$Revision: 80 $ Richard Scheuermann Barry Smith Cristian Cocos Richard Bruskiewich Melanie Courtot Jeffrey Grethe Gilberto Fragoso Jessica Turner Dawn Field This file is based on checkout of our SVN repository revision $Revision: 3042 $ Norman Morrison Frank Gibson Bjoern Peters Pierre Grenon Susanna-Assunta Sansone An ontology for the annotation of biomedical and functional genomics experiments. Joe White Chris Taylor Holger Stenzhorn Philippe Rocca-Serra Chris Mungall Jennifer Fostel Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Jie Zheng Trish Whetzel free, no license required. Luisa Montecchi Allyson Lister OWL-DL Philip Lord Dirk Derom Tina Hernandez-Boussard Monnie McGee Eric Deutsch Yongqun He 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. Daniel Schober Stefan Wiemann Robert Stevens Kevin Clancy John Westbrook Larisa Soldatova Jay Greenbaum Mervi Heiskanen Alan Ruttenberg Helen Parkinson James Malone Elisabetta Manduchi Lawrence Hunter Bill Bug Chris Stoeckert 2010-08-19 Daniel Rubin Matthew Pocock Helen C. Causton Tanya Gray Ryan R. Brinkman en Liju Fan Ontology for Biomedical Investigation An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ $Revision$ en Institute for Formal Ontology and Medical Information Science (IFOMIS) http://www.ifomis.org/bfo/1.1 Andrew Spear Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE" Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain" http://creativecommons.org/licenses/by/3.0 Barry Smith: "Beyond Concepts: Ontology as Reality Representation" Holger Stenzhorn Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization" Barry Smith: "Against Fantology" Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics" Pierre Grenon application/rdf+xml Barry Smith: "Basic Tools of Formal Ontology" Basic Formal Ontology (BFO) 1.1.1 en Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations" Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO" Alan Ruttenberg en An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ $Revision$ $Revision: 80 $ $Revision: 80 $ cjm relationship <p>This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology</p><div class="notes"><p>In the definitions, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes</p><p> For a discussion of instance-level relations and also of additional axioms needed to infer transitivity and other properties of the relations listed above see <a href="http://genomebiology.com/2005/6/5/R46">http://genomebiology.com/2005/6/5/R46</a> or the OBO relations page hosted at <a href="http://obo.sourceforge.net/relationship">http://obo.sourceforge.net/relationship</a></div> cvs version $Revision: 1.5 $ release version 1.01 relationship This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi en obsolete classes from the information artifact ontology. see http://code.google.com/p/information-artifact-ontology/ $Revision$ en $Revision$ 14:07:2006 00:00 cjm ro_bfo_bridge Domain and range constraints for OBO_REL, in terms of BFO ro_bfo_bridge This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi Thermobifida fusca Thermobifida fusca IEDB IEDB metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. T cell epitope (3H-Thymidine) cell proliferation assay T cell epitope (3H-Thymidine) cell proliferation assay T cell epitope specific proliferation assay that measures T cell proliferation utilizing the Thymidine incorporation assay. Greco-Latin square design is a study design which relates to Latin square design graeco latin square design PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. graeco latin square design pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor. Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and only 2 articles in pubmed ->probably irrelevant Coniferopsida Coniferopsida metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. PERSON:Daniel Schober A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. GROUP:<http://msi-ontology.sourceforge.net> chromatography device, check on definition ! http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 column cartridge column cartridge Density plot of SSC-H and FSC-H. 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. example to be eventually removed OBI_0000179 density plot group:Flow Cytometry community density plot person:Chris Stoeckert person:Allyson Lister Sciurognathi Sciurognathi obsolete_portion of tissue Philippe Rocca-Serra a tissue is a multicellular entity of organismal origin with is made a one or more cell type which has recognisable morphological and functional characteristics CARO Definition: Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. obsolete_portion of tissue adapted from OED and possible import from CARO PMID:18173349 # J Neurosurg Spine. 2008 Jan;8(1):67-73..OBJECT: Hydrogels are nontoxic, chemically inert synthetic polymers with a high water content and large surface area that provide mechanical support for cells and axons when implanted into spinal cord tissue. FWER correction family wise error rate correction method Monnie McGee A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 family wise error rate correction method PERSON: James Malone James Malone, Helen Parkinson error correction objective Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. error correction objective person:Jennifer Fostel 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. eMedical record article-without-pmid-or-doi:CDISCglossary cell-cell binding detection by flow cytometry assay Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. cell:cell conjugate detection assay An assay which uses a flow cytometer to detect pairs of cells that are interacting by staining them with different fluorescent labels. cell-cell binding detection by flow cytometry assay PERSON:Bjoern Peters length length A 1-D extent quality which is equal to the distance between two points. A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. CD3 subunit with immunoglobulin domain CD3 subunit with immunoglobulin domain Viruses Viruses mast cell A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. mast cell curve fitting data transformation ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." curve fitting data transformation James Malone A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. Elisabetta Manduchi Melanie Courtot WEB: http://en.wikipedia.org/wiki/Curve_fitting Philippe Rocca-Serra hyper graeco latin square design hyper graeco latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and no example found in pubmed->not in use in the community PRS to do Paxilineae Paxilineae PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:\n Significant S/N gains (with moderately salty samples also)\n Short pulse widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient. Bruker CryoProbe Bruker CryoProbe NMR probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 Macropus eugenii Macropus eugenii scaling data transformation James Malone A scaling data transformation is a data transformation that has objective scaling. scaling data transformation PERSON: James Malone left handed left handed ambidexterous ambidexterous right handed right handed PERSON:Alan Ruttenberg handedness categorical measurement datum A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally handedness categorical measurement datum PERSON:Jessica Turner OBI_0000266 Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) curation status specification curation status specification GROUP:OBI:<http://purl.obolibrary.org/obo/obi> requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. to be replaced with external ontology term Alan Ruttenberg Terms with this status should eventually replaced with a term from another ontology. group:OBI organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg 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. PERSON:Bill Bug culture medium role OBI culture medium role a role that inheres in a material entity and is realized in the use of that material entity by an organism grown in vitro to provide all needed nourishment. A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 culture medium Person: Jennifer Fostel Streptophyta Streptophyta Staphylococcaceae Staphylococcaceae 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. PERSON: Phillippe Rocca-Serra PERSON: Daniel Schober microtome All classes yet to be suitably placed in a hierarchy obsolete__move to quality? James Malone obsolete__move to quality? Zinnia Zinnia Thlaspi caerulescens Thlaspi caerulescens ethylenediaminetetraacetic acid ethylenediaminetetraacetic acid A tetracarboxylic acid that has formula C10H16N2O8. MO_699 reference design Philippe Rocca-Serra on behalf of MO reference design PMID: 12933549 A reference experiment design type is where all samples are compared to a common reference. epitope specific T cell proliferation IEDB A biological process where T cells proliferate resulting from the recognition of a T cell epitope. IEDB epitope specific T cell proliferation unplanned occurrence effecting an investigation Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used unplanned occurrence effecting an investigation a process which is external in origin to the investigation that has an impact on the outcome. OBI PERSON: Bjoern Peters Elisabetta Manduchi A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. James Malone Melanie Courtot PERSON: Melanie Courtot 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 out, the resulting data set corresponds to a row submatrix of the original set. row submatrix extraction row submatrix extraction PERSON: Elisabetta Manduchi PERSON: James Malone Cryptopygus antarcticus Cryptopygus antarcticus Person:Chris Stoeckert Data representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. GROUP: OBI sequence data A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. cross validation objective rotation estimation objective cross validation objective James Malone WEB: http://en.wikipedia.org/wiki/Cross_validation An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 Bruker UltraShield Plus NMR magnet Bruker UltraShield Plus NMR magnet NMR instrument Haemosporida Haemosporida Bartonella grahamii Bartonella grahamii Desulfovibrio desulfuricans Desulfovibrio desulfuricans Rhabditoidea Rhabditoidea Euacanthopterygii Euacanthopterygii failed exploratory term Person:Alan Ruttenberg The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job A device function is a function inhering in a device enabling it to participate in a critical process in the context of a specific investigation plan. device function Schober: Bill, please check ID and definition. PERSON:Daniel Schober obsolete_device function latin square design Philippe Rocca-Serra PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and latin square design Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. IEDB T cell epitope (BrdU) cell proliferation assay IEDB T cell epitope specific proliferation assay that measures T cell proliferation utilizing the BrdU incorporation assay. T cell epitope (BrdU) cell proliferation assay obsolete_right handedness obsolete_right handedness Jennifer Fostel obsolete_role of being member of special population Special population Geriatric subset of eligible population 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 is an eligible population role played by a population with characteristics that make it especially important to target for enrollment James Malone submatrix extraction submatrix extraction Melanie Courtot 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.) WEB: http://en.wikipedia.org/wiki/Submatrix 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. Elisabetta Manduchi 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. CARO obsolete_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. organ Philippe Rocca-Serra http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 PERSON:Daniel Schober Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> atomic emission detector AED atomic emission detector James Malone A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. EDITOR sequence analysis data transformation sequence analysis data transformation Actinobacteria (class) Actinobacteria (class) A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. pressure pressure Monacrosporium haptotylum Monacrosporium haptotylum Triticeae Triticeae IEDB EL-4 cell culture http://www.biotech.ist.unige.it/cldb/cl1160.html A cell line derived from mouse (C57BL/6N) lymphoma cells. IEDB EL-4 cell culture A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage life cycle stage Stolidobranchia Stolidobranchia obsolete_digital quality Need to rework digital entity. Digital quality was suggested by Barry. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 hypothesis Tamoxifen cures cancer Gene A regulates pathway B Investigation has objective (hypothesis testing objective) which has part hypothesis Melanie Courtot Jennifer Fostel GROUP:OBI obsolete_hypothesis Hypothesis is an information content entity that is an assertion which is intended to be tested. Bartonella henselae Bartonella henselae PERSON: Jie Zheng fresh specimen fresh specimen PERSON: Chris Stoeckert a liver freshly removed from a rat a specimen that is output of a specimen creation process used for an investigation without storage. MO Mycobacterium Mycobacterium Methylophilaceae Methylophilaceae Streptomyces avermitilis Streptomyces avermitilis data set of features data set of features PERSON: Monnie McGee PERSON: James Malone A data set of features is a data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. experimental infection of cell culture experimental infection of cell culture is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture IEDB IEDB Apicomplexa Apicomplexa A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) microscope wikipedia PERSON: Phillippe Rocca-Serra microscope PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6 Thermoplasmataceae Thermoplasmataceae Vibrio cholerae Vibrio cholerae Penaeus Penaeus merging of columns from two different data sets combining objective James Malone PERSON: Data Transformation Branch merging objective A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. merging objective a processed material created to have a function and which requires electrical power to execute obsolete_electrically powered device obsolete_electrically powered device diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Jennifer Fostel diagnosis textual entity Mycobacteriaceae Mycobacteriaceae Thiomonas Thiomonas Cryptopygus Cryptopygus A cell line derived from mouse dendritic cells. IEDB IEDB JAWS II cell culture http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology JAWS II cell culture A clustered data set is a data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. A clustered data set is the output of a K means clustering data transformation AR thinks could be a data item instead clustered data set PERSON: Monnie McGee PERSON: James Malone data set with assigned discovered class labels clustered data set loess transformation loess transformation Philippe Rocca-Serra James Malone 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. OTHER: Editor's generalization based on MGED Ontology term Melanie Courtot Elisabetta Manduchi Cyanothece Cyanothece Macropus Macropus Desulfovibrionaceae Desulfovibrionaceae Pinaceae Pinaceae Desulfovibrio Desulfovibrio A parameter value application is part of a protocol application in which the values of the parameter are set. Setting the centrifuge to 1200 RPM. obsolete_parameter_value_application obsolete_parameter_value_application OBI http://www.biotech.ist.unige.it/cldb/cl1597.html A cell line derived from human cervical cancer cells. HeLa cell culture HeLa cell culture IEDB IEDB editor edge weighting Tina Hernandez-Boussard was classified under algorithm class which is not acceptable super-class TO BE DEALT WITH STILL BY RICHARD. JAMES edge weighting Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. Staphylococcus aureus subsp. aureus Staphylococcus aureus subsp. aureus Stegomyia Stegomyia Coccidia Coccidia setting datum A settings datum is a datum that denotes some configuration of an instrument. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. scalar score from composite inputs questionaire score scalar score from composite inputs PlanAndPlannedProcess Branch sample preparation for assay study OBI branch derived sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. Magnaporthaceae Magnaporthaceae assigning a centrally registered identifier A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity Actinomyces Actinomyces Coffea arabica Coffea arabica glucose molecules glucose in solution Glucose present in blood glucose in solution A scattered aggregate of glucose molecules in a liquid PERSON: Jie Zheng Brucellaceae Brucellaceae Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m. soil soil A line graph is a type of graph created by connecting a series of data points together with a line. WEB: http://en.wikipedia.org/wiki/Line_chart PERSON:Chris Stoeckert line graph line chart GROUP:OBI line graph PERSON:Melanie Courtot glucose metabolic process The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. glucose metabolic process Vibrio Vibrio Corynebacteriaceae Corynebacteriaceae Pipoidea Pipoidea alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. alive Sulfolobaceae Sulfolobaceae Liliopsida Liliopsida IEDB IEDB epitope specific IL-10 release by T cells epitope specific IL-10 release by T cells A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope. liquid chemical solution 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. A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute. PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch chemical solution chemical solution PERSON: Bjoern Peters documenting wikipedia http://en.wikipedia.org/wiki/Documenting a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Bjoern Peters Paracoccidioides brasiliensis Paracoccidioides brasiliensis Mycobacterium leprae Mycobacterium leprae Poeae Poeae PERSON:Daniel Schober imaging NMR probe imaging NMR probe NMR device GROUP:<http://msi-ontology.sourceforge.net> An NMR probe that is designed for generating pictures from sample states via NMR imaging. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 Awaiting English definition from Monnie McGee Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean spread calculation objective spread calculation objective Person:Helen Parkinson James Malone is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set Philippe Rocca-Serra copy number variation profiling copy number variation profiling CNV analysis Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796 copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping. conclusion textual entity A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case conclusion textual entity 2009/10/23 Alan Ruttenberg: We need to work on the definition still that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 Staphylococcus aureus Staphylococcus aureus Estrildidae Estrildidae Polytrichum juniperinum Polytrichum juniperinum Actinomyces naeslundii Actinomyces naeslundii in-line filter in-line filter PERSON:Daniel Schober WEB:<http://www.appliedporous.com/frits-chromatography.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. Drosophila simulans Drosophila simulans JEOL ECA NMR spectrometer PERSON:Daniel Schober NMR instrument WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> JEOL ECA NMR spectrometer The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 James Malone PERSON: Ryan Brinkman Ryan Brinkman Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. PERSON: Richard Scheuermann gating gating PERSON:Melanie Courtot Richard Scheuermann Josef Spidlen Melanie Courtot PERSON: James Malone PERSON: Josef Spidlen http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. fraction collector PERSON:Daniel Schober fraction collector A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. James Malone data vector reduction data transformation data vector reduction data transformation PERSON: James Malone Cyprinus carpio Cyprinus carpio IEDB epitope specific GM-CSF release by T cells epitope specific GM-CSF release by T cells IEDB A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope. Ciona savignyi Ciona savignyi obsolete__move to relations? obsolete__move to relations? James Malone All classes yet to be suitably placed in a hierarchy lymphotoxin A production The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. lymphotoxin A production TNF beta production obsolete_peptide 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. Philippe Rocca-Serra peptide Susanna Sansone TERM: CHEBI:16670 James Malone left cerebral hemisphere left cerebral hemisphere http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 NMR device indirect detection probe An NMR probe designed to allow the indirect detection of acquisition nuclei. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> indirect detection probe Leishmania braziliensis species complex Leishmania braziliensis species complex amino acids amino acids Carboxylic acids containing one or more amino groups. Synechococcus Synechococcus PERSON: Elisabetta Manduchi 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 samples out, the resulting data set corresponds to a column submatrix of the original set. Elisabetta Manduchi PERSON: Melanie Courtot A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. column submatrix extraction Melanie Courtot PERSON: James Malone James Malone column submatrix extraction GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 gel filtration column A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. PERSON:Daniel Schober gel filtration column Jennifer Fostel a reagent supplier role is realized by the process of supplying reagents for an investigation or part of an investigation obsolete_reagent supplier role Reagent supplier center calculation data transformation PERSON: James Malone A center calculation data transformation is a data transformation that has objective of center calculation. center calculation data transformation James Malone Eumalacostraca Eumalacostraca Oryzeae Oryzeae mass mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. Pancrustacea Pancrustacea right cerebral hemisphere right cerebral hemisphere Philippe Rocca-Serra Peptides containing ten or more amino acid residues TERM: CHEBI:16670 James Malone obsolete_polypeptide Susanna Sansone polypeptide An NMR instrument that is manufactured by tecmag. PERSON:Daniel Schober tecmag NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 GROUP:<http://msi-ontology.sourceforge.net> NMR instrument tecmag NMR instrument descriptive statistical calculation data transformation PERSON: James Malone A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. James Malone descriptive statistical calculation data transformation Viannia Viannia 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) PERSON: Monnie McGee A mean calculation 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 PERSON: James Malone Philippe Rocca-Serra mean calculation mean calculation Monnie McGee Trichoderma reesei QM6a Trichoderma reesei QM6a Mandibulata Mandibulata dead dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. WEB: http://en.wikipedia.org/wiki/Protein hemoglobin Philippe Rocca-Serra protein 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. TERM: CHEBI:16541 Susanna Sansone obsolete_protein (obsolete) James Malone scaling objective is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Person:Helen Parkinson Awaiting English definition from Monnie McGee Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 scaling objective James Malone PERSON: Elisabetta Manduchi PERSON: Monnie McGee descriptive statistical calculation objective PERSON: James Malone Elisabetta Manduchi PERSON: Melanie Courtot Monnie McGee James Malone A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. Melanie Courtot descriptive statistical calculation objective An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. affinity column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 affinity column PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> Fabaceae Fabaceae Coffea Coffea A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope. epitope specific IFN-g release by T cells IEDB IEDB epitope specific IFN-g release by T cells Trifolium Trifolium Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class). site Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria. Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities. Cyprinus Cyprinus tumor necrosis factor production The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. tumor necrosis factor production TNF alpha production Pyuridae Pyuridae Triticum Triticum NMIA RNA structure mapping assay single nucleotide resolution mapping assay using NMIA probe a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses NMIA as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure NMIA RNA structure mapping assay RNA ontology Person:Philippe Rocca-Serra SHAPE mapping assay PMID: 15796531 length unit length unit length unit A base unit which is a standard measure of the distance between two points. length unit substance detection the detection of phycoerytherin by means of flow cytometry substance detection PERSON:Kevin Clancy any protocol which results in the detection of a specified substance OBI branch derived obsolete_instrument OBI InstrumentBranch OBI InstrumentBranch An instrument is a device which provides a mechanical or electronic function. was: An instrument is a device which provides a mechanical or electronic advantage as a participant in a process An example of an instrument is a mass spectrometer or a flow cytometer instrument Archaeoglobus Archaeoglobus recombinant YAC cloning http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21 recombinant YAC cloning Helen Parkinson Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material PMID:19696660#The thrombin time was determined using thromboclotin assay kit. thrombin time assay 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs thrombin time assay Person:Alan Ruttenberg obsolete_laboratory role Laboratory is an administrative unit role played by an organization and its members who perform clinical assays or non-clinical trials Laboratory Jennifer Fostel Pisum sativum Pisum sativum Drosophila erecta Drosophila erecta left side of A relational spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. left side of Xanthomonas campestris Xanthomonas campestris Veillonella parvula Veillonella parvula Triticum aestivum Triticum aestivum Pisum Pisum Archaeoglobus fulgidus Archaeoglobus fulgidus PMID:10772868 RNA ontology Person:Philippe Rocca-Serra Terbium RNA structure mapping assay Terbium RNA structure mapping assay single nucleotide resolution mapping assay using Terbium probe a single-nucleotide-resolution nucleic acid structure mapping assay which uses Terbium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure 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 Instrument branch device A device is a material that is manufactured by an organization or person, designed with the intent to perform a specific function or functions. hardware obsolete_device Instrument branch A device can be any instrument such as a mass spectrometer or lab ware such as a petri dish When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture maintaining cell culture maintaining cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing PlanAndPlannedProcess Branch OBI branch derived A mass spectrometry assay is an assay to measure and analyze the molecules of a sample based on it's mass and charge. definition_source: OBI. obsolete_mass spectrometry assay obsolete mass spectrometry assay OBI branch derived PlanAndPlannedProcess Branch A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated single blind study execution http://clinicaltrials.gov/ct2/info/glossary#single single blind study execution 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg Thraupini Thraupini Campylobacter jejuni Campylobacter jejuni Actinobacillus Actinobacillus Veillonella Veillonella Streptococcus agalactiae Streptococcus agalactiae Sphingobacteriales Sphingobacteriales a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAase U2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure RNA ontology PMID:409999 RNASE U2 structure mapping assay single nucleotide resolution mapping assay using RNAse U2 RNASE U2 structure mapping assay Person:Philippe Rocca-Serra Hypodermis Hypodermis Halobacteriales Halobacteriales ---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined. artificially induced cell membrane lysis a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate PlanAndPlannedProcess Branch http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent. OBI branch derived artificially induced cell membrane lysis nuclear magnetic resonance assay www.nature.com/nrd/journal/v2/n5/glossary/nrd1086_glossary.html OBI branch derived nuclear magnetic resonance assay PlanAndPlannedProcess Branch an assay used to identify the chemical structure of a compound or biological macromolecule. filled capsule 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A pill in the form of a small rounded gelatinous container with medicine inside. http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n filled capsule Person:Alan Ruttenberg Pasteurellaceae Pasteurellaceae Cercopithecinae Cercopithecinae Triticum turgidum subsp. durum Triticum turgidum subsp. durum CD8-positive, alpha-beta cytotoxic T cell A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. CD8-positive, alpha-beta cytotoxic T cell Halobacteriaceae Halobacteriaceae OBI branch derived Helen Parkinson longitudinal mass measurement assay longitudinal mass measurement assay A process in which the mass of a material is measured at two or more time points The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection connected_spatiotemporal_region Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion]. Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus activated partial thromboplastin time (aPTT) assay An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms. 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs 2009/09/28 Alan Ruttenberg. Fucoidan-use-case WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06 activated partial thromboplastin time (aPTT) assay PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent. Person:Alan Ruttenberg population PERSON: 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 adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process 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. population Streptococcus pneumoniae Streptococcus pneumoniae phage display library PERSON: Bjoern Peters display library WEB: http://www.immuneepitope.org/home.do PERSON: Philippe Rocca-Serra a phage 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. PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction phage display library 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] Bacillus subtilis Bacillus subtilis Cellia Cellia isolation of cell culture supernatant isolation of cell culture supernatant OBI branch derived PlanAndPlannedProcess Branch Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube. a protocol which results in the separation of supernatant material from a cell culture This does not apply to the case where the cells are lysed research organization The SALK institute is a research organization. Person:Bjoern Peters An organization formed with a goal to have its members conduct investigations research organization ssDNA viruses ssDNA viruses Mucosa of oropharynx Mucosa of oropharynx eluate eluate 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 PERSON: Philippe Rocca-Serra OBI Bionaterial need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263 eluted material Linum Linum Streptococcus pyogenes Streptococcus pyogenes Deinococcaceae Deinococcaceae IEDB An assay that measures MHC:epitope complex binding to TCR utilizing flow cytometry. The MHC molecules are prepared into multimers, loaded with epitope, and are fluorescently labeled in order to visualize the T cells that bind. The data that is generated provides information on the presence of epitope specific T cells in the cell population that was tested. T cell epitope MHC tetramer/multimer staining assay IEDB T cell epitope MHC tetramer/multimer staining assay Catarrhini Catarrhini portion of tissue portion of tissue Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. a processed material which is used to introduce or draw fluids from a material entity. A 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 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 OBI Instrument adapted from Wikipedia syringe Philippe Rocca-Serra syringe pathology review board Person: Jennifer Fostel role of pathology review board role of pathology review board a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation Thlaspi Thlaspi drug added to a buffer contained in a tube; substance injected into an animal; OBI material to be added role Role Branch material to be added role material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process 9 March 09 from discussion with PA branch Sordariales Sordariales OBI branch derived The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA artificially induced reverse transcription PERSON:Kevin Clancy a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) artificially induced reverse transcription We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. Linum usitatissimum Linum usitatissimum A dose of medicine or placebo in the form of a small pellet. Person:Alan Ruttenberg pill pill 2009/09/28 Alan Ruttenberg. Fucoidan-use-case http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n Solanum tuberosum Solanum tuberosum Plasmodium berghei Plasmodium berghei Ferroplasma acidarmanus Ferroplasma acidarmanus Cercopithecidae Cercopithecidae extracted material GROUP: OBI Biomatrial Branch Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 PERSON: Philippe Rocca-Serra extract extract an extract is a material entity which results from an extraction process Neognathi Neognathi data format specification obsolete_data format specification A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file PlanAndPlannedProcess Branch OBI branch derived Festuca rubra subsp. littoralis Festuca rubra subsp. littoralis 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over Person:Alan Ruttenberg A planned process, part of a study design execution, during which the treatment of subjects is ongoing treatment portion of study execution treatment portion of study execution 2009/09/28 Alan Ruttenberg. Fucoidan-use-case feature extraction PERSON: Jie Zheng feature extraction A planed process with objective of obtaining quantified values from an image. MO_928: feature_extraction Methanobacteria Methanobacteria Plasmodium Plasmodium scattered_temporal_region Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which. Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair Drosophila orena Drosophila orena 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. protocol optimization Jennifer Fostel protocol optimization Halobacterium Halobacterium obsolete_trypsinized material A trypsinized suspension of cells A material entity that has undergone a process of digestion with trypsin Test Class: to evaluate OBI design pattern decided to be deprecated on Aug 2, 2010 dev call obsolete_trypsinized material Person:Bjoern Peters Felidae Felidae single nucleotide resolution mapping assay using OH-radical probe MOHCA assay RNA ontology OH-radical structure mapping assay a single-nucleotide-resolution nucleic acid structure mapping assay which uses hydroxyl radical as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure PMID:2501870 OH-radical structure mapping assay Person:Philippe Rocca-Serra OH footprinting assay A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo to be treated with placebo role to be treated with placebo role Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Festuca rubra subsp. fallax Festuca rubra subsp. fallax Linaceae Linaceae The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. cytotoxic T cell degranulation cytotoxic T cell degranulation Campylobacter Campylobacter Thermoprotei Thermoprotei Nicotiana Nicotiana Actinobacillus pleuropneumoniae Actinobacillus pleuropneumoniae glucose glucose imaging assay imaging assay OBI branch derived PlanAndPlannedProcess Branch An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. Felis Felis OBI Biomaterial decapitated organism decapitated organism Philippe Rocca-Serra Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 decapitated organism is an organism which has had it's head removed OBI Biomaterial Philippe Rocca-Serra injection injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 injection quantitative confidence value group:OBI person:Chris Stoeckert quantitative confidence value A quantitative confidence value is a information content entity which is used to indicate the degree of uncertainty about a measurement. A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension cell pellet GROUP: OBI Biomaterial Branch Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214 GROUP: CEBS cell pellet PERSON: Philippe Rocca-Serra PERSON: Helen Parkinson Trichodesmium Trichodesmium Spermatophyta Spermatophyta loop design A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design Philippe Rocca-Serra on behalf of MO MO_912 loop design PMID: 12933549 adaptive immune receptor IEDB IEDB adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. Acidithiobacillales Acidithiobacillales Lactobacillaceae Lactobacillaceae Sapindales Sapindales Chlamydophila Chlamydophila Spirurida Spirurida Anabaena variabilis Anabaena variabilis IEDB Bjoern Peters Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules enrollment enrollment Drosophila melanogaster Drosophila melanogaster (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) enzyme person: Melanie Courtot MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. GROUP:OBI enzyme solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615 GROUP: IEDB Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. cell culture supernatant cell culture supernatant PERSON: Bjoern Peters Picea Picea OBI biomaterial branch microscope slide PERSON: Phillippe Rocca-Serra a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument microscope slide PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. Trichodesmium erythraeum Trichodesmium erythraeum Tracheophyta Tracheophyta immunogen a material entity bearing the immunogen role immunogen IEDB IEDB Nidovirales Nidovirales balanced incomplete block design 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 http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html 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' Philippe Rocca-Serra Acidithiobacillaceae Acidithiobacillaceae scientific observation assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. measuring OBI branch derived assay A planned process with the objective to produce information about some evaluant PlanAndPlannedProcess Branch Pyretophorus Pyretophorus Drosophila mauritiana Drosophila mauritiana OBI transcription profiling 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 transcription profiling Philippe Rocca-Serra gene expression profiling trancription profiling is a process which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot denatured polymer denatured polymer PERSON: Alan Ruttenberg Is a polymer which has lost secondary or tertiary structure http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 Drosophila pseudoobscura Drosophila pseudoobscura B cell A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive. B cell PERSON: Phillippe Rocca-Serra a processed material which has the function to define a bounded habitat which is amenable to keeping animals. animal cage animal cage laboratory cage PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice. OBI biomaterial branch http://www.tufts.edu/~gdallal/ranblock.htm Philippe Rocca-Serra randomized complete block design A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) randomized complete block design IEDB IEDB Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent environmental exposure to infectious agent environmental exposure to infectious agent 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 interrogation point. arc lamp The Jablochkoff Candle http://en.wikipedia.org/wiki/Arc_lamp arc lamp John Quinn Pleuronectoidei Pleuronectoidei averaging objective Elisabetta Manduchi A mean calculation 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 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. substance unit A base unit which is a standardized quantity of an element or compound with uniform composition. substance unit Drosophila sechellia Drosophila sechellia MHC protein complex MHC protein complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. macrophage macrophage microarray function obsolete_microarray function A liquid state is a state in which the entity has no fixed shape but a fixed volume, generally at a temperature between its freezing and boiling points. OBI obsolete_liquid_state obsolete_liquid_state Aconoidasida Aconoidasida Anurophorinae Anurophorinae An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. FACS Calibur, Luminex 100 flow cytometer analyzer http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm John Quinn flow cytometer analyzer Rosoideae Rosoideae A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. parallel group design independent measure design http://www.holah.karoo.net/experimentaldesigns.htm parallel group design Philippe Rocca-Serra Drosophilini Drosophilini Nostoc Nostoc RNA microarray function obsolete_RNA microarray function we could generalize this for other input materials cell fixation should include capturing what qualities are being preserved OBI branch derived a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus cell fixation PERSON:Bjoern Peters temperature unit A base unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit Magnetospirillum Magnetospirillum matched pairs design 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. Philippe Rocca-Serra 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. Embryophyta Embryophyta analog-to-digital converter A2D The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. analog-to-digital converter http://en.wiktionary.org/wiki/Analog-to-Digital_Converter John Quinn Melanie Courtot A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. Paxillus involutus Paxillus involutus PERSON: Bjoern Peters David Osumi Sutherland an assay of changes in phenotype due to increased or decreased dosage of a single allele of a gene. gene dosage assay gene dosage assay A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. host of immune response In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation. IEDB host of immune response An organism in which an immune response process occurs. IEDB rhodium rhodium A cobalt group element that has formula Rh. Mollicutes Mollicutes Brugia Brugia Philippe Rocca-Serra observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. observation design PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. observation design OBI branch derived Pasteuria Pasteuria PRS:20090901: addition of alternative term = histopathology histopathology 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 PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney OBI branch derived histology histology the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated 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 revisit? PERSON:Alan Ruttenberg OBI branch derived adverse event trigger adverse event trigger Chlamydophila pneumoniae Chlamydophila pneumoniae n-to-1 design Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) 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 Philippe Rocca-Serra obsolete_transcription analysis function transcription analysis function John Quinn A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice 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. A40-MiniFCM A40-MiniFCM http://www.apogeeflow.com/flow_cytometry_products.htm RNA ontology Person:Philippe Rocca-Serra single nucleotide resolution mapping assay using Fe-BABE probe a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-BABE as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Fe-BABE RNA structure mapping assay PMID: 7862644 Fe-BABE RNA structure mapping assay Campylobacterales Campylobacterales Drosophilina Drosophilina sequential design MUSC Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does sequential design PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. Provenance: OCI Philippe Rocca-Serra Brugia malayi Brugia malayi time unit time unit time unit time unit A base unit which is a standard measure of the dimension in which events occur in sequence. transcription factor binding site identification a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors transcription factor binding site identification Philippe Rocca-Serra 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 Carnivora Carnivora Skeletal muscle tissue Skeletal muscle tissue Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm. John Quinn A10-Analyzer 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. http://www.apogeeflow.com/flow_cytometry_products.htm PERSON:Kevin Clancy OBI branch derived The use of agarase to digest an agar gel non specific enzymatic cleavage a protocol application to digest the fraction of input material that is susceptible to that enzyme non specific enzymatic cleavage Archaeoglobales Archaeoglobales cross over design PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) cross over design a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control Philippe Rocca-Serra The administration of a substance into the peritoneum of an organism intraperitoneal administration Person:Bjoern Peters intraperitoneal administration Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h erythrocyte A red blood cell. In mammals, mature erythrocytes are non-nucleated, biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte Lead structure mapping assay a single-nucleotide-resolution nucleic acid structure mapping assay which uses lead as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure RNA ontology PMID:2686708 single nucleotide resolution mapping assay using Lead probe Lead structure mapping assay Person:Philippe Rocca-Serra obsolete_NMR spectroscopy function obsolete_NMR spectroscopy function 293-T cell culture 293-T cell culture http://www.biotech.ist.unige.it/cldb/cl5008.html IEDB A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication. IEDB right side of right side of A relational spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. Xanthomonas Xanthomonas validated information OBI Person:Philippe Rocca-Serra an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means. PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." validated information a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage PERSON: Jie Zheng paraffin storage UPenn Group paraffin storage need to specify paraffin or wax is one of specified input of the process PERSON: Chris Stoeckert 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. http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design repeated measure design PlanAndPlannedProcess Branch 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 in container assay an assay in which a measurement is made by observing entities located in a container. in container assay the use physical means to remove a portion of a substance from the rest excision excision Cutting out the portion of a gel which contains a DNA fragment Alan Ruttenberg, Kevin Clancy www.crohnsresource.com/glossary.jsp (via google define:resection) obsolete_labware OBI labware Daniel Schober 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). Archaeoglobaceae Archaeoglobaceae mass unit mass unit mass unit mass unit A base unit which is a standard measure of the amount of matter/energy of a physical object. RNA ontology Person:Philippe Rocca-Serra a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure PMID:6207483 RNASE T2 structure mapping assay single nucleotide resolution mapping assay using RNAse T2 RNASE T2 structure mapping assay C1R cell culture IEDB C1R cell culture IEDB A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). metabolic profiling function obsolete_metabolic profiling function Saccharomyces mikatae Saccharomyces mikatae An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. PERSON: Erik Segerdell electron paramagnetic resonance spectrometer electron paramagnetic resonance spectrometer http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance T cell epitope ELISPOT IL-10 assay IEDB A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ELISPOT methodology. IEDB T cell epitope ELISPOT IL-10 assay Rhizobiaceae Rhizobiaceae quality of a single physical entity quality of a single physical entity A physical object quality which inheres in a single-bearer. Gallus Gallus Cryptosporidium parvum Cryptosporidium parvum Gallus gallus Gallus gallus Proteobacteria Proteobacteria characteristic path length calculation characteristic path length calculation Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices PERSON: Tina Hernandez-Boussard PERSON: Tina Hernandez-Boussard data item extraction from journal article a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing Person:Alan Ruttenberg solute role solute role solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) Philippe Rocca-Serra PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure. positive reference substance role positive reference substance role MMS mutagen a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response positive reference substance Person: Jennifer Fostel specimen labeling function specimen labeling function WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> Varian MERCURY spectrometer Varian MERCURY spectrometer MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. NMR instrument PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 James Malone Fisher's exact test Fisher's exact test Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. WEB:http://mathworld.wolfram.com/FishersExactTest.html http://www.faqs.org/patents/app/20090196797 A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. electronic repeater pipette electronic repeater pipette PERSON: Erik Segerdell A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). water bath A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. Daniel Schober water bath PERSON: Daniel Schober Cyprinoidea Cyprinoidea Philippe Rocca-Serra adapted from Wikipedia before possible import from CHEBI polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether 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 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. author role author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot unsupervised classification data transformation PERSON: James Malone A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. class discovery data transformation class discovery data transformation clustering data transformation James Malone PERSON: Tina Hernandez-Boussard PERSON: James Malone continuum mass spectrum continuum mass spectrum A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. PERSON: Tina Boussard A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package OBI Helen Parkinson An training objective which is fulfilled by the provision of some training training objective training objective hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments hematology hematology blood analysis, haematology Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943 Philippe Rocca-Serra OBI branch derived study design study design PERSON: Chris Stoeckert a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. PERSON: Erik Segerdell analytical balance analytical balance A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. http://en.wikipedia.org/wiki/Weighing_scale Monnie McGee data imputation 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. ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. data imputation The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production Pinus resinosa Pinus resinosa Cricetinae Cricetinae Joseph Spliden b transformation Elisabetta Manduchi WEB: http://flowcyt.sourceforge.net/gating/latest.pdf b transformation This type of transformation is typically used in flow cytometry. A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. Ryan Brinkman Enterogona Enterogona Spirochaetes (class) Spirochaetes (class) detection of analyte in blood sample clinical chemistry assay a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism. 3/26/09: There needs to be a restriction set that specifies which type of evaluants are used in the assay, somewhere along the lines of 'sample derived of bodily fluid' clinical chemistry assay Person: Philippe Rocca-Serra adapted from Wikipedia chemical pathology Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Mueller T, Schimetta W, Dieplinger B, Loeffler P, Rehm M, Kreimeier U, Poelz W, Haltmayer M. Clin Chem Lab Med. 2008;46(4):558-62. PMID: 18605936 B cell tolerance induction A process involving any mechanism for tolerance induction in B cells. B cell tolerance induction WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 PERSON:Daniel Schober column heater The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. column heater a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation Bjoern Peters OBI branch derived investigation Could add specific objective specification Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation James Malone curve fitting objective Elisabetta Manduchi curve fitting objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. PERSON: Elisabetta Manduchi Escherichia coli Escherichia coli categorical label categorical label PlanAndPlannedProcess Branch PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] The definition needs to be extended to other things than simply patients clinical study design clinical study design Clinical Research Glossary Version 4.0 CDICS glossary group t cell epitope prediction 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. t cell epitope prediction PERSON: Helen Parkinson Helen Parkinson A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). rocker PERSON: Erik Segerdell PERSON: Erik Segerdell rocker Actinobacteridae Actinobacteridae A physical entity quality which exists in relation towards some other entity. quality of related physical entities quality of related physical entities droplet sorter 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. OBI Instrument branch droplet sorter An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 Bruker Metabolic Profiler PERSON:Daniel Schober Bruker Metabolic Profiler hyphenated NMR instrument platform NMR instrument WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> Escherichia Escherichia Spirochaetes Spirochaetes in live cell assay An assay in which a measurement is made by observing entities located in a live cell. in live cell assay background correction objective background correction objective James Malone Elisabetta Manduchi A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. PERSON: Elisabetta Manduchi single cell gel electrophoresis assay a comet assay is an assay which utilizes gel electrophoresis 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. SCGE assay comet assay PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review. PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra comet assay GROUP: Role Branch When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. OBI evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role a role that inheres in an entity that is realized in an assay in which data is generated about the bearer of the evaluant role Aculeata Aculeata Bifidobacteriales Bifidobacteriales IEDB infection infection the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB Populus deltoides Populus deltoides Rosales Rosales http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 NMR probe The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 µl flowcell with an NMR active volume of 2.5 µl, and a 10 µl flowcell with an NMR active volume of 5 µl. The fluidic connections are 75 µm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. PERSON:Daniel Schober WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> JEOL CapNMR probe JEOL CapNMR probe Coregonus Coregonus trial monitor role trial monitor role a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study trial monitor 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. Person:Jennifer Fostel Onchocercidae Onchocercidae Rubus idaeus Rubus idaeus James Malone partial least square discriminant analysis PLS-DA WEB: http://www.camo.com/rt/Resources/pls-da.html PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. partial least square discriminant analysis mitosporic Trichocomaceae mitosporic Trichocomaceae Actinomycineae Actinomycineae Populus trichocarpa x Populus deltoides Populus trichocarpa x Populus deltoides IEDB IEDB Immunization in vitro Process of administering an object playing the role of immunogen to a cell culture Immunization in vitro Mycoplasma Mycoplasma DNA methylation profiling Philippe Rocca-Serra DNA methylation profiling is a process which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. DNA methylation profiling OBI branch derived Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979 Rosaceae Rosaceae Filarioidea Filarioidea obsolete_Surgical intervention Surgical intervention device is an intervention variable in which the varying parameter is a surgical procedure or medical device Test of a new pacemaker Surgical intervention Jennifer Fostel PERSON: Bjoern Peters peptide construct peptide construct IEDB a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617 PERSON: Elisabetta Manduchi classification objective class prediction objective supervised classification objective 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 technique. 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 eh transformation Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf eh transformation Elisabetta Manduchi An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. OBI_0000099 PERSON: Melanie Courtot a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. report 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion PERSON: Alan Ruttenberg 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON:Chris Stoeckert GROUP: OBI disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. report Vitales Vitales 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. digital-to-analog converter PERSON: Daniel Schober digital-to-analog converter Daniel Schober microcentrifuge http://en.wikipedia.org/wiki/Laboratory_centrifuge microcentrifuge A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. PERSON: Erik Segerdell PERSON:Daniel Schober gas purifier gas purifier http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> gas chromatography equipment Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. Mycoplasmataceae Mycoplasmataceae Cannabaceae Cannabaceae Populus trichocarpa Populus trichocarpa Environmental characteristic variable 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 Varying the collection location for environmental samples in study of chromium levels and effects Jennifer Fostel obsolete_Environmental characteristic variable class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. PERSON: James Malone discriminant analysis objective clustering objective class discovery objective unsupervised classification objective James Malone PERSON: Elisabetta Manduchi Xanthomonas campestris pv. campestris Xanthomonas campestris pv. campestris Herdmania Herdmania buffer role Person:Philippe Rocca-Serra OBI buffer role Person:Helen Parkinson a role which inheres in some molecular entity realized during the process of buffering buffer A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3−) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution partial least square regression analysis Tina Hernandez-Boussard Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. partial least square regression analysis ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. PLS-RA An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample). An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period. oil bath Daniel Schober PERSON: Daniel Schober oil bath Corynebacterineae Corynebacterineae Cannabis Cannabis gas chromatography detector PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> gas chromatography detector chromatography detector, defined class/xps A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 FID Saccharomyces kudriavzevii Saccharomyces kudriavzevii Dictyostelium Dictyostelium Tetraodontoidei Tetraodontoidei center calculation objective 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. James Malone center calculation objective A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. PERSON: James Malone reagent application function reagent application function Insertion of approved cardiac pace maker Reference medical device is a reference treatment used in a clinical investigation of medical device behavior; it is played by an approved medical device. obsolete_Reference medical device Jennifer Fostel Reference medical device http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 PERSON:Daniel Schober acquisition computer acquisition computer GROUP:<http://msi-ontology.sourceforge.net> A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. NMR instrument solvent role adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) solvent role Philippe Rocca-Serra PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors. solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation Herdmania momus Herdmania momus 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. WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant analysis Tina Hernandez-Boussard discriminant analysis mitosporic Onygenales mitosporic Onygenales 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 epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s 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 multiple linear regression analysis WEB: http://www.answers.com/animal?cat=health human obsolete_animal Melanie Courtot James Malone A multicellular organism of the kingdom Animalia, differing from plants in certain typical characteristics such as capacity for locomotion, nonphotosynthetic metabolism, pronounced response to stimuli, restricted growth, and fixed bodily structure. animal preparative autosampler http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 GROUP:<http://msi-ontology.sourceforge.net> preparative autosampler For preparative LC with injection of sample volumes ranging from L to mL ranges. PERSON:Daniel Schober Hypocreaceae Hypocreaceae Triticum turgidum Triticum turgidum flow HR-probe flow high resolution probe Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. NMR probe GROUP:<http://msi-ontology.sourceforge.net> flow high resolution probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 PERSON:Daniel Schober Collembola Collembola Solanum lycopersicum Solanum lycopersicum anterior to anterior to A relational spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. frontal IEDB T cell epitope intracellular cytokine staining (ICS) IL-17 assay T cell epitope intracellular cytokine staining (ICS) IL-17 assay A T cell epitope specific cytokine production assay that measures production of IL-17 by T cells utilizing the ICS methodology. IEDB WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. principal component regression Tina Hernandez-Boussard principal component regression Salmoniformes Salmoniformes Melanie Courtot WEB: http://en.wikipedia.org/wiki/Fungus James Malone Saccharomyces cerevisiae obsolete_fungus fungus 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. PERSON:Daniel Schober Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> splitless GC injector splitless GC injector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 Ustilaginomycetidae Ustilaginomycetidae Felis catus Felis catus Mycoplasma genitalium Mycoplasma genitalium Brassicales Brassicales T cell epitope intracellular cytokine staining (ICS) IL-10 assay IEDB T cell epitope intracellular cytokine staining (ICS) IL-10 assay A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ICS methodology. IEDB Polytrichopsida Polytrichopsida WEB: http://en.wikipedia.org/wiki/Reverse_transcribing_viruses Melanie Courtot obsolete_reverse transcribing virus reverse transcribing virus A reverse transcribing virus is any virus which replicates using reverse transcription, the formation of DNA from an RNA template. hepatitis B virus James Malone Susanna Sansone Peloderinae Peloderinae Papilionoideae Papilionoideae linear discriminant functional analysis 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. PERSON: Tina Hernandez-Boussard linear discriminant functional analysis First subject treated First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study first subject treated. First subject who receives the test article or placebo in a clinical trial. obsolete_role of being first subject treated OBI Rat 1A; first enrolled patient to receive treatment Role Branch Listeria innocua Listeria innocua Neosartorya fennelliae Neosartorya fennelliae JEOL NMR probe PERSON:Daniel Schober An NMR probe that is manufactured by JEOL. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 NMR device GROUP:<http://msi-ontology.sourceforge.net> JEOL NMR probe 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. Alan Ruttenberg: 2009/11/01 - probably a duplicate for object acquisition. https://sourceforge.net/tracker/?func=detail&aid=2890523&group_id=177891&atid=886178 Bjoern Peters acquisition acquisition IEDB Culicini Culicini plant James Malone tree WEB: http://www.answers.com/topic/plant?cat=biz-fin obsolete_plant Melanie Courtot 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. regression analysis method Tina Hernandez-Boussard BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. regression analysis method Streptomyces coelicolor Streptomyces coelicolor Thermoanaerobacter Thermoanaerobacter WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> chromatography device PERSON:Daniel Schober liquid chromatography valve liquid chromatography valve A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 T cell epitope intracellular cytokine staining (ICS) IL-4 assay A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ICS methodology. IEDB IEDB T cell epitope intracellular cytokine staining (ICS) IL-4 assay exposure of material to environment IEDB a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. Bjoern Peters Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. exposure of material to environment Alan says there will be problmes, e.g. with selection by survival 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. partitioning objective James Malone partitioning objective 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 PERSON: Elisabetta Manduchi Chroococcales Chroococcales PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases. polymerase chain reaction-single strand conformation polymorphism assay PCR-SSCP assay a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure. PERSON: Philippe Rocca-Serra PCR-SSCP assay PERSON:Daniel Schober vial GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 vial A vial is a cylindrical container often made from glass tubing. A DNA virus is a virus that has DNA as its genetic material and replicates using a DNA-dependent DNA polymerase. Melanie Courtot DNA virus WEB: http://en.wikipedia.org/wiki/DNA_virus obsolete_DNA virus James Malone papillomavirus A relational spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. dorsal to dorsal to a study personnel role played by a party who reports the outcome of a study component MO:submitter mapped to this term. So, alternative term 'submitter' was added. reporting party role OBI reporting party The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm submitter Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. Jennifer Fostel reporting party role Ovis Ovis chi square test The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. PERSON: Tina Boussard PERSON: James Malone chi square test Festuca rubra Festuca rubra injection function PERSON: Alan Ruttenberg adapted from WEB: http://www.dictionary.net/injection PERSON: Melanie Courtot injection function The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. IEDB T cell epitope intracellular cytokine staining (ICS) TNF assay T cell epitope intracellular cytokine staining (ICS) TNF assay IEDB A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ICS methodology. flame ionization detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. PERSON:Daniel Schober WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> flame ionization detector FID Holm false discovery rate correction method