl.obolibrary.org/obo/IAO_0000064 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). http://purl.obolibrary.org/obo/OBI_0002467 alignment counting application http://purl.obolibrary.org/obo/IAO_0000594 software application A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes. http://purl.obolibrary.org/obo/OBI_0002468 base calling algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer http://purl.obolibrary.org/obo/OBI_0002469 base calling application http://purl.obolibrary.org/obo/IAO_0000594 software application A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis. http://purl.obolibrary.org/obo/OBI_0002461 BCL format http://purl.obolibrary.org/obo/IAO_0000098 data format specification 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. http://purl.obolibrary.org/obo/OBI_0002470 bcl2fastq software application http://purl.obolibrary.org/obo/OBI_0002469 base calling 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. http://purl.obolibrary.org/obo/OBI_0002471 date process started http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is the date when a process was initiated. http://purl.obolibrary.org/obo/OBI_0002462 ERCC RNA spike-in http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids. http://purl.obolibrary.org/obo/OBI_0002473 material amplification role http://purl.obolibrary.org/obo/OBI_0000116 worker role A worker role played by the person who runs the enzymatic amplifying process. http://purl.obolibrary.org/obo/OBI_0002474 material sequencing library preparation role http://purl.obolibrary.org/obo/OBI_0000116 worker 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. http://purl.obolibrary.org/obo/OBI_0002487 microraft http://purl.obolibrary.org/obo/OBI_0000932 material separation device A material separation device also commerically known as Isoraft, that is used to isolate single cells. http://purl.obolibrary.org/obo/OBI_0002476 number of rounds of amplification http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is the number of times an amplification reaction happened. http://purl.obolibrary.org/obo/OBI_0002488 pipette http://purl.obolibrary.org/obo/OBI_0000968 device 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. http://purl.obolibrary.org/obo/OBI_0002477 reference genome role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role A reference substance role that is played by a reference genome when used during sequence alignment. http://purl.obolibrary.org/obo/OBI_0002478 reference genome-transcriptome alignment algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome. http://purl.obolibrary.org/obo/OBI_0002481 single-end library http://purl.obolibrary.org/obo/OBI_0000047 processed material A cDNA library that is a collection of short tags from only one end of DNA fragments. http://purl.obolibrary.org/obo/OBI_0002463 SIRV RNA spike-in http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material that 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. http://purl.obolibrary.org/obo/OBI_0002483 spike-in dilution factor http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that indicates the dilution of spike-in added to a specimen. http://purl.obolibrary.org/obo/OBI_0002484 star algorithm http://purl.obolibrary.org/obo/OBI_0002478 reference genome-transcriptome alignment 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. http://purl.obolibrary.org/obo/OBI_0002485 transcript analysis by single-end sequencing http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. http://purl.obolibrary.org/obo/OBI_0002486 verse algorithm http://purl.obolibrary.org/obo/OBI_0002466 alignment counting 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. http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/NCIT_C25364 Identifier http://purl.obolibrary.org/obo/NCIT_C19498 Document One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) http://purl.obolibrary.org/obo/IAO_0000010 software http://purl.obolibrary.org/obo/IAO_0000104 plan specification Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. http://purl.obolibrary.org/obo/IAO_0000017 model number http://purl.obolibrary.org/obo/IAO_0000028 symbol 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. http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant A generically dependent continuant that is about some thing. http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000027 data item An information content entity whose concretizations indicate to their bearer how to realize them in a process. http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000104 plan specification 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. http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity 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 http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity 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. http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000027 data item A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measuring a temporal interval http://purl.obolibrary.org/obo/IAO_0000594 software application http://purl.obolibrary.org/obo/IAO_0000010 software A software application is software that can be directly executed by some processing unit. http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000015 process A processual entity that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/OBI_0000047 processed material http://purl.obolibrary.org/obo/BFO_0000040 material entity Is a material entity that is created or changed during material processing. http://purl.obolibrary.org/obo/OBI_0000091 detector reagent role http://purl.obolibrary.org/obo/BFO_0000023 role a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role http://purl.obolibrary.org/obo/BFO_0000023 role 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. http://purl.obolibrary.org/obo/OBI_0000181 population http://purl.obolibrary.org/obo/BFO_0000040 material entity 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 http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/BFO_0000040 material entity 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. http://purl.obolibrary.org/obo/OBI_0000272 protocol http://purl.obolibrary.org/obo/IAO_0000104 plan specification 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. http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay 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. http://purl.obolibrary.org/obo/OBI_0000832 measurement device http://purl.obolibrary.org/obo/OBI_0000968 device A device in which a measure function inheres. http://purl.obolibrary.org/obo/OBI_0000835 manufacturer http://purl.obolibrary.org/obo/BFO_0000040 material entity A person or organization that has a manufacturer role http://purl.obolibrary.org/obo/OBI_0000932 material separation device http://purl.obolibrary.org/obo/OBI_0000968 device A device with a separation function realized in a planed process http://purl.obolibrary.org/obo/OBI_0000947 service provider role http://purl.obolibrary.org/obo/BFO_0000023 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 http://purl.obolibrary.org/obo/OBI_0000973 sequence data http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. http://purl.obolibrary.org/obo/OBI_0001140 spike-in quality control role http://purl.obolibrary.org/obo/OBI_0000025 reference substance 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 http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measurement of age of an organism http://purl.obolibrary.org/obo/OBI_0001169 age since birth measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age 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. http://purl.obolibrary.org/obo/OBI_0001468 cell specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. http://purl.obolibrary.org/obo/OBI_0001494 linear amplification http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. http://purl.obolibrary.org/obo/OBI_0001852 paired-end library preparation http://purl.obolibrary.org/obo/OBI_0000711 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. http://purl.obolibrary.org/obo/OBI_0001891 sequencing facility organization http://purl.obolibrary.org/obo/OBI_0000245 organization An organization that provides sequence determination service http://purl.obolibrary.org/obo/OBI_0001895 specimen collector http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens A person who collects the specimen http://purl.obolibrary.org/obo/OBI_0001933 value specification http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that specifies a value within a classification scheme or on a quantitative scale. http://purl.obolibrary.org/obo/OBI_0001959 sequencing library multiplexing http://purl.obolibrary.org/obo/OBI_0000094 material processing 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. http://purl.obolibrary.org/obo/OBI_0001967 multiplexing sequence identifier http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid 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 http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/BFO_0000040 material entity 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. http://purl.obolibrary.org/obo/OBI_0100051 specimen http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that has the specimen role. http://purl.obolibrary.org/obo/OBI_0400099 flow cytometer sorter http://purl.obolibrary.org/obo/OBI_0000932 material separation device 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. http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay http://purl.obolibrary.org/obo/OBI_0000070 assay the use of a chemical or biochemical means to infer the sequence of a biomaterial http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification http://purl.obolibrary.org/obo/OBI_0000094 material processing the use of enzymes to increase the number of molecules of a biomaterial http://purl.obolibrary.org/obo/OGMS_0000090 treatment http://purl.obolibrary.org/obo/OBI_0000011 planned process A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder http://purl.obolibrary.org/obo/OMIABIS_0000100 study principle investigator or responsible http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens The principle investigtor or responsible person for a study or a sample collection. http://purl.obolibrary.org/obo/NCIT_C25402 Accession Number http://purl.obolibrary.org/obo/NCIT_C70663 Unique Identifier A control number unique to an object. It is used to identify the object among other objects in a collection. http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. http://purl.obolibrary.org/obo/CL_0000000 cell http://purl.obolibrary.org/obo/BFO_0000040 material entity 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. http://purl.obolibrary.org/obo/CL_0000127 astrocyte http://purl.obolibrary.org/obo/CL_0000000 cell 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. http://purl.obolibrary.org/obo/CL_0000449 brown fat cell http://purl.obolibrary.org/obo/CL_0000000 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. http://purl.obolibrary.org/obo/CL_0000540 neuron http://purl.obolibrary.org/obo/CL_0000000 cell 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. http://purl.obolibrary.org/obo/CL_0000746 cardiac muscle cell http://purl.obolibrary.org/obo/CL_0000000 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. http://purl.obolibrary.org/obo/GO_0005575 cellular_component http://purl.obolibrary.org/obo/BFO_0000040 material entity A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). http://purl.obolibrary.org/obo/GO_0044464 cell part http://purl.obolibrary.org/obo/GO_0005575 cellular_component Any constituent part of a cell, the basic structural and functional unit of all organisms. http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Anatomical entity that has mass. http://purl.obolibrary.org/obo/GENEPIO_0000069 sequencing run date http://purl.obolibrary.org/obo/IAO_0000027 data item date the sequencing run was performed http://purl.obolibrary.org/obo/GENEPIO_0000081 sequencing kit http://purl.obolibrary.org/obo/OBI_0000047 processed material 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. http://purl.obolibrary.org/obo/GENEPIO_0000085 library preparation kit http://purl.obolibrary.org/obo/OBI_0000047 processed material 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. http://purl.obolibrary.org/obo/SO_0001505 reference_genome http://www.ebi.ac.uk/efo/EFO_0004420 genome A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. http://purl.obolibrary.org/obo/TAXRANK_0000000 taxonomic_rank http://purl.obolibrary.org/obo/GENEPIO_0001170 organism datum A level of depth of a taxon in a taxonomic hierarchy. http://www.ebi.ac.uk/efo/EFO_0005630 CEL data file format http://purl.obolibrary.org/obo/IAO_0000098 data format specification 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. http://purl.obolibrary.org/obo/NCIT_C19498 Document http://purl.obolibrary.org/obo/NCIT_C25198 Record A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable. http://purl.obolibrary.org/obo/OBIws_0000015 pairwise sequence alignment algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences). http://purl.obolibrary.org/obo/OBIws_0000088 BLAST algorithm http://purl.obolibrary.org/obo/OBIws_0000015 pairwise sequence alignment 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. http://purl.obolibrary.org/obo/OBIws_0000140 BLASTn http://purl.obolibrary.org/obo/OBIws_0000088 BLAST algorithm A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level. http://purl.obolibrary.org/obo/OBIws_0000192 RNA sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data A sequence data that is about the primary structure of RNA. http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0044464 cell part 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. http://purl.obolibrary.org/obo/GO_0030425 dendrite http://purl.obolibrary.org/obo/GO_0044464 cell part A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses 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. http://purl.obolibrary.org/obo/GO_0044297 cell body http://purl.obolibrary.org/obo/GO_0044464 cell part The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. http://www.ebi.ac.uk/efo/EFO_0000683 replicate http://purl.obolibrary.org/obo/BFO_0000023 role 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. http://www.ebi.ac.uk/efo/EFO_0004155 FASTQ format http://purl.obolibrary.org/obo/IAO_0000098 data format specification FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. http://www.ebi.ac.uk/efo/EFO_0004157 BAM format http://purl.obolibrary.org/obo/IAO_0000098 data format specification BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format http://www.ebi.ac.uk/efo/EFO_0004420 genome http://purl.obolibrary.org/obo/BFO_0000040 material entity A genome is the full genetic content of an organism, contained in either DNA or RNA (such as for viruses). http://www.ebi.ac.uk/efo/EFO_0004421 transcriptome http://purl.obolibrary.org/obo/BFO_0000040 material entity 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. http://purl.obolibrary.org/obo/CL_2000029 central nervous system neuron http://purl.obolibrary.org/obo/CL_0000540 neuron Any neuron that is part of a central nervous system. http://purl.obolibrary.org/obo/NCIT_C25198 Record http://purl.obolibrary.org/obo/NCIT_C20181 Conceptual Entity Anything (e.g., a document) providing permanent evidence of or information about past events. http://purl.obolibrary.org/obo/NCIT_C70663 Unique Identifier http://purl.obolibrary.org/obo/NCIT_C25364 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. http://purl.obolibrary.org/obo/OBI_0002127 single cell specimen http://purl.obolibrary.org/obo/OBI_0001468 cell specimen A cell specimen that contains only one cell. http://purl.obolibrary.org/obo/ORNASEQ_0000001 date of specimen amplification http://purl.obolibrary.org/obo/OBI_0002471 date process started amplified date http://purl.obolibrary.org/obo/ORNASEQ_0000002 date of specimen library preparation http://purl.obolibrary.org/obo/OBI_0002471 date process started library preparation date http://purl.obolibrary.org/obo/ORNASEQ_0000003 enzymatic amplification protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol amplification protocol http://purl.obolibrary.org/obo/ORNASEQ_0000017 verse http://purl.obolibrary.org/obo/OBI_0002467 alignment counting application http://purl.obolibrary.org/obo/ORNASEQ_0000012 RNA harvest compound http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/ORNASEQ_0000013 specimen harvest source type http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/ORNASEQ_0000014 specimen harvest source unit http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/ORNASEQ_0000008 number of flow cell lanes http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/ORNASEQ_0000009 number of flow cells http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/ORNASEQ_0000004 experiment name http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/NCBITaxon#_taxonomic_rank taxonomic rank http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/GENEPIO_0001170 organism datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/ORNASEQ_0000010 pairwise sequence alignment application http://purl.obolibrary.org/obo/IAO_0000594 software application http://purl.obolibrary.org/obo/ORNASEQ_0000007 library preparation protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/ORNASEQ_0000011 region of material anatomical entity http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity http://purl.obolibrary.org/obo/ORNASEQ_0000005 Illumina TruSeq Rapid SBS Kit v2 http://purl.obolibrary.org/obo/GENEPIO_0000081 sequencing kit http://purl.obolibrary.org/obo/ORNASEQ_0000006 Illumina TruSeq Stranded http://purl.obolibrary.org/obo/GENEPIO_0000085 library preparation kit http://purl.obolibrary.org/obo/TAXRANK_0000006 species http://purl.obolibrary.org/obo/TAXRANK_0000000 taxonomic_rank http://purl.obolibrary.org/obo/ORNASEQ_0000015 star http://purl.obolibrary.org/obo/ORNASEQ_0000010 pairwise sequence alignment application http://purl.obolibrary.org/obo/ORNASEQ_0000016 TIVA tag http://purl.obolibrary.org/obo/ORNASEQ_0000012 RNA harvest compound http://purl.obolibrary.org/obo/NCIT_C20181 Conceptual Entity An organizational header for concepts representing mostly abstract entities. http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of http://purl.obolibrary.org/obo/RO_0000056 participates in A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/RO_0002223 starts http://purl.obolibrary.org/obo/BFO_0000050 part of inverse of starts with http://purl.obolibrary.org/obo/RO_0000087 has role http://purl.obolibrary.org/obo/RO_0000053 bearer of a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002131 overlaps http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000050 part of http://purl.obolibrary.org/obo/RO_0002131 overlaps a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/RO_0000053 bearer of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000056 participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to A mereological relationship or a topological relationship