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