Joe White Eric Deutsch draft version Daniel Schober Robert Stevens Frank Gibson Allyson Lister Jeffrey Grethe Alan Ruttenberg 1.0.1213 Philippe Rocca-Serra James Malone Liju Fan Barry Smith Tanya Gray Richard Scheuermann Monnie McGee Helen Parkinson Bill Bug Dawn Field Ryan R. Brinkman Ontology for Biomedical Investigation Susanna-Assunta Sansone Helen C. Causton Melanie Courtot Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Chris Stoeckert Kevin Clancy Elisabetta Manduchi Luisa Montecchi Daniel Rubin Stefan Wiemann An ontology for the annotation of biomedical and functional genomics experiments. OWL-DL free, no license required. Chris Taylor Cristian Cocos Jennifer Fostel en Gilberto Fragoso Norman Morrison Mervi Heiskanen Trish Whetzel Tina Hernandez-Boussard Bjoern Peters 2008-11-28 The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. buffer role Philippe Rocca-Serra buffer OBI http://medical.merriam-webster.com/medical/cytometer A cytometer is an instrument for counting and measuring cells. cytometer Melanie Courtot cytometer image aquisition function An image aquisition function is a function to aquire an image of a material Frank Gibson image aquisition function Jennifer Fostel Clinical laboratory is a worker role involved in carrying out assay protocols on specimens derived from a study; this activity occurs outside the study timeline Clinical laboratory clinical laboratory role source pending biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. example_of_usage to be added biological feature identification objective Jennifer Fostel Special population is an eligible population role played by a population with characteristics that make it especially important to target for enrollment Geriatric subset of eligible population role of being member of special population Jennifer Fostel CDISC Definition: special populations. Subsets of study populations of particular interest included in clinical trials to ensure that their specific characteristics are considered in interpretation of data [e.g., geriatric]. Special population dorsal to dorsal to A relational spatial quality where on entity is located toward the back or upper surface of an organism relative to another entity. protocol application role analyte measurement objective is an assay objective to determine the presence or concentration of an analyte in the evaluant Environmental characteristic variable is a direct experimental factor (role) in which the component which varies is a part of the environment or the environmental history of study participants source pending Jennifer Fostel Environmental characteristic variable obsolete_Environmental characteristic variable Varying the collection location for environmental samples in study of chromium levels and effects excised OBI Biomaterial Glioma-like proliferation within tissues excised as tubers in patients with tuberous sclerosis complex. Acta Neuropathol. 2008 Jul;116(1):67-77. PMID: 1858112 Philippe Rocca-Serra excised is a conferred qualify which inheres in material resulting from an excision process has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch sequencing OBI branch derived sequencing the use of a chemical or biochemical means to infer the sequence of a biomaterial The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template Elisabetta Manduchi This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf Joseph Spliden s transformation Ryan Brinkman s transformation An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. person:Allyson Lister A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content obsolete_report table replaced by IAO_0000097 report table group:OBI person:Alan Ruttenberg Frank Gibson Daniel Schober Melanie Courtot sort function A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. James Malone this class should eventually be removed source pending All classes yet to be suitably placed in a hierarchy obsolete__move to relations? example_of_usage to be added repeated measure design http://www.holah.karoo.net/experimentaldesigns.htm PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. PlanAndPlannedProcess Branch MSI A repeated measure design is a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs repeated measure design Archaea Archaea Helen Parkinson Susanna Sansone A diplotype is the association of two alleles of a haplotype (or simple gene allele) in a diploid organism. disomic genotype haplotype pair PMID: 11842208. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2228-33. "...Theory to estimate the covariance D for a random sample of haplotypes or disomic genotypes (diplotypes) may be extended to the association probability...." PMID:15274749. BMC Genet. 2004 Jul 26;5:20."..The combination of two haplotypes is called the diplotype..." TCCG/CCTG at the ADH1B Philippe Rocca-Serra diplotype Tina Boussard/PharmGBK obsolete_diplotype MC: is diplotype a diploid genotype? (cf haplotype) PRS: see reference, it stands for disomic genotype and it is also referred to as " The combination of two haplotypes is called the diplotype" from PMID:15274749 even though no details are given on the type of combinaition is a process to place an administered material into a target location administering substance Philippe Rocca-Serra Helen Parkinson Bjoern Peters Alan Ruttenberg call Jan11 2008: Proposal to keep Biomaterial as name of the branch, but with the following definition: object and has_role (sample role or reagent role).. While Device would be an object and ((has_role some instrument_role) or (has_part some (has_role some instrument_role))) Daniel Schober _biomaterial(deprecated) Susanna Sansone Melanie Courtot James Malone Tina Boussard Jennifer Fostel A biomaterial entity is an object of biological origin. definition_source: OBI. Domain of an object property "has_role_which_can_only_be_played_by_biomaterial_entity" in obi before split, Range: ?role_which_can_only_be_played_by_biomaterial_entity (LF 040907). _biomaterial(deprecated) example_of_usage to be added obsolete__biomaterial(deprecated) population population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. rem1: collection somehow always involve a selection process adapted from Oxford English Dictionnary Philippe Rocca-Serra 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 The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial definition blessed by Allyson, Bjoern, Jay & Randi non-specific labeling OBI branch derived non-specific labeling The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. PlanAndPlannedProcess Branch _instrument by virtue of part PERSON:Alan Ruttenberg obsolete_gaseous_state A gaseous state is a state in which the entity is distinguished from the solid and liquid states by: relatively low density and viscosity; relatively great expansion and contraction with changes in pressure and temperature; the ability to diffuse readily; and the spontaneous tendency to become distributed uniformly throughout any container. definition_source: http://wordnet.princeton.edu/perl/webwn?s=gaseous%20state, Jan 3, 2007. PlanAndPlannedProcess Branch replaced by IAO_0000104 obsolete_plan specification a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan Part of range for an object property is_potentially_realizable_as in obi before split (LF 040907) PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI branch derived Recruited population CDISC definition: The group of eligible participants that agreed to participate in the trial and signed the informed consent. Recruited population is an eligible population role played by the set of members who have signed the informed consent form Jennifer Fostel Group of people who have agreed to participate, before they are completely enrolled role of being member of recruited population Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. Jennifer Fostel protocol testing objective example_of_usage to be added source pending protocol testing objective The use of a protease to digest a protein into peptides a protocol application to digest the fraction of input material that is susceptible to that enzyme OBI branch derived PERSON:Kevin Clancy specific enzymatic cleavage specific enzymatic cleavage Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation single Helen Parkinson Elisabetta Manduchi Melanie Courtot This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). OTHER: Adjusted from MGED Ontology James Malone total intensity transformation single A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. A concentration which relative low. diluted diluted A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter. BioSorter 1000 at TSRI Flow Cytometry Core Facility John Quinn BioSorter1000 BioSorter1000 http://www.unionbio.com/products/BioSorter.html obsolete_labware The class labware is here as a place holder class to accout for entities such as test tubes, beakers, centrifuge tubes etc. It is expected as we identify subclasses we will be in a better position to identify the hierarchy, the definition and possibly the label for this class. An example of labware are test tubes, petri dishes, glass beakers. Labware is a device that has low overall complexity and usually facilitates less process steps than other devices. Its low complexity is signified through the fact that it is often regarded as passive (not active). Labware needs a proactive agent (human or computer) to facilitate a process (its intended use). Daniel Schober labware OBI Guava Personal Cell Analysis http://www.guavatechnologies.com/main/products/PCA-new.cfm Guava_PCA A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. Guava Personal Cell Analysis John Quinn editor All classes yet to be suitably placed in a hierarchy _unclassified James Malone _unclassified this class should be removed hemoglobin protein Susanna Sansone TERM: CHEBI:16541 Philippe Rocca-Serra Melanie Courtot Naturally occurring polypeptides synthesized at the ribosome.(CHEBI) Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES HAS MADE_UP_OF RELATION WITH POLYPEPTIDE CONCEPT. JAMES James Malone WEB: http://en.wikipedia.org/wiki/Protein obsolete_protein (obsolete) The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells OBI branch derived definition blessed by Allyson, Bjoern, Jay & Randi specific labeling PlanAndPlannedProcess Branch a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material specific labeling obsolete__move to information_content_entity frontal anterior to A relational spatial quality where on entity is located toward the front of an organism relative to another entity. anterior to PERSON: Elisabetta Manduchi An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster. Elisabetta Manduchi average linkage hierarchical clustering average linkage hierarchical clustering standard deviation calculation standard deviation calculation From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. Monnie McGee PERSON: Monnie McGee Monnie McGee A false discovery rate correction method is a multiple testing procedure that controls for the expected value of the proportion of false positives among the rejected hypotheses. FDR correction method false discovery rate correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 false discovery rate correction method is the role of the substance that is being detected in a analyte measuring assay analyte role plant Melanie Courtot obsolete_plant Any of various photosynthetic, eukaryotic, multicellular organisms of the kingdom Plantae characteristically producing embryos, containing chloroplasts, having cellulose cell walls, and lacking the power of locomotion. WEB: http://www.answers.com/topic/plant?cat=biz-fin James Malone tree PERSON: James Malone A mode calulcation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. Monnie McGee James Malone From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) mode calculation mode calculation PERSON: Monnie McGee polynomial degree The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. PERSON: Elisabetta Manduchi polynomial degree Elisabetta Manduchi quantitative confidence value person:Chris Stoeckert group:OBI quantitative confidence value A quantitative confidence value is a information content entity which is used to indicate the degree of uncertainty about a measurement. Jennifer Fostel Saline solution Negative reference substance negative reference substance role A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. FIlters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells. Influx Cell Sorter John Quinn Influx Cell Sorter at TSRI Flow Cytometry Core Facility http://www.cytopeia.com/sorter.htm Influx Cell Sorter Test of new psychological therapy Psychological intervention is an intervention variable in which the varying parameter is a psychological therapy obsolete_Psychological intervention Psychological intervention Jennifer Fostel source pending PRS: 22-02-2008: need to submit immortal to PATO none Bjoern Peters immortal cell a single Hela cell immortal cell added as hierarchy term a cell derived from a multicellular organism that has the potential to replicate indefinately dialysis tubing function PERSON:William Bug@2007/07/10 obsolete_dialysis tubing function obsolete_solid_state A solid state is a state in which the entity has no tendency to flow under moderate stress; resists forces (such as compression) which tend to deform it; and retains a definite size and shape. definition_source: http://wordnet.princeton.edu/perl/webwn?s=solid%20state, Jan 3, 2007. Jennifer Fostel software testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. software testing objective source pending example_of_usage to be added xenograft WEB: http://en.wikipedia.org/wiki/Xenograft Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world a xenograft is an entity of organismal origin which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. MC: xenotransplantation should be submited to material_transformation Melanie Courtot Philippe Rocca-Serra xenotransplant xenograft instruction OBI branch derived obsolete_realizable information entity replaced by IAO_0000033 is the specification of a process that can be concretized and realized by an actor realizable information entity PlanAndPlannedProcess Branch obsolete_chromium_release_assay_target_role sep:00107 filter paper filter paper Frank Gibson Fliter paper is a device manufacture with the intent to provide a porous unsized paper used for filtering. obsolete_software CEBS, Biomaterial_branch Jennifer Fostel killing sacrifice euthanisia killing difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing. Philippe Rocca-Serra Terminal sacrifice of animals by cervical dislocation at the end of an investigation. death status type A protocol application in which an organism is intentionally put to death life termination person:Chris Stoeckert group:OBI patent content patent content need to distinguish the patent submission (which I think the term refers to) and the patent itself, which is what confers the rights. (Alan) Renamed from patent to patent submission. [Isn't the submission like a recipe, i.e. a realizable information entity, in that it tells you how to do something? no] Cristian: what is the difference b/w some document that has been patented, and the same document that has not been patented? The (informational) content is the same. It is just that the former has been encapsulated within some social mechanism, hence it has acquired some role. Hence 'patent' is a role. A patent content is a report for the purpose of obtaining a license from a government conferring for a set period the sole right to make, use, or sell some process or invention impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who role of being impartial witness Impartial witness According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html Jennifer Fostel James Malone this class should eventually be removed All classes yet to be suitably placed in a hierarchy obsolete__unclassified source pending example_of_usage to be added averaging data transformation averaging data transformation James Malone An averaging data transformation is a data transformation that has objective averaging. PERSON: James Malone A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. Joseph Spliden This type of transformation is typically used in flow cytometry. Elisabetta Manduchi biexponential transformation biexponential transformation Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf volunteer. A person volunteering to participate as a subject in a clinical trial, often a healthy person agreeing to participate in a Phase 1 trial. See Jennifer Fostel role of being healthy volunteer Healthy volunteer Healthy volunteer is a potential study participant role played by a person who is healthy in all aspects relevant to the trial Person with controlled diabetes but high blood pressure (with respect to a study of blood pressure therapy) longitudinal data analysis longitudinal data analysis graph_position_temporary OBI branch derived weight assessment an assay in which the weight of an organism is measured over time The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection PlanAndPlannedProcess Branch weight assessment Alan says something is funny\n---\nThis is a description of what you did as opposed to the description of the assay. This should be more generic. something like 'mass_assay'\n output of a process obsolete_Metabolite source pending output of a process A metabolite is a role characterized by being the product of catabolism or metabolism by a living organism N-acetyl-benzoquinoneimine (NAPQI) produced from acetaminophen Metabolite Jennifer Fostel culture medium role Jennifer Fostel Culture medium OBI A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 recombinant vector cloning pa_branch (Alan, Randi, Kevin, Jay, Bjoern) recombinant vector cloning insertion of a DNA fragment into a cloning vector which creates. Has input vectors + DNA fragments. Has output: recombinant vectors OBI branch derived methylated OBI Biomaterial Philippe Rocca-Serra Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 methylated is a conferred qualify which inheres in material resulting from an methylation process Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. A logicle transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. logicle transformation Elisabetta Manduchi WEB: http://flowcyt.sourceforge.net/gating/latest.pdf logicle transformation filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device Philippe Rocca-Serra OBI-Branch: adapted from wikipedia and wordnet PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. filtration intraperitoneal administration A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application. obsolete_Conclusion Conclusion source pending example_of_usage to be added replaced by IAO_0000035 Jennifer Fostel target role purified Gene expression analysis of RNA purified from embryonic stem cells and embryoid body-derived cells using a high-throughput microarray platform. Curr Protoc Stem Cell Biol. 2007 Sep;Chapter 1:Unit 1B.2. PMID: 18785160 OBI Biomaterial purified is a conferred qualify which inheres in material resulting from an purification process Philippe Rocca-Serra synthetic polypeptide original term: protein fragment split into synthetic polypeptide and fragment derived from protein DS: Is this synthetic an oxymoron to the biomaterial? the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application IEDB Bjoern Peters a synthetic polypeptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment synthetic polypeptide Eukaryota Eukaryota Clustering is the partitioning of a data set into related subsets (clusters), the input is a single cluster of data and the output is partitioned data or information on cluster labels editor James Malone obsolete_clustering method clustering method detection of label Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present OBI branch derived PERSON:Bjoern Peters detection of label the detection of the amount of a label which is a proxy for the detection of the labeled biomaterial gas_ aser http://en.wikipedia.org/wiki/Gas_laser A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emmission amplification. The gas is excited to emit light via an external light source or an electric current dischargeing through the gas. gas laser John Quinn helium-neon gas laser used to erradiate cells in a flow cytometer. Daniel Schober logarithmic voltage amplifier HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportioal o the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. logarithmic voltage amplifier John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 OBI branch derived data collection Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC Is an aquisition of information from an organization that provides information. This is not an assay. It consists of specifiying a query what information is desired, putting this query to an organization, and retrieveing the requested information from the organization. Bjoern Peters data collection thiamine; A vitamin is an organic compound required as a nutrient in tiny amounts by an organism Wikipedia, March 2008 Vitamin vitamin role Jennifer Fostel Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 OBI trancription profiling is a process which aims to provide information about gene expression and transcription activity using ribonucleic acids collected froma entity of organismal origin using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot transcription profiling gene expression profiling Philippe Rocca-Serra Susanna Sansone Melanie Courtot Helen Parkinson PMID: 18241317, Alcohol Clin Exp Res. 2008 Jan 30. Association of the Epsilon2 Allele of Apoe Gene to Hypertriglyceridemia and to Early-Onset Alcoholic Cirrhosis. bin under common 'Genotype' Placeholder. Do we also want recessive_allele etc? as Children or are these qualities. HP will check with PATO http://en.wikipedia.org/wiki/Allele An allele is a viable DNA coding that occupies a given locus (position) on a chromosome. It represents one of two or more alternative forms of a gene or marker sequence at a given locus and differing from other alleles at one or more mutational sites based on phenotype or sequence. allele MO_58 obsolete_allele Philippe Rocca-Serra Bacteria Bacteria James Malone PERSON: Melanie Courtot Elisabetta Manduchi Melanie Courtot PERSON: James Malone PERSON: Elisabetta Manduchi dimensionality reduction data projection dimensionality reduction A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, …, x_m) into an output n-dimensional vector (y_1, y_2, …, y_n), where n is smaller than m. relational quality of continuant relational quality of continuant A quality of continuant which inheres in multiplicity of bearers. Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer. DNA polymerase activity DNA polymerase activity microarray Daniel Schober PERSON: Daniel Schober DS: The subclasses might be thought of as XPS like: microarray has_probe any biomolecule microarray A microarray is a device that is used as physical 2D immobilisation matrix for defined biomolecule sequences in ordered spatial position. The array-bound DNA fragments, antibodies, or proteins are used as targets for a hybridising probes form a sample to be investigated. The array typically consists of a glass, filter, or silicon wafer (chip). rem1:link to Cell Type Ontology (CO) OBI Biomaterial derived OBI Biomaterial derived cell of organismal origin cell of organismal origin hepatocyte A cell of organismal origin is an entity of organismal origin that contains nuclear and cytoplasmic material enclosed by a semipermeable membrane. example_of_usage to be added Daniel Schober supernatant collection system harvesting frame google supernatant collection system harvesting frame The Supernatant Collection system is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. editor_note pending ion detector ion detector An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. http://en.wikipedia.org/wiki/Mass_spectrometry#Detector The ion detector of the Voyager-DE™ STR Biospectrometry Workstation Frank Gibson A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby cristal solid state laser. solid state laser Daniel Schober http://en.wikipedia.org/wiki/Solid-state_laser Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command solid state laser Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. podzol podzol a liquid solvent containing one or more solutes Bjoern Peters liquid chemical solution obsolete_liquid chemical solution moved here following BM140308-call from molecular mixture (a class which has been deprecated, i.e. moved to obsolete.owl PBS, RPMI added as hierarchy term PERSON: Melanie Courtot PERSON: Ryan Brinkman James Malone Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. data partioning PERSON: Richard Scheuermann data partioning immobilize funtion An immobilize function is a contain function to fix an entity in a defined position and prevent its movement immobilize function Frank Gibson Melanie Courtot Daniel Schober DNA polymerase Melanie Courtot obsolete_DNA polymerase Taq polymerase is a commonly used DNA polymerase to copy DNA templates in PCR reactions. WEB: http://en.wikipedia.org/wiki/DNA_polymerase A DNA polymerase is an enzyme that assists in DNA replication. Such enzymes catalyze the polymerization of deoxyribonucleotides alongside a DNA strand, which they "read" and use as a template. The newly-polymerized molecule is complementary to the template strand and identical to the template's partner strand. Guava Personal Cell Analysis-96 Guava_PCA-96 http://www.guavatechnologies.com/main/products/PCA-96new.cfm John Quinn Guava Personal Cell Analysis-96 The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 flourescent parameters. It includes a photodiode forward scatter collector.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. polymerized is a conferred qualify which inheres in material resulting from an polymerization process OBI Biomaterial polymerized Biodegradable and radically polymerized elastomers with enhanced processing capabilities. Biomed Mater. 2008 Sep;3(3):034104. PMID: 18689916 Philippe Rocca-Serra Melanie Courtot heat function A heat function is a function that increases the internal kinetic energy of a material heat function Frank Gibson Bill Bug Daniel Schober blocked Philippe Rocca-Serra subgraph indegree calculation Richard Scheuermann A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. subgraph indegree calculation PERSON: Richard Scheuermann jackknifing method jackknifing method A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008) variance calculation Monnie McGee PERSON: Monnie McGee variance calculation scaling data transformation scaling data transformation A scaling data transformation is a data transformation that has objective scaling. James Malone PERSON: James Malone eMedical record An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel eMedical record article-without-pmid-or-doi:CDISCglossary Elisabetta Manduchi Community submitted term (MSI) A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. Philippe Rocca-Serra PMID:16762068 pareto scaling pareto scaling Jennifer Fostel Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. example_of_usage to be added methodology testing objective source pending methodology testing objective epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. epithelium Philippe Rocca-Serra Endoscopic surgery for intraventricular brain tumors in patients without hydrocephalus. Neurosurgery. 2008 Jun;62(6 Suppl 3):1042-8.PMID: 18695524 OBI Biomaterial intraventricular intraventricular is a positional quality which inheres in a ventricule site (e.g. heart ventricule or brain ventricule) Elisabetta Manduchi pearson correlation coefficient calculation A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. PERSON: Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Correlation pearson correlation coefficient calculation stopping rule PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy. a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen PRS stopping rule MSI PRS would have to inhere in data - nono. Is this related to the objective Philippe Rocca-Serra normalized replaced by IAO_0000025 R, Perl, Java person:Alan Ruttenberg person:Chris Stoeckert group:OBI programming language obsolete_programming language A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. tris A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. tris metal vapor laser metal vapor laser Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer. John Quinn Gold vapor laser, Helium-cadmium metal-vapor laser global modularity calculation PERSON: Richard Scheuermann Richard Scheuermann A network graph quality calculation in which an input data set of subgraph modules and their indegree and outdegree qualities is used to calculate the average modularity of subgraphs within the network. global modularity calculation OBI Biomaterial washed washed is a conferred qualify which inheres in material resulting from an washing process Philippe Rocca-Serra Effect of extraction conditions on the yield and purity of apple pomace pectin precipitated but not washed by alcohol. J Food Sci. 2007 Jan;72(1):C001-9. PMID: 17995865 a format standard is a digital entity that consists of rules applied to information, as opposed to rules applied to objects (which are termed plans) obsolete_format standard PERSON:Jennifer Fostel PERSON:Chris Stoeckert Susanna Sansone example_of_usage to be added cell line cell OBI Biomaterial derived A cell line is an entity of organismal origin that represents generations of a primary culture. cell line cell adapted from wordnet (wkipedia) validation validation is a process by which the accuracy or the quality of a claim or prediction satisfies criteria and is assessed by comparing with independent results PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. Philippe Rocca-Serra enrolled OBI Biomaterial Philippe Rocca-Serra Characteristics and outcome of pediatric patients enrolled in phase I oncology trials. Oncologist. 2008 Jun;13(6):679-89. PMID: 18586923 enrolled is a conferred qualify which inheres in material resulting from an enrollment process Melanie Courtot WEB: http://en.wikipedia.org/wiki/Submatrix Elisabetta Manduchi A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) submatrix extraction When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. submatrix extraction James Malone Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. transcription analysis function transcription analysis function multiple linear regression analysis multiple linear regression analysis Tina Hernandez-Boussard multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term ε. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where β0 is the intercept ("constant" term), the βis are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. WEB:http://en.wikipedia.org/wiki/Linear_regression John Quinn optical filter An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. 720 LP filter, 580/30 BP filter optical filter http://en.wikipedia.org/wiki/Optical_filter catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Catalytic activity (disposition) catalytic activity Catalytic activity (disposition) transplantation OBI branch derived PlanAndPlannedProcess Branch transplantation a protocol application to replace an organ or tissue of an organism Ryan Brinkman A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. http://flowcyt.sourceforge.net/gating/latest.pdf ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." hyperlog transformation Elisabetta Manduchi Joseph Spliden hyperlog transformation This type of transformation is typically used in flow cytometry protocol optimization source pending Jennifer Fostel Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. example_of_usage to be added protocol optimization WEB: http://en.wikipedia.org/wiki/Canonical_analysis canonical variate analysis canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. canonical variate analysis CVA Tina Hernandez-Boussard person:Chris Stoeckert agree replaced by IAO_0000003 A measurement unit is an information content entity associated with a physical magnitude that has been conventionally assigned a number. measurement unit obsolete_measurement unit group:OBI Examples of measurement unit are liters, inches, weight per volume. person:Cristian Cocos Philippe Rocca-Serra edited Monnie McGee A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. tail probability for the proportion of false positives correction method tail probability for the proportion of false positives correction method TPPFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 Saline treated rat; one of three identically-treated subjects OBI Reference participant role is a reference role in which the characteristics or responses of the participant playing the reference participant role are used for comparison or reference. Jennifer Fostel reference participant role Reference participant trial statistician role CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9] Trial statistician is a worker who analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. Jennifer Fostel Trial statistician Pathology review board is a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation Jennifer Fostel role of pathology review board Pathology review board allotransplantation allotransplantation is the transplantation of organs between members of the same species. PlanAndPlannedProcess Branch OBI branch derived agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269 agarose gel OBI biomaterial Philippe Rocca-Serra Kaplan Meier Kaplan Meier MO reference design MO_699 A reference experiment design type is where all samples are compared to a common reference. Philippe Rocca-Serra on behalf of MO reference design PMID: 12933549 expectation maximization PERSON: James Malone James Malone expectation maximization EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximateed probability function. PCR product is double stranded DNA that is the output of a polymerase chain reaction should we use PCR (or the written out words)? These are also in the Sequence Ontology, should we take them from there? Needs DNA added to the logical definition A count function is a measure function to numerically quantify an entitiy with certain qualities Melanie Courtot Bill Bug Daniel Schober Frank Gibson count function count function obsolete__to_be_fixed report graph A report graph is a report figure that presents one or more tuples of information my mapping those tuples in to a two dimensional space in a non arbitrary way. group:OBI person:Alan Ruttenberg person:Allyson Lister report graph autotransplantation is the transplantation of tissue from one part of \nthe body to another in the same individual. ) autotransplantation PlanAndPlannedProcess Branch OBI branch derived WEB: http://flowcyt.sourceforge.net/gating/latest.pdf split-scale transformation split-scale transformation Ryan Brinkman Joseph Spliden This type of transformation is typically used in flow cytometry A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuos with a continuous derivative at the transition point t. Elisabetta Manduchi A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 chromium-51 CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study. Trial monitor trial monitor role Trial monitor is a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study Jennifer Fostel acrylamide acrylamide James Malone Elisabetta Manduchi A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess transformation loess transformation inclusion rule PMID: 17599746-RESULTS: Fifteen trials met our inclusion criteria. The summary effect size was 0.35 (95% confidence interval 0.14, 0.56). I(2) was 0.80. inclusion rule MSI PRS Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group an inclusion rule (criterion) is_ rule* in a protocol that prospective subjects must meet to be eligible for participation in a study quantitative node degree calculation Richard Scheuermann PERSON: Richard Scheuermann A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. quantitative node degree calculation network graph construction A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. Richard Scheuermann PERSON: Richard Scheuermann network graph construction number of lost events electronic person:Kevin Clancy number of lost events electronic A number of lost events electronic is a datum measuring the the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer insturment. The datum has a qualitative role. quantity 74, 0, 14 events lost due to data acquisition electronic coincidence. Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt peptides Amides derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. peptides inter-rater agreement inter-rater agreement mhc binding prediction Helen Parkinson An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. PERSON: Helen Parkinson mhc binding prediction Jennifer Fostel Pathologist Pathologist is a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline pathologist role Cell Lab Quanta SC John Quinn http://www.beckmancoulter.com/cell-lab A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 flourescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of inividal cells. Cell Lab Quanta SC Bjoern Peters liquid chemical solution OBI Biomaterial derived chemical entities in solution a solution of chemicals is a material which is made up of at least 2 chemical entities, one chemical entity playing the role of solvent and the other one playing the role of solute. PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution. Philippe Rocca-Serra PERSON: Elisabetta Manduchi no longer required as gating has been dealt with using objectives data vector reduction and partioning Melanie Courtot James Malone Elisabetta Manduchi obsolete_random vector selection An author_role is a role attributed to someone creating an information_object author role synthesizing function Frank Gibson synthesizing function Daniel Schober Melanie Courtot Bill Bug A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. molecular feature identification objective Jennifer Fostel molecular feature identification objective example_of_usage to be added source pending Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. Bill Bug Frank Gibson transfer function Daniel Schober Melanie Courtot A transfer function is a function to displace a material from one location to another. transfer function OBI branch derived PlanAndPlannedProcess Branch RNA extraction A RNA extraction is a nucleic acid extration where the desired output material is RNA requested by Helen Parkinson for MO RNA extraction Time interval variable source pending Time interval variable is a direct experimental factor in which the varying parameter is a time interval describing the time of exposure of study participants to a treatment, intervention or other perturbational protocol. A time course study design obsolete_Time interval variable Jennifer Fostel OBI Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 Feed feed role Jennifer Fostel Philippe Rocca-Serra organ PRS:22022008:possible import from CARO dbxref=CARO:0000055 obsolete_multi-tissue structure CARO Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. SCGE assay PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. a comet assay is an assay which utilizes gel electropheris on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions. Philippe Rocca-Serra single cell gel electrophoresis assay comet assay comet assay PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review. Philippe Rocca-Serra blotted An extraneous process is a process which is external in origin to the investigation that has an impact on the outcome. spontaneous process OBI Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used Healthcare provider is a worker role of providing medical care either within or outside the study timeline Health care provider health care provider role Jennifer Fostel obscuration bar John Quinn Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 obscuration bar Daniel Schober obscuration bar in a flow cytometer An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. Data transformation role is a role whereby a data analysis entity is transformed into a different data analysis entity source pending Integrated dataset, normalized dataset, clustered dataset obsolete_Data transformation role Jennifer Fostel Data transformation role see P-Value standard error Standard error is a quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. standard error person:Chris Stoeckert group:OBI John Quinn helium neon ion laser A helium neon laser can by used to irradiate cells in a flow cytometer. A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm. Daniel Schober helium neon ion laser http://en.wikipedia.org/wiki/Laser#Gas_lasers A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 flourescent parameters. The FACS_Canto is an analyser usually used in clinical applications. FACS Canto http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf John Quinn FACS Canto OBI Biomaterial pooled Philippe Rocca-Serra pooled is a conferred qualify which inheres in material resulting from an material pooling process SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur J Hum Genet. 2008 Oct 15. PMID: 18854868 http://www.miltenyi.com John Quinn MACS Quant A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and dectors to collect 7 flourescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications. MACS Quant PERSON:Kevin Clancy enzymatic amplification OBI branch derived the use of enzymes to increase the number of molecules of a biomaterial the use of a polymerase chain reaction to amplify a fragment of DNA enzymatic amplification _dispositions PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. randomization is a group assignemnt which relies on chance to assign materials to a group of materials in order to avoid biais in experimental set up. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] randomization legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary] Legally acceptable representative Parent of minor patient; Definition of legally acceptable representative An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE role of legally acceptable representative Jennifer Fostel OBI, CDISC acquisition This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition the process of obtaining a continuant from a source. IEDB Bjoern Peters acquisition NMR spectroscopy function NMR spectroscopy function polystyrene tube function polystyrene tube function Potential study participant role of potential study participant Jennifer Fostel People with diabetes in range of a trial site for a new diabetes therapy; SD rats living in Charles River Labs when an order for rats is placed there study participant role Study participant Study participant is a role of actual or potential entities of, used in or produced by a study; NB: this does not include the study personnel who perform the study Jennifer Fostel http://www.answers.com/artefact artifact object Frank Gibson An artefact_object is an object that is produced or shaped by human craft, especially a tool, weapon, or ornament of archaeological or historical interest, i.e. something that is manufactered. artifact object Examples include the siblings of device and other objects such as gel matrices; used in gel electrophoresis, filter paper, parafilm and buffer solutions. editor_note pending circular circular A quality of a nucleotide polymer that has no terminal nucleotide residues. obsolete_frozen_state A frozen state is a state in which the entity is kept below its freezing point. OBI OBI Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031 Philippe Rocca-Serra transcription factor binding site identification transcription binding site identification is a process which aims at finding DNA region specifically recognized by proteins whose function is transcription factors Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Cosine.html cosine transformation cosine transformation A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. gel dryer sep:00094 A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels gel dryer Frank Gibson inductive reasoning wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning It is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. Bjoern Peters Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer. OBI Instrument adapted from Wikipedia Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 Philippe Rocca-Serra syringe a syringe is a device which is used to introduce or draw fluids from a material entity. Syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 C30644E - InGaAs Avalanche Photodiode John Quinn avalanche photodiode avalanche photodiode An avalanche photodiode is typically used to collect photons emmitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode wih high quantom efficiency and a mechanism for producing gains as high as a few thousand. John Quinn Cyan http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm Cyan A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine flourescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of inividal cells. algorithm adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) obsolete_algorithm replaced by IAO_0000064 an algorithm is a plan which describes inputs, 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. PlanAndPlannedProcess Branch Philippe Rocca-Serra PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. MC: should be a child of DNA polymerase A reverse transcriptase is a DNA polymerase enzyme that transcribes single-stranded RNA into single-stranded DNA. WEB: http://en.wikipedia.org/wiki/Reverse_transcriptase reverse transcriptase obsolete_reverse transcriptase Avian reverse transcriptase transcribes RNA into complementary DNA. RNA-dependent DNA polymerase Melanie Courtot electricity supply function power supply An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity. Melanie Courtot Frank Gibson Daniel Schober electricity supply function multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. multi-tissue structure http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points OBI branch derived material pooling physical combination of several instances of like material 2 sample pooling PlanAndPlannedProcess Branch material pooling like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. directed network graph construction PERSON: Richard Scheuermann Richard Scheuermann A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. directed network graph construction PERSON: James Malone A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. center calculation objective center calculation objective James Malone A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. OBI Biomaterial Vaccinia peptides eluted from HLA-DR1 isolated from virus-infected cells are recognized by CD4+ T cells from a vaccinated donor. J Proteome Res. 2008 Jul;7(7):2703-11. PMID: 18507432 Philippe Rocca-Serra eluted is a conferred qualify which inheres in material resulting from an elution process eluted A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 flourescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters. FACSAria http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf FACSAria at TSRI Flow Cytometry Core Facility FACSAria John Quinn lateral to A relational spatial quality where on entity is located toward the side relative to another entity. lateral to PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate multiple testing correction method Monnie McGee multiple testing procedure a process by which an event or an entity is described before it actually happens or is being discovered and identified. OBI prediction Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190 Philippe Rocca-Serra arrayer FG: definition normalised from raw import Trish Whetzel MO An arrayer is an instrument which deposits biological material onto a substrate in a defined pattern. BioRobotics Microgrid II TAS, Affymetrix GMS 417 arrayer PERSON: Elisabetta Manduchi partitioning objective partitioning objective A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. James Malone A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. Elisabetta Manduchi environmental matter Norman Morrison PRS: 110508: Possible Import from ENVO:00010483 Matter in or on which organisms may live (From ENVO) OR an environmental sample is an object that contains an array of objects that may or may not contain a biomaterial. definition_source: OBI. (formerly known as environmental sample) PMID: 3109018.Schriftenr Ver Wasser Boden Lufthyg. 1987;71:71-82. German. An environmental sample bank for human organ samples in Munster--hair analyses (NOTE: Only 2 occurences in Pubmed Title line) A dirt sample containing different populations of bacteria. A sample of martian water. A sample of gut flora. OBI Biomaterial derived PRS:19032008: change label from site_sample to environmental sample to match definition. site_sample demoted to alternative term site_sample Philippe Rocca-Serra Susanna Sansone PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings] PERSON: Philippe Rocca-Serra a collection is a bfo:aggregate object, that is a set of material object of the same kind collection (of entities of organismal origin) added during 22-02-2008 biomaterial call to distinguish library and population PRS: How can we distinguish with 'collection' as the process of collecting entities, (eg. data collection, urine collection) set, group, ensemble OBI branch derived the detection of phycoerytherin by means of flow cytometry any protocol which results in the detection of a specified substance substance detection substance detection PERSON:Kevin Clancy is a process through which a disease manifests itself _disease course a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. clinical diagnosis (maybe CIO) OBI branch derived PlanAndPlannedProcess Branch clinical diagnosis quantile transformation quantile transformation Elisabetta Manduchi This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. PERSON: Elisabetta Manduchi A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. Philippe Rocca-Serra on behalf of MO PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. Groups of assays that are related as part of a time series. time series design MO_887 time series design MO canonical realisation of device function Elisabetta Manduchi A data transformation is a protocol application which produces output data from input data - e.g. the application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. data processing data analysis Melanie Courtot Philippe Rocca-Serra Richard Scheuermann a protocol application which has the objective to produce output data from input data Helen Parkinson Tina Hernandez-Boussard data transformation James Malone Branch editors data transformation Ryan Brinkman A protocol application which has the objective to produce output data from input data signal conversion function signal conversion function A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. Frank Gibson Daniel Schober Bill Bug Melanie Courtot standard compliance rule standard compliance rule example to be added a standard compliance rule is a compliance rule which defines conformity to a representation standard PRS MSI PRS Philippe Rocca-Serra Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina (From CARO:) OR epithelium is a tissue composed of layers of cells that line the cavities and surfaces of structures throughout the body (adapted from Wikipedia). obsolete_epithelium Wikipedia and possible import from CARO:0000066 PMID: 18431835. Alteration of medial-edge epithelium cell adhesion in two Tgf-beta3 null mouse strains. Differentiation. 2008 Apr;76.4.417-30 light source light source A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiberoptics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interogation point. The light source in a flow cytometer is usually a laser. Olga Tchuvatkina John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 DS: this is a role I guess, not an instrument. Elizabeth M. Goralczyk All classes yet to be suitably placed in a hierarchy source pending James Malone this class should eventually be removed example_of_usage to be added obsolete__move to quality? skewness calculation skewness calculation WEB: http://www.riskglossary.com/link/skewness.htm Monnie McGee From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment person:Chris Stoeckert A software interpreter is a generically dependent realizable entity that takes, as input, some digital entity, and takes action driven by the information content of that digital entity R program, Perl interpreter, Java virtual machine obsolete_software interpreter replaced by IAO_0000065 group:OBI software interpreter person:Alan Ruttenberg Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter data set obsolete_data set A data set is an information content entity that is an aggregate of other information_content_entities that have something in common and are considered to form a unit. group:OBI person:Allyson replaced by IAO_0000100 An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel CDISC glossary electronic case report form electronic case report form Monnie McGee data imputation data imputation ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. leave one out cross validation method leave one out cross validation method CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations CytoBuoy John Quinn, Melanie Courtot CytoBuoy A CytoBuoy is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files.They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. http://www.cytobuoy.com/ recombinant plasmid A vector is a vehicle for transferring genetic material into a cell. It is an autonomous replicating vehicle which can be modified by the insertion of foreign DNA and when introduced into recipient cells does not alter the viability of those cells. obsolete_vector Melanie Courtot plasmid vector Susanna Sansone Adapted from http://en.wikipedia.org/wiki/Vector_%28biology%29 vector Philippe Rocca-Serra viral vector PRS: Vector should treated as a role ->submission to tracker The DNA expressing the protein of interest was inserted within pM13 which was then transfected into a cell line to facilitate expression of the protein. a display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. WEB: http://www.immuneepitope.org/home.do display_library phage display library phage display library PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction Bjoern Peters Philippe Rocca-Serra PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] Shave animals but do not apply treatment to skin obsolete_Sham treatment Sham treatment is a reference treatment designed to mimic the harmless portion of an intervention; e.g. treatment with vehicle alone, placebo or sham surgery. Jennifer Fostel Sham treatment source pending 500, 200, 0 number of particles in subset number of particles in subset quantity A number of particles in subset is a datum measuring the the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. OBI branch derived PlanAndPlannedProcess Branch imaging assay imaging assay Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. Portion of tissue Portion of tissue portion of tissue portion of tissue Helen Parkinson organ section CEBS + OBI Biomaterial organ section A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521 An organ_section is entity of organismal origin which derives from an organ and results from a process of dissection or histological sample preparation a portio(formerly an organ section is portionn of an organ removed from the context of the organ) section needs to be added as process PRS 22-02-2008: organ has input_role in protocol_application histological preparation. Also how different it is from a fragment Philippe Rocca-Serra Philippe Rocca-Serra labeled is a conferred qualify which inheres in material resulting from an labeling process Analysis of the Spatial Distribution of Identical and Two Distinct Virus Populations Differently Labeled with Cyan and Yellow Fluorescent Proteins in Coinfected Plants. Phytopathology. 2007 Oct;97(10):1200-1206. PMID: 18943677 use role labeled OBI Biomaterial a process to determine the weight of an evaluant weight measurement assay Regulation-assigned role Jennifer Fostel Approval letter regulation-assigned role Regulation-assigned role is a regulatory role defined by legislation or governmental orders PlanAndPlannedProcess Branch A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. 2 Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay cell co-culturing cell co-culturing OBI branch derived obsolete_investigation site role solution2: site is related to trial used located_in relation - site can bear the role site is a material (building) having the role site Investigation site solution1: is a physical location, should maybe go under processual context, and then be used in conjunction with the located relation source pending Jennifer Fostel A field, a laboratory, a medical institute, a pharmaceutical company PERSON: Richard Scheuermann A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. node outdegree calculation Richard Scheuermann node outdegree calculation PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes. Tina Boussard PBS buffer phosphate buffered saline solution Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). http://en.wikipedia.org/wiki/Phosphate_buffered_saline Philippe Rocca-Serra phosphate buffered saline solution Melanie Courtot arc lamp http://en.wikipedia.org/wiki/Arc_lamp Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interogation point. The Jablochkoff Candle John Quinn arc lamp heart A physical document is an object serving as a record of information by means of symbolic marks. physical document OBI BP: moved and renamed for BFO information_content_entity "is_encoded_in" some physical_document in obi before split (040907). a book is a physical document OBI branch derived is the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vectors cell growth mediated amplification needs defined relationship to cell culture PlanAndPlannedProcess Branch cell growth mediated amplification trypsinized is a conferred qualify which inheres in material resulting from an trypsination process Philippe Rocca-Serra trypsinized Carbohydrate-induced modulation of cell membrane. VIII. Agglutination with mammalian lectin galectin-1 increases osmofragility and membrane fluidity of trypsinized erythrocytes. FEBS Lett. 2006 Mar 6;580(6):1691-5. PMID: 16497300 Why do we need this? There is always the actual record of the specific type of digestion that was done. - Alan Because OBI will probably be used by text-mining tools so the context is different. Having such terms related to the processes causing them to appear is probably something useful - Philippe cell permeabilization definition blessed by Jay, Alan, Randi need to add output cell has_quality permeable OBI branch derived PERSON:Bjoern Peters Electroporation of HeLa cells to allow transfection with pUC19. A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application cell permeabilization "http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11" editor_note pending John Quinn FACS Calibur "FACS Calibur at TFL, BCCRC, Vancouver" The FACS Calibur is one of the most popular cytometers in use for research. FACS Calibur PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html MSI Philippe Rocca-Serra balanced incomplete block design balanced incomplete block design object acquisition Acquiring 50 C57BL/6 mice in the investigators animal facilities. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. Bjoern Peters, Alan Ruttenberg object acquisition Bjoern is concerned that information such as model number and serial number are to be associated with the process. Others contend that these are associated, perhaps as labels, to the instances that are the participants. an object acquisition is an acquisition of an object from an investigator, institution or vendor. Participant roles include source, destination, carrier, container, transaction record, payer... IEDB sep:00092 blot module blot module A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised Frank Gibson role of being member of screened population Jennifer Fostel Group of potential subjects who pass the screening criteria Screened population Screened population is a potential study participant role of individuals who have been interviewed or screened for participation eligibility adapted from Wikipedia before possible import from CHEBI polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. Philippe Rocca-Serra triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties Column chromatography in chemistry is a tube (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. chromatography column http://en.wikipedia.org/wiki/Column_chromatography chromatography column example_of_usage to be added Frank Gibson PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application Helen Parkinson whole mount sample whole mount tissue whole mount tissue OBI A whole_mount tissue is an entity of organismal origin resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide Philippe Rocca-Serra PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity OBI branch derived PlanAndPlannedProcess Branch assay AltDef: An assay is a protocol application which is a process of measuring. rem1: Imaging is covered by this definition. rem2: material: used in the context of studying some biological problem, example: hybridization assay An assay is a process with the objective to create as an output information about a material entity (bearing evaluant role). gene expression gene expression The process by which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role) assay objective injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally administering substance in vivo needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor. administering substance in vivo IEDB Different routes and means of administration should go as children underneath this Bjoern Peters a substance is intentionally given to an organism through a specified route of administration A network subgraph quality calculation in which an input data set of subgraph indegree and outdegree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. subgraph modularity calculation subgraph modularity calculation Richard Scheuermann PERSON: Richard Scheuermann Jennifer Fostel hardware testing objective Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. example_of_usage to be added source pending hardware testing objective modular decomposition editor Tina Hernandez-Boussard modular decomposition Molecular decompostion is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. John Quinn Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less freqeuntly nitorgen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. LSR2 fluid pressure regulator fluid_pressure_regulator Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 fluid pressure regulator mean calculation PERSON: Monnie McGee A mean calulcation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the “center of gravity” for the data set. It is also known as the first moment. James Malone From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008) Monnie McGee PERSON: James Malone mean calculation Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. loess global transformation one-channel Elisabetta Manduchi loess global transformation one-channel OTHER: Editor's generalization based on MGED Ontology term A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 the introduction and integration of genetic material into a cell or organism in order to alter its genetic make-up genetic transformation PERSON:Kevin Clancy OBI branch derived genetic transformation discriminant analysis WEB: http://www.statsoft.com/textbook/stdiscan.html Tina Hernandez-Boussard discriminant analysis Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. exponential base The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). WEB: http://en.wikipedia.org/wiki/Exponential_function exponential base Elisabetta Manduchi biosource provider Helen Parkinson THIS IS A ROLE. James The Jackson Laboratory is a biosource_provider obsolete_biosource provider MO_230 The resource or individual (e.g. company, hospital, commerical supplier) used to obtain or purchase the biomaterial. James Malone probabilistic algorithm A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. PERSON: James Malone probabilistic algorithm example_of_usage to be added obsolete_genetic information content genetic information content move to dependent.owl A radiation quality inhering in bearer vy virtue of its exhibiting or being caused by radioactivity. radioactive radioactive correction objective PERSON: James Malone A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation. correction objective James Malone PERSON: Melanie Courtot Type I error correction Philippe Rocca-Serra obsolete_biomaterial OBI Biomaterial derived Frank Gibson Melanie Courtot Bill Bug perturbe function A perturbe function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. perturbe function Daniel Schober http://en.wikipedia.org/wiki/Perturbation_biology waste_tank Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished. waste tank John Quinn LSR2 waste tank Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 The act or process of identifying or determining the nature and cause of a disease or injury through evaluation Jennifer Fostel example_of_usage to be added Diagnosis Diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Diagnosis source pending Place holder class, see editor note This is a placeholder class to collect all protocl applications where the name conflicts with natural processes that could be classes in other ontologies. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict with natural processes.\nThe terms: translation and transcription were also requested. PlanAndPlannedProcess Branch _induction of natural processes OBI branch derived _induction of natural processes spectrophotometer MO Helios Gamma Spectrophotometer Melanie Courtot Trish Whetzel A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. spectrophotometer non-negative matrix factorization A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software differential expression analysis objective differential expression analysis objective PERSON: Elisabetta Manduchi Elisabetta Manduchi prokaryote Melanie Courtot The prokaryotes are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. bacteria James Malone obsolete_prokaryote WEB: http://en.wikipedia.org/wiki/Prokaryote rem0: (AL) One of in-vitro state/ex-vivo state should be deleted, and made a synonym of the remaining term. An ex-vivo state is a state in which the entity is in an artificial environment outside the living organism. definition_source: http://wordnet.princeton.edu/perl/webwn?s=in%20vitro, Jan 3, 2007. obsolete_ex-vivo_state http://www.apogeeflow.com/flow_cytometry_products.htm A A40-MiniFCM is a flow_cytometer_analyser that allows for the choise of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. John Quinn A40-MiniFCM A40-MiniFCM OBI Instrument branch A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. The instrument branch needs to identify parts of instruments. The above def is needed to disambiguate between flow cytometer and flow cytometer sorter. The part between () is optional. A flow cytometer sorter has all the parts a flow cytometer has and is also has a "droplet sorter" droplet sorter droplet sorter OBI Instrument branch Philippe Rocca-Serra OBI Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism metabolite profiling Bjoern Peters PRS:22-02-2008: output role in protocol application lavage and need to submit protocol application bronchial alveolar lavage solution containing lung derived T cells, eosinophils, and TNFa. IEDB Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. bronchial alveolar lavage BAL Daniel Schober Melanie Courtot mechanical function http://en.wikipedia.org/wiki/Mechanical_work A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force. mechanical function Bill Bug Frank Gibson _relative position Philippe Rocca-Serra PERSON: Helen Parkinson t cell epitope prediction t cell epitope prediction Helen Parkinson A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. pH indicator dye phenol red in RPMI; pH=4 indicator dye (also carries reference role) Jennifer Fostel pH indicator dye role Body substance Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. Examples: saliva, semen, cerebrospinal fluid, inhaled air, urine, feces, blood, plasma, lymph. Body substance Philippe Rocca-Serra Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) example to be added MSI n-to-1 design N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). n-to-1 design discriminant function analysis WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant function analysis Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. Tina Hernandez-Boussard BioSorter250 John Quinn BioSorter250 A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 flourescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. BioSorter 250 at TSRI Flow Cytometry Core Facility http://www.unionbio.com/products/BioSorter.html obsolete_funder http://www.medterms.com/script/main/art.asp?articlekey=18426 Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells An incubator is an instrument in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled incubator incubator Frank Gibson Jennifer Fostel reporter reagent role Reporter Molecular entity molecular entities A molecular entity is any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entities Molecular entity Philippe Rocca-Serra OBI Plan 2 group assignment group assignment is a process which results in the creation of at least 2 sub population from the starting population, also understood as assigning objects/subject to groups group assignment splitting an enrolled population into a treated and controlled sub-group; randomized group assignment A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal. A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound. Daniel Schober digital-to-analog converter digital-to-analog converter PERSON: Daniel Schober PRS: this class has been added during major biomaterial.owl cleanup for evaluation and testing of imports from CARO adipose tissue is a tissue which main constituants are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. Philippe Rocca-Serra OBI Biomaterial derived PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4. adipose tissue eluate need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role OBI Bionaterial Philippe Rocca-Serra a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase eluted material Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263 Causality assessment example_of_usage to be added source pending Causality assessment Jennifer Fostel Causality assessment is an assessment role in which the contribution of a study factor towards causing the observed outcome or data is estimated and reported drug role Drug role is a role assigned to an entity by a regulatory agency that is designed to diagnose, treat or prevent an abnormal medical condition Drug role OBI, CDISC Jennifer Fostel James Malone An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi A mean calulcation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the “center of gravity” for the data set. It is also known as the first moment. PERSON: Elisabetta Manduchi averaging objective averaging objective CDISC definition: a meaningful interpretation of data or observations resulting from planned evaluations. Finding Jennifer Fostel Finding source pending Finding is an assessment of data, observations or evaluations from a clinical study which can be used to form a diagnosis example_of_usage to be added Elisabetta Manduchi loess group transformation one-channel A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. OTHER: Editor's generalization based on MGED Ontology term loess group transformation one-channel A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. http://www.guavatechnologies.com/main/products/easyCyteMini.cfm A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 flourescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputing cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. John Quinn Guava EasyCyte Mini Guava EasyCyte Mini PlanAndPlannedProcess Branch OBI branch derived hypothesis generating investigation hypothesis generating investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis Jennifer Fostel Statistical factor Statistical factor is an outcome role consisting of being a variable used in the main analysis of the study source pending obsolete_Statistical factor example_of_usage to be added contour plot A contour plot is a report graph which is a graphical representation of a 3-dimensional surface by plotting constant z slices, called contours, on a 2-dimensional format. That is, given a value for z, lines are drawn for connecting the (x,y) coordinates where that z value occurs. generically_dependent_continuants person:Chris Stoeckert person:Allyson contour plot Contour plot of SSC-H, FSC-H, and FL1-H. group:Flow Cytometry community http://www.luminexcorp.com/support/faqs.html Luminex 200 Luminex 200 A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation John Quinn Jay/Bjoern think this is problematic. There are so many different types of chromatography. This term may be overloaded. May be best to define each type separately underneath material_separation. Also, example seems to be an assay. the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity OBI branch derived chromatography chromatography The use of gas chromatography in order to identify the presence of pesticides in a sample of eggs PERSON:Kevin Clancy electrocuted Philippe Rocca-Serra CDISC definition: investigational treatment. An intervention under investigation in a clinical trial. A test of exposure to different compounds or procedures Treatment variable is a direct experimental factor in which the varying parameter is a component of a treatment, intervention or perturbational protocol. obsolete_Treatment variable Treatment variable Jennifer Fostel source pending Excluded study participant is a study participant role of not meeting the inclusion criteria or being excluded by the exclusion criteria role of being excluded study participant CDISC definition: screen failure. Potential subject who did not meet one or more criteria required for participation in a trial. See also screening of subjects. screen/screening (of substances). Screening is the process by which substances are evaluated in a Person too old for trial inclusion Jennifer Fostel Excluded study participant Richard Scheuermann network subgraph quality calculation network subgraph quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. PERSON: Richard Scheuermann obsolete__PATO_quality B cell A type of lymphocyte whose defining characteristic is the expression of an immunoglobulin complex. B cell source pending obsolete_Biologic CDISC: variable. 1. Any quantity that varies; any attribute, phenomenon or event that can have different qualitative or quantitative values. 2. In SDTM variables are used to describe observations. Such describing variables have roles that determine the type of information conveyed by the variable about each observation and how it can be used; FCR: Variables concepts that can be assigned values and thus must be defined operationally by the methods for measuring or evaluating them; CDISC: study variable. A term used in trial design to denote a variable to be captured on the CRF. See also variable, supporting variable Biologic Biologic is an intervention variable in which the varying parameter is a drug or investigational compound Test of investigational drug Jennifer Fostel polymerization PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3. OBI-Branch polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. ploymerization results in molecular entity of high molecular weight Philippe Rocca-Serra PRS:22102008: need to import catalyst from CHEBI 35223 Biological replicate biological replicate role Jennifer Fostel A member of a dose-time group; a patient in a given arm of a trial OBI CEBS, Biomaterial_branch placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress Jennifer Fostel acclimatization A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. acclimatization person:Kevin Clancy 0, 125, 787 events lost due to computer busy. quantity Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events computer A number of lost events is a datum recording the the number of measurement events lost due to overloading of the analysis chip in a flow cytometer insturment. The datum has a qualitative role number of lost events computer sponsor role Sponsor CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators Jennifer Fostel Sponsor is a responsible party role involved with any of the following activities: initiating, managing and funding a study Rat 1A; first enrolled patient to receive treatment Jennifer Fostel role of being first subject treated First subject treated First subject treated is a subject role played by the subject first to have treatment applied first subject treated. First subject who receives the test article or placebo in a clinical trial. labeling PERSON:Kevin Clancy The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. OBI branch derived labeling the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future definition blessed by Allyson, Bjoern, Jay & Randi A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. Density plot of SSC-H and FSC-H. group:Flow Cytometry community generically_dependent_continuants density plot density plot person:Chris Stoeckert person:Allyson group:Flow Cytometry community list-mode data file list-mode data file One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people. person:Chris Stoeckert An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used. A list-mode data file is a digital entity where events are stored sequentially, parameter by parameter. example_of_usage to be added Assessment Jennifer Fostel source pending Assessment is a conclusion derived from the processes used to learn about a patient's condition. In part from NCI Assessment An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. MA transformation PERSON: Elisabetta Manduchi Elisabetta Manduchi MA transformation MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. krypton ion laser Daniel Schober John Quinn A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerfull line), and 676 nm all at once. They have much lower gain than argon lasers however. krypton ion laser Lexel 95L krypton laser PERSON: Phillippe Rocca-Serra A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. microtome PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. microtome PERSON: Daniel Schober edge betweenness calculation PERSON: Richard Scheuermann Richard Scheuermann An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. edge betweenness calculation Philippe Rocca-Serra cross linked is a conferred qualify which inheres in material resulting from an cross linking process cross-linked OBI Biomaterial Degradable Disulfide Core-Cross-Linked Micelles as a Drug Delivery System Prepared from Vinyl Functionalized Nucleosides via the RAFT Process. Biomacromolecules. 2008 Oct 9.PMID: 18842025 PERSON: James Malone Exclude all x_i's which do not fulfill a pre-formulated condition. projection PERSON: Elisabetta Manduchi PERSON: Melanie Courtot Melanie Courtot Elisabetta Manduchi James Malone obsolete_projection A projection is a dimensionality reduction where the transformation is a simple projection into a subset of the components, i.e. (x_1, x_2, ..., x_m) is transformed into (x_i1, x_i2, ..., x_in) for some 1<=i1... <=m and n<m. A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. OBI AL: Original definition_editor was Kevin Clancy, and then I (Allyson Lister) added to it. I changed the editor to OBI, but am not sure if I should have put both our names in. fluorometer Allyson Lister fluorometer laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 Kevin Lister http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer Frank Gibson A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific mass spectrometer obsolete_curation status PERSON:Bill Bug The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. GROUP:OBI:<http://obi.sourceforge.net> curation status replaced by IAO_0000078 A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) microtiter plate microtiter plate microplate http://en.wikipedia.org/wiki/Microtiter_plate Melanie Courtot A microtiter_plate is a flat plate with multiple wells used as small test tubes. ratio of collected to emitted light person:Chris Stoeckert quantity 10% Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt ratio of collected to emitted light person:Kevin Clancy A ratio of collected to emitted light is a datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role obsolete_Subject characteristic variable Selection of subjects of different sexes for testing Subject characteristic variable is a direct experimental factor in which the component which varies results from the selection of subjects with non-uniform characteristics source pending Subject characteristic variable Jennifer Fostel James Malone obsolete_fungus Saccharomyces cerevisiae A fungus is any eukaryotic organism that is a member of the kingdom Fungi. The fungi are heterotrophic organisms characterized by a chitinous cell wall, and in the majority of species, filamentous growth as multicellular hyphae forming a mycelium; some fungal species also grow as single cells. WEB: http://en.wikipedia.org/wiki/Fungus fungus Melanie Courtot quantile proportion of false positives correction method quantile proportion of false positives correction method Monnie McGee A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distriubition of the proportion of false positives among the rejected hypothesis (false discovery rate). Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 QPFP correction method SomaScope Mark II Automatic Economical "http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10" SomaScope The SomaScope is an instrument to quantify somatic cells in milk. SomaScope Josef Spidlen editor_note pending ion laser ion laser Daniel Schober 2 Watt Lexel 88 Argon Ion laser http://en.wikipedia.org/wiki/Ion_laser An ion laser is a gas laser which uses an ionized gas as its lasing medium. John Quinn obsolete_emulsion MC: should be a state A mixture of immiscible (unblendable) substances, that are finely dispersed and not separate through the action of gravity alone lipid emulsion, oil in water emulsion, perfluoro-chemical emulsion, photographic emulsion Susanna PSI emulsion Daniel Schober ionization function http://en.wikipedia.org/wiki/Ionization The ion source in amass spectrometer ionization function Bill Bug Frank Gibson An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. Melanie Courtot is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans PlanAndPlannedProcess Branch xenotransplantation xenotransplantation OBI branch derived A protocol application is a process carried out to bring about the objective defined in the protocol applied. Every protocol_application has one or more inputs and outputs definition_source: OBI. a protocol_application is a planned process realizes a process in which the objective of the protocol is achieved. The manipulation of materials and information on materials as part of an investigation PlanAndPlannedProcess Branch rem1: This is an actual part of the experiment. It includes the protocol that the experimenter intends to carry out, deviations from this and unintended variables, such as the earthquake that occurred while the experiment was taking place. protocol application OBI protocol_application part_of_process some sample_preparation_for_assay in obi before split (LF 040907) protocol application Elisabetta Manduchi A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. log-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. James Malone ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 Melanie Courtot Ryan Brinkman log-log curve fitting OBI branch derived BFO to do concretized protocol PlanAndPlannedProcess Branch concretized protocol measuring a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables. homogeneous polynomial transformation homogeneous polynomial transformation WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html Elisabetta Manduchi A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. obsolete_analytical instrument function PERSON:William Bug@2007/07/10 analytical instrument function Bill Bug An instrument function where the process in which the instrument participates results in a quality measurement of the material under examination which is critical in the context of a specific investigation plan. E.g. the function of a spectrophotometer to provide a measure of the relative absorbance of a liquid sample for a particular wavelength (or set of wavelengths) of light. Reference is a role that can support the observation of similarities, differences, relative magnitude or change reference role control Jennifer Fostel OBI Reference MC: should be a state solution Susanna obsolete_solution A homogeneous mixture of two or more substances PSI criteria come from plan / clinical trial branch enrollment of humans based on eligibility criteria for an investigation Bjoern Peters IEDB enlisting familiy members of HIV patients into a study human subject enrollment human subject enrollment spread calculation data transformation A spread calculation is a data transformation that has objective spread calculation. James Malone spread calculation data transformation CytoSence http://www.cytobuoy.com/ John Quinn CytoSence A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. loess scale group transformation OTHER: Editor's generalization based on MGED Ontology term Elisabetta Manduchi Melanie Courtot A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. James Malone loess scale group transformation OBI branch derived PERSON:Kevin Clancy the use of a clonal cell line to produce a biomaterial E coli expressing the gene for M avium p35 were cultured in order to produce p35. amplification of a clone amplification of a clone long pass filter long pass filter A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. http://en.wikipedia.org/wiki/high-pass_filter John Quinn 750 LP filter person:Alan Ruttenberg group:OBI replaced by IAO_0000091 person:Allyson Lister obsolete_report display element There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text report display element A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. thermocycler Melanie Courtot thermal cycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. Piko™ 96-well Thermal Cycler Trish Whetzel MO Polymerase_Chain_Reaction_ machine PCR_machine thermal cycler DNA_amplifier obsolete_in-vitro_state An in-vitro state is a state in which the entity is in an artificial environment outside the living organism. definition_source: http://wordnet.princeton.edu/perl/webwn?s=in%20vitro, Jan 3, 2007. linear discriminant functional analysis PERSON: Tina Hernandez-Boussard Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. Tina Hernandez-Boussard linear discriminant functional analysis FACSvantage FACSvantage http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 John Quinn The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parametersand side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. FACSvantage at TSRI Flow Cytometry Core Facility several roles are implied in this: There must be one or more actors that realizes the plan, potentially a planner that devised the plan, potentially a supervisor monitoring the plan. OBI branch derived is a process that is the realization of some plan PlanAndPlannedProcess Branch planned process planned process PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. OBI-Branch enzymatic ligation is a process which fragments of molecule can be united or or open molecules can be circularized by covalent bond through the action of enzyme or other agent with ligase activity enzymatic ligation Philippe Rocca-Serra planning is the process of creating or modifying a plan. Bjoern Peters planning Bjoern Peters Alan Ruttenberg person PRS: a person is material entity instantiating an organism human Philippe Rocca-Serra Susanna Sansone a human being regarded as an individual PMID: 18333287.AIDS Read. 2008 Feb;18(2):100-4.Progression of Kaposi sarcoma associated with iatrogenic Cushing syndrome in a person with HIV/AIDS. adapted from OED and OBI James Malone Melanie Courtot loess global transformation A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possiby all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess global transformation The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. http://web.mit.edu/solab/Research/ImageCytometry.html image cytometer An image_cytometer is an instrument for image-based study or measurement of cells. Melanie Courtot image cytometer elution PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13. the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions) Philippe Rocca-Serra wordnet.princeton.edu/perl/webwn analog-to-digital converter Melanie Courtot original definition says "part of the electronic subsystem" http://en.wiktionary.org/wiki/Analog-to-Digital_Converter A-D A2D The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. John Quinn analog-to-digital converter Jennifer Fostel Vulnerable subject Vulnerable subject is a potential study participant role characterized by being unduly influenced by the expectation that participation in the trial will provide direct benefit vulnerable subjects. Individuals whose willingness to volunteer in a clinical trial may be unduly influenced by the expectation, whether justified Person who believes the trial medication will cure them of cancer role of being vulnerable subject coordinating committee (also executive committee, steering committee MUSC; study-committee, RCT schema) Coordinating committee is a responsible party role overseeing the progress of a multicenter trial Jennifer Fostel Study committee study committee role cloned is a conferred qualify which inheres in material resulting from an cloning process cloned Trichostatin A improved epigenetic modifications of transfected cells but did not improve subsequent cloned embryo development. Anim Biotechnol. 2008;19(4):211-24. PMID: 18855246 Philippe Rocca-Serra OBI Biomaterial node quality calculation PERSON: Richard Scheuermann Richard Scheuermann node quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. obsolete_precipitate role Philippe Rocca-Serra OBI Biomaterial derived cellular compartment possible import from GO or From CARO PMID: 15342780 .The PEN1 syntaxin defines a novel cellular compartment upon fungal attack and is required for the timely assembly of papillae. Mol Biol Cell. 2004 Nov;15(11):5118-29. Epub 2004 Sep 1. a cellular compartment is a cellular component which is defined or enlosed by a lipidic membrane (golgi) and nucleic acid material (nucleole). obsolete_cellular compartment James Malone Jennifer Fostel role of acclimating subject Fish captured in the wild being acclimated to the housing conditions of the laboratory; lab animals being temporally progressed so that their night occurs during normal daylight hours Acclimating subject Acclimating potential subject is a potential subject kept in controlled physical conditions prior to the study A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. PERSON: Richard Scheuermann subgraph degree calculation subgraph degree calculation Richard Scheuermann monadic quality of continuant monadic quality of continuant A quality of continuant which inheres in a single-bearer. a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material concentrate concentrate OBI branch derived Evaporation of the solution containing DNA to increase the concentration of the DNA molecules PERSON:Kevin Clancy OBI Biomaterial derived TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES PRS 210608: moved from biomaterial branch following deprecation of biomolecule class (note: polymer has been moved under quality (since polymer describes the result of a polymerization process where as monomer indicates that a chemical entity has the potential to be used as a monomer such polymerization reaction) placeholder, possible import from CHEBI to be added (possibly) Susanna Sansone monomer monomer A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning techique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone PERSON: James Malone class prediction objective class prediction objective PERSON: Elisabetta Manduchi supervised classification objective DS: This and its subclasses are experimantal classes added purely for experimentation and implementation of a simple use case. microarray function microarray function subject/trial subject. An individual who participates in a clinical trial, either as recipient of the investigational product(s)) or as a control. [ICH] See also healthy volunteer, human subject.; human subject. Individual who is or becomes a participant in research, either as a recipient of the test article or as a control. A subject may be either a healthy human or a patient. [21 CFR50.3]. Synonym: subject/trial subject. Study subject is a Study participant role that is played by the objects of the study during the study timeline. In most cases, a study subject is considered to be a population representative Study subject study subject role Jennifer Fostel loess fitting Monnie McGee ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. loess fitting A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between ¼ and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda). Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html Worker Jennifer Fostel worker role Worker is 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 Each of these are related to material separation. I'm not sure if they should be named or not, and whether any of them are historical in the sense described in historical role _related_to_material_separation Body substance which consists of plasma and blood cells Blood Blood activated is a conferred qualify which inheres in material resulting from an activation process activated OBI Biomaterial Philippe Rocca-Serra Reduction of Nuclear Peroxisome Proliferator-Activated Receptor gamma Expression in Methamphetamine-Induced Neurotoxicity and Neuroprotective Effects of Ibuprofen. Neurochem Res. 2008 Oct 23. PMID: 18946735 sequence feature identification objective example_of_usage to be added Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. source pending Jennifer Fostel sequence feature identification objective viral RNA extraction obsolete_cell derived from multicellular organism lymphocyte cell derived from multicellular organism Bjoern Peters A cell derived from a multicellular organism none added as hierarchy term HMMM.. THE CONCEPT HERE IS CELL, ITS ORIGIN IS A DIFFERENT CONCEPT LINKED BY A RELTION SUCH AS ORIGNATED_FROM OR SIMILAR. SUGGEST REMOVE THIS AND ADD APPROPRIATE RELATION. JAMES matched pairs design MSI PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. http://www.holah.karoo.net/experimentaldesigns.htm matched pairs design A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. Philippe Rocca-Serra Holm false discovery rate correction method Holm false discovery rate correction method cloning insert role is the role a DNA or RNA fragment plays that is inserted into a cloning vector in a cloning process. Jennifer Fostel obsolete_variables Variables are specifications, part of plan Was 'value' PERSON:Chris Stoeckert obsolete_number A number is an information content entity which provides a magnitude for the result of a measurement. the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated histology need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n OBI branch derived PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney histology the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. fluorescence compensation matrix generically_dependent_continuants fluorescence compensation matrix group:Flow Cytometry community person:Chris Stoeckert ((1.053096, -0.22476), (-0.24877, 1.053096)) Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. molecular_function molecular_function Stage II breast cancer, The timepoint of recovery from a disease _disease stage is a fiat_process_part which is part_of a disease_process which is associated with position in the normal progression of the disease http://www.apogeeflow.com/flow_cytometry_products.htm A10-Analyzer A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. A10-Analyzer John Quinn Jennifer Fostel Placebo treatment source pending Placebo treatment is a sham treatment role played in a clinical investigation by a treatment appearing similar to an investigational product but lacking the active chemical component Delivery of a pill consisting of inert materials obsolete_Placebo treatment OBI branch derived PlanAndPlannedProcess Branch a material separation to recover the nuceic acid fraction of an input material requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction nucleic acid extraction Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. A cell pellet is a entity of organismal origin which results from the aggegration of cells produced by the application of centrifugal force to a liquid containing cells in suspension