"Mickael Silva" João Carriço OWL NGSOnto This ontology aims to describe and anotate all pipelines of a NGS process, starting from DNA extraction from an isolate to the assembled draft genome, allowing the reproducibility of the processes. nConstructed from BFO (Basic Formal Ontology), an upper level ontology (http://www.ifomis.org/bfo) and designed based on NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) and EMBL-EBI European Nucleotide Archive (http://www.ebi.ac.uk/ena/) public data. editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred term editor preferred term example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term has role Sequenced on used function has protocol has step has workflow starts with ends with adaptor ammount DNA buffer end repair enzyme extraction method file file extension fragmentation method library type name parameter designation parameter value range of fragments size reference genome scaffolding script file script language sequence coverage size selector software version strategy study description study title study type tailing uri version date index DNA Extraction kit name password Activation username Task ID mail box ns1:data_2527 beta12orEarlier "Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org] Slightly narrower in the sense of changing the characteristics of a system/function. data data:0961 data:1773 data:2029 bioinformatics data edam Parameter Parameter or primitive Tool parameter Tool-specific parameter parameter Parameter Parameter or primitive Tool parameter Tool-specific parameter parameter Jon Ison "Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org]nnhttp://edamontology.org/data_2527 Parameter Parameter ns1:operation_0310 For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. beta12orEarlier "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] operation bioinformatics edam operations Jon Ison Sequence assembly ns1:operation_0369 beta12orEarlier "Cut (remove) characters or a region from a molecular sequence." [http://edamontology.org] operation bioinformatics edam operations Jon Ison Sequence cutting ns1:operation_0523 The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. beta12orEarlier "Sequence assembly by combining fragments using an existing backbone sequence." [http://edamontology.org] operation bioinformatics edam operations Jon Ison Sequence assembly (mapping assembly) ns1:operation_0524 De-novo assemblers are much slower and more memory intensive than mapping assemblers. beta12orEarlier "Sequence assembly by combining fragments into a new, previously unknown sequence." [http://edamontology.org] operation bioinformatics edam operations Jon Ison Sequence assembly (de-novo assembly) ns1:operation_3218 Raw sequence data quality control. Sequencing QC 1.1 Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems. Sequencing quality control 1 1 oboOther:IAO_0000010 software see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.nnhttp://purl.obolibrary.org/obo/IAO_0000010 software oboOther:IAO_0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. 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 that reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item oboOther:IAO_0000104 plan specification To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes. a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 plan specification 1 oboOther:IAO_0000591 software method A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 software method 1 oboOther:IAO_0000595 software script PERSON: Melanie Courtot PERSON: Michel Dumontier http://code.google.com/p/information-artifact-ontology/issues/detail?id=80 A manual script is string or file whose instructions can be executed using a software interpreter. software script oboOther:NCBITaxon_9606 Homo sapiens oboOther:NGS_0000001 Collection of the 5' and 3' ends of DNA or cDNA fragments. Represents the output of a Library Preparation process. Library oboOther:NGS_0000003 Reads that have suffered some processing. Processed Reads oboOther:NGS_0000004 Raw output of a Sequencing Process. Raw Reads 1 1 1 oboOther:NGS_0000006 A single process execution that may occur within a NGS pipeline. Next Generation Sequencing Process oboOther:NGS_0000007 Post Sequencing processing of the reads. Data processing oboOther:NGS_0000008 Selection of a set of reads considering a set of parameters. Filtering oboOther:NGS_0000061 A result output of a single process. This output may be an input for another process . Message 1 1 oboOther:NGS_0000064 Data Processing protocol oboOther:NGS_0000065 Sequence cutting protocol oboOther:NGS_0000066 Resource that provides access to software, applications, or toolkits that perform alter the spatial-temporal spectral content of data.nnhttp://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Filtering Filtering protocol 1 oboOther:NGS_0000067 DNA Extraction Protocol 1 1 1 1 1 1 oboOther:NGS_0000068 Library Preparation Protocol 1 1 oboOther:NGS_0000069 Sequence assembly protocol 1 1 oboOther:NGS_0000070 de-novo assembly protocol oboOther:NGS_0000071 mapping assembly protocol 1 oboOther:NGS_0000072 sequencing protocol 1 oboOther:NGS_0000073 An index that represents the place in an ordered sequence. Step 1 oboOther:NGS_0000074 Index of a sequence of worklfows used in the concretization of a pipeline. Execution step 1 oboOther:NGS_0000075 Index of a sequence of protocols performed in a workflow. NGS Workflow step 1 1 oboOther:NGS_0000088 Sequencing quality control protocol 1 1 oboOther:NGS_0000090 Allele Call Protocol oboOther:OBI_0000011 planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process 1 1 1 oboOther:OBI_0000066 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification study investigation oboOther:OBI_0000202 investigation agent role oboOther:OBI_0000245 organization oboOther:OBI_0000257 DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction 1 oboOther:OBI_0000272 protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. 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. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol oboOther:OBI_0000435 Allele Call Allele call oboOther:OBI_0000471 study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that realizes the concretization of a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. pipeline study design execution 1 oboOther:OBI_0000626 DNA sequencing Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858 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. Philippe Rocca-Serra OBI Branch derived nucleotide sequencing DNA sequencing oboOther:OBI_0000711 library preparation PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. 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. Philippe Rocca-Serra library construction library preparation oboOther:OBI_0000747 material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample oboOther:OBI_0000968 device 1 oboOther:OBI_0001051 DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract oboOther:OBI_0001305 Allele Matrix 1 1 oboOther:OBI_0001573 DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. DNA sequence data 1 1 1 oboOther:OBI_0400103 DNA sequencer ABI 377 DNA Sequencer, ABI 310 DNA Sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.nntnnhttp://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer 1 oboOther:OBI_0500000 study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design 1 1 oboOther:SO_0000149 A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. SO:0000149 SOFA http://en.wikipedia.org/wiki/Contig A set of overlapping DNA segments that together represent a consensus region of DNA. Represents the output of a De-novo assembly process contig 1 oboOther:SO_0000150 A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. SO:0000150 SOFA A string or a file that contains a nucleotid sequence representing that read. read ns4:Sample ns6:Isolate material entity An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Examples: collection of random bacteria, a chair, dorsal surface of the body Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. material entity process the life of an organism the process of cell-division the process of sleeping A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. process has part has_part has part Possession relation between an agent and a study or pipeline. Belong To used Parameter used Software execute is a Run of has performer performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system) has performer p has input c if either: p has direct input c or p has indirect input c. See subrelations for definitions. consumes has input p has output c if either: p has direct output c or p has output input c. See subrelations for definitions. produces has output "Mickael Silva" João Carriço OWL NGSOnto This ontology aims to describe and anotate all pipelines of a NGS process, starting from DNA extraction from an isolate to the assembled draft genome, allowing the reproducibility of the processes. nConstructed from BFO (Basic Formal Ontology), an upper level ontology (http://www.ifomis.org/bfo) and designed based on NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) and EMBL-EBI European Nucleotide Archive (http://www.ebi.ac.uk/ena/) public data.