Richard Scheuermann Barry Smith Cristian Cocos Richard Bruskiewich Melanie Courtot Jeffrey Grethe Gilberto Fragoso Jessica Turner Dawn Field 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 2009-07-31 Jie Zheng Trish Whetzel free, no license required. Luisa Montecchi Allyson Lister OWL-DL Philip Lord 2009-11-06 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 John Westbrook Kevin Clancy Larisa Soldatova Jay Greenbaum This file is based on checkout of our SVN repository revision $Revision: 2489 $ Mervi Heiskanen Alan Ruttenberg Helen Parkinson James Malone Elisabetta Manduchi Lawrence Hunter Bill Bug Chris Stoeckert http://purl.obolibrary.org/obo/obi/2009-11-06/obi.owl Daniel Rubin Matthew Pocock Helen C. Causton Tanya Gray Ryan R. Brinkman en Liju Fan Ontology for Biomedical Investigation Bacillus cereus Bacillus cereus Capsicum annuum Capsicum annuum editor A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. data pooling data combination data combination Richard Scheuermann Magnoliaceae Magnoliaceae age age A time quality inhering in a bearer by virtue of how long the bearer has existed. A time quality inhering in a bearer by virtue of how long has existed. Triticum Triticum Halobacteria Halobacteria 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. A relational spatial quality where on entity is located toward the back or upper surface of an organism relative to another entity. dorsal to dorsal to Sylviidae Sylviidae electronic case report form CDISC glossary An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel electronic case report form http://www.guavatechnologies.com/main/products/PCA-96new.cfm Guava Personal Cell Analysis-96 Guava Personal Cell Analysis-96 The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. John Quinn Guava_PCA-96 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 Actinobacteria (class) Actinobacteria (class) Brassica napus Brassica napus A repeated measure design is a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs PlanAndPlannedProcess Branch repeated measure design http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design 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. Coxiella burnetii Coxiella burnetii pool of specimens PERSON: Jennifer Fostel check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish pool of specimens GROUP: CEBS A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. Archaea Archaea Linum Linum a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance material maintenance Ureaplasma urealyticum Ureaplasma urealyticum IEDB BrdU incorporation assay wiki http://en.wikipedia.org/wiki/BrdU The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. A BrdU incorporation assay is an assay to detect actively replicating cells. BrdU is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication. Antibodies specific for BrdU can then be used to detect the incorporated chemical, thus indicating cells that were actively replicating their DNA. BrdU incorporation assay A normalized data set is a data set that is produced as the output of a normalization data transformation. PERSON: Melanie Courtot PERSON: James Malone normalized data set normalized data set Brugia Brugia PERSON: Elisabetta Manduchi 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. class prediction objective supervised classification objective James Malone class prediction objective PERSON: James Malone Spirochaetaceae Spirochaetaceae Spirochaetales Spirochaetales Philippe Rocca-Serra on behalf of MO dye swap design An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. MO_858 dye swap design Xanthomonas axonopodis pv. citri Xanthomonas axonopodis pv. citri asterids asterids trial monitor role trial monitor role Trial monitor is a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study Jennifer Fostel Hypocreales Hypocreales A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. cell co-culturing Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay 2 PlanAndPlannedProcess Branch OBI branch derived cell co-culturing Ralstonia solanacearum Ralstonia solanacearum Thiomonas sp. 3As Thiomonas sp. 3As Canis Canis Brucella Brucella Cytophaga hutchinsonii Cytophaga hutchinsonii Thermoproteaceae Thermoproteaceae Is a disease characterized by an immune response of an organism against parts of itself autoimmune disease IEDB IEDB autoimmune disease adapted from wikipedia Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292 document editing editing is a process which checks for and corrects errors in spelling, punctuation, capitalization, grammar, and usage; curation, proofreading document editing Philippe Rocca-Serra Bjoern Peters and Nicole Washington cell cycle synchronization is a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle cell cycle synchronization OBI PA cell cycle synchronization Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs. Tracheophyta Tracheophyta placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress CEBS, Biomaterial_branch acclimatization A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. acclimatization Jennifer Fostel Dothideomycetes et Chaetothyriomycetes incertae sedis Dothideomycetes et Chaetothyriomycetes incertae sedis A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air. Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter jet_in_air_flow_chamber http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm jet_in_air_flow_chamber John Quinn a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. OBI branch derived PlanAndPlannedProcess Branch clinical diagnosis clinical diagnosis Parent of minor patient; Definition of legally acceptable representative An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE role of legally acceptable representative Jennifer Fostel role of legally acceptable representative OBI, CDISC legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary] IEDB A disease characterized by abnormal and uncontrolled cell division cancer cancer IEDB 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 Desulfovibrio desulfuricans Desulfovibrio desulfuricans Sus Sus IEDB The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex. effector T cell function IEDB effector T cell function WEB: http://en.wikipedia.org/wiki/Xenograft PERSON: Philippe Rocca-Serra xenograft xenotransplant Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. PERSON: Melanie Courtot xenograft Homo/Pan/Gorilla group Homo/Pan/Gorilla group Dinosauria Dinosauria A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role material sample role a blood sample taken to represent all the blood in an organism; a human taken to represent others in a cohort. mature NK T cell mature NK T cell A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. Physcomitrella Physcomitrella first subject treated. First subject who receives the test article or placebo in a clinical trial. OBI role of being first subject treated Role Branch Rat 1A; first enrolled patient to receive treatment role of being 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 WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. ozone-induced chemiluminescence detector ozone-induced chemiluminescence detector PERSON:Daniel Schober 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. Bjoern Peters 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. IEDB exposure of material to environment exposure of material to environment A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. homogenizer mortar, blender http://en.wikipedia.org/wiki/Homogenizer Trish Whetzel Melanie Courtot homogenizer Ralstonia Ralstonia Bjoern Peters PERSON: Jennifer Fostel the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions PERSON: Bjoern Peters interpreting data Identifiying and removing outliers from data by eye. Examining data to and deriving a new hypothesis. interpreting data Elisabetta Manduchi A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. Loess scale group normalization applied to data from a two-channel expression microarray assay. OTHER: Adjusted from MGED Ontology loess scale group transformation two-channel loess scale group transformation two-channel hepatocyte hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. GROUP: Role branch supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. supernatant role supernatant role OBI Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia Lachancea kluyveri Lachancea kluyveri Ehrhartoideae Ehrhartoideae Coprinopsis cinerea Coprinopsis cinerea The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> electrical conductivity detector electrical conductivity detector Pleuronectiformes Pleuronectiformes Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant adjuvent role Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response. Vaccine Ontology, Wikipedia, OBI adjuvent role GROUP: Role branch 11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'. Pyretophorus Pyretophorus diagnosis textual entity diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Jennifer Fostel revisit? PERSON:Alan Ruttenberg OBI branch derived adverse event trigger adverse event trigger CD3 subunit with immunoglobulin domain CD3 subunit with immunoglobulin domain 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. Asteraceae Asteraceae cell lysis cell lysis BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41. adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. Philippe Rocca-Serra mode calculation Monnie McGee PERSON: James Malone A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. James Malone PERSON: Monnie McGee mode calculation Cyprininae Cyprininae Endopterygota Endopterygota Tylenchoidea Tylenchoidea Ixoroideae Ixoroideae Role Branch dropout role Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. dropout role OBI Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study) Protacanthopterygii Protacanthopterygii Solanum lycopersicum Solanum lycopersicum Oryza sativa (indica cultivar-group) Oryza sativa (indica cultivar-group) Metazoa Metazoa A material separation where blood is taken from an organism. IEDB blood harvesting blood harvesting IEDB http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 FACSvantage at TSRI Flow Cytometry Core Facility FACSvantage FACSvantage The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. John Quinn Drosophila pseudoobscura Drosophila pseudoobscura Rubrivivax gelatinosus Rubrivivax gelatinosus PERSON:Daniel Schober A chromatography device where the column cartridge is inserted into and stabilised. GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 column cartridger column cartridger Filobasidiales Filobasidiales is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP intraperitoneal injection intraperitoneal injection 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 avalanche photodiode avalanche photodiode Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand. C30644E - InGaAs Avalanche Photodiode John Quinn GROUP:IEDB PERSON: Philippe Rocca-Serra transgenic organism PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162 transgenic organism PERSON: Bjoern Peters Lolium perenne Lolium perenne http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 Bruker CryoProbe Bruker CryoProbe 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: Significant S/N gains (with moderately salty samples also) Short pulse widths Short ring down times Linear behavior in power response Gradient capability CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher All high resolution probes have a lock circuit All high resolution probes have Z-gradient. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober BP purification objective The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest PERSON:Bjoern Peters isolation objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. purification objective error corrected data set error corrected data set PERSON: Monnie McGee PERSON: James Malone An error corrected data set is a data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). The objective to obtain multiple aliquots of an enzyme preparation. is the objective to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective portioning objective Lactobacillus gasseri Lactobacillus gasseri Dictyostelium discoideum Dictyostelium discoideum Philippe Rocca-Serra k-means clustering James Malone A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). Elisabetta Manduchi k-means clustering WEB: http://en.wikipedia.org/wiki/K-means 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 James Malone partial least square discriminant analysis PLS-DA 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. WEB: http://www.camo.com/rt/Resources/pls-da.html partial least square discriminant analysis Paracanthopterygii Paracanthopterygii platelet activating factor production platelet activating factor production The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels. article-without-pmid-or-doi:CDISCglossary eSource document an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures eSource document person:Jennifer Fostel Metatheria Metatheria any protocol resulting in information on the 3-dimensional qualities of a biomaterial The use of NMR Spectroscopy to determine the 3D-Structure of the binding of an epitope to an MHC molecule PERSON:Kevin Clancy structure assay OBI branch derived structure assay Protostomia Protostomia Bacteria Bacteria Antirrhineae Antirrhineae A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. platform OBI Instrument branch OBI Instrument branch platform Solanoideae Solanoideae 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 A physical entity quality which exists in relation towards some other entity. quality of related physical entities quality of related physical entities Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 proportion of expected false positives correction method proportion of expected false positives correction method A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. Monnie McGee PEFP correction method Magnaporthe grisea Magnaporthe grisea Schistosoma mansoni Schistosoma mansoni IEDB IEDB T cell epitope ELISA IL-10 assay A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ELISA methodology. T cell epitope ELISA IL-10 assay Brucellaceae Brucellaceae Pinus [NCBITaxon:139271] Pinus [NCBITaxon:139271] Corynebacterium glutamicum ATCC 13032 Corynebacterium glutamicum ATCC 13032 Coffea Coffea IEDB A T cell epitope specific cytokine production assay that measures production of IL-1b by T cells utilizing the ELISA methodology. IEDB T cell epitope ELISA IL-1b assay T cell epitope ELISA IL-1b assay Aspergillus fumigatus Aspergillus fumigatus Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. podzol podzol Trypanosomatidae Trypanosomatidae Paxillus involutus Paxillus involutus isocratic pump system isocratic pump system A pump system optimized for isocratic chromatography. WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 PERSON:Daniel Schober he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm OBI responsible party role responsible party role A responsible party role is a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Jennifer Fostel interleukin-11 production interleukin-11 production The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Festuca rubra subsp. fallax Festuca rubra subsp. fallax A cell line derived from mouse dendritic cells. IEDB IEDB JAWS II cell culture JAWS II cell culture http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology Cannabaceae Cannabaceae OBI branch derived the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands a protocol application to repair damaged DNA molecules artificially induced DNA repair PlanAndPlannedProcess Branch artificially induced DNA repair Funariidae Funariidae BioSorter250 BioSorter250 John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter 250 at TSRI Flow Cytometry Core Facility A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. Tetraodon Tetraodon cell culture splitting The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. cell culture splitting PlanAndPlannedProcess Branch OBI branch derived Bordetella bronchiseptica Bordetella bronchiseptica Coronaviridae Coronaviridae Eutheria Eutheria Daniel Schober Frank Gibson A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. synthesizing function Melanie Courtot synthesizing function Bill Bug Geospiza conirostris Geospiza conirostris Mycoplasma genitalium Mycoplasma genitalium Philippe Rocca-Serra staining staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> open tubular column open tubular column An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. PERSON:Daniel Schober allotransplantation OBI branch derived is the transplantation of organs between members of the same species. PlanAndPlannedProcess Branch allotransplantation Orbiliaceae Orbiliaceae http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n Person:Alan Ruttenberg filled capsule filled capsule A pill in the form of a small rounded gelatinous container with medicine inside. Stolidobranchia Stolidobranchia PERSON:Daniel Schober carbon nanotube column carbon nanotube column http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. Sapindales Sapindales Philippe Rocca-Serra Elisabetta Manduchi linlog transformation A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. PMID: 16646782 linlog transformation This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. column compartment column compartment PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 GROUP:<http://msi-ontology.sourceforge.net> cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. cloning insert role PERSON:Alan Ruttenberg Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" GROUP: Role branch OBII and Wikipedia cloning insert role epithelium epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 Patient is a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch patient role OBI, CDISC Rickettsiales Rickettsiales Gastropoda Gastropoda Deinococcus Deinococcus Methanothermobacter Methanothermobacter protocol testing objective protocol testing objective Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. Jennifer Fostel GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. PERSON:Daniel Schober NMR sample tube NMR sample tube washing washing OBI-Branch PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. Philippe Rocca-Serra A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] group randomization group randomization 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 Aedes aegypti Aedes aegypti Oscillatoriales Oscillatoriales Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html reference substance role reference substance role OBI Jennifer Fostel a role inhering in a substance that is realized when characteristics or responses elicited by the substance are used for comparison or reference. Cryptopygus antarcticus Cryptopygus antarcticus A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. James Malone Helen Parkinson OTHER: Adjusted from MGED Ontology Melanie Courtot total intensity transformation single This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). Philippe Rocca-Serra Elisabetta Manduchi total intensity transformation single PERSON: James Malone class prediction data transformation class prediction data transformation James Malone supervised classification data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. Betaproteobacteria Betaproteobacteria a planned process that realizes the concretization of a study design branch derived study design execution study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. Schizosaccharomycetales Schizosaccharomycetales Dicondylia Dicondylia TRAIL production TRAIL production The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Mycoplasmatales Mycoplasmatales IEDB IEDB is an administration of an infectious agent to a host organism administration in vivo with infectious agent administration in vivo with infectious agent A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IL-6 release by T cells epitope specific IL-6 release by T cells Lamiales Lamiales Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. catalytic activity catalytic activity Bruker AMX series NMR instrument Bruker AMX series NMR instrument http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 PERSON:Daniel Schober WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. Funariaceae Funariaceae Mycoplasmataceae Mycoplasmataceae Euacanthopterygii Euacanthopterygii Bordetella pertussis Bordetella pertussis Crustacea Crustacea Cyprinidae Cyprinidae 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 yeast artificial chromosome vector YAC A yeast artificial chromosome vector is a DNA molecule that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences Kevin Clancy, Bjoern Peters this should be a child of 'chromosome' if we import that from another source yeast artificial chromosome vector background correction objective background correction objective James Malone Elisabetta Manduchi PERSON: 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. Methanococcoides Methanococcoides Physcomitrella patens Physcomitrella patens mass spectrometer Frank Gibson LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum Bjoern Peters Bjoern Peters specimen creation objective A specimen creation objective is to obtain and store a material entity for potential use as an input during an investigation specimen creation objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. Salmoniformes Salmoniformes Neisseria Neisseria A laser is the most common way to irradiate a cell in a flow cytometer. laser light amplification by the stimulated emission of radiation John Quinn laser http://en.wikipedia.org/wiki/Laser Daniel Schober A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. 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 Glires Glires Saline solution negative reference substance role Reference substance is a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response Jennifer Fostel negative reference substance role Pyuridae Pyuridae Sordariomycetes incertae sedis Sordariomycetes incertae sedis Euteleostei Euteleostei Ralstonia syzygii Ralstonia syzygii photodiode photodiode Avalanche photodiode http://cyto.mednet.ucla.edu/Protocols/flow.htm A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer. John Quinn Thermococcaceae Thermococcaceae Basommatophora Basommatophora Xenopodinae Xenopodinae Pongo pygmaeus Pongo pygmaeus PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. adapted from wordnet (wkipedia) Philippe Rocca-Serra a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results validation validation replicate design replicate design MO_885 Philippe Rocca-Serra on behalf of MO A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Pleuronichthys verticalis Pleuronichthys verticalis Planorbidae Planorbidae A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ICS methodology. T cell epitope intracellular cytokine staining (ICS) IL-2 assay IEDB IEDB T cell epitope intracellular cytokine staining (ICS) IL-2 assay peptide peptide Amide 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. Aquifex Aquifex BEP clade BEP clade Actinobacteridae Actinobacteridae Richard Scheuermann global modularity calculation global modularity calculation A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. PERSON: Richard Scheuermann Legionellales Legionellales A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. node shortest path identification node shortest path identification PERSON: Richard Scheuermann Richard Scheuermann Thermoprotei Thermoprotei unplanned occurrence effecting an investigation unplanned occurrence effecting an investigation Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used a process which is external in origin to the investigation that has an impact on the outcome. OBI PERSON: Bjoern Peters Enterococcus faecalis Enterococcus faecalis Selaginellaceae Selaginellaceae http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 An NMR console manufactured by tecmac. GROUP:<http://msi-ontology.sourceforge.net> tecmag NMR console tecmag NMR console PERSON:Daniel Schober http://en.wikipedia.org/wiki/Dichroic_filter A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. Cy3 Dichroic Filter dichroic filter dichroic filter John Quinn mass spectrometry PRIDE: PRIDE:0000027 Philippe Rocca-Serra This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically. mass spectrometry assay mass spectrometry assay Identification of Human Pituitary Growth Hormone Variants by Mass Spectrometry. Kohler M, Thomas A, Püschel K, Schänzer W, Thevis M. J Proteome Res. 2009 Jan 5. PMID: 19123788 Pan troglodytes Pan troglodytes Actinobacillus pleuropneumoniae Actinobacillus pleuropneumoniae Group 2 species Group 2 species Rubrobacteraceae Rubrobacteraceae material portioning a material processing in which the input substance is partitioned into a number of portions that are similar in composition. OBI branch derived pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock PERSON:Bjoern Peters apportioning aliquoting material portioning Streptophyta Streptophyta Chlamydiae (class) Chlamydiae (class) The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-7 production interleukin-7 production Medicago sativa Medicago sativa Festuca arundinacea Festuca arundinacea magic angle spinning rotor PERSON:Daniel Schober A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. magic angle spinning rotor WEB:<http://www.freepatentsonline.com/4352066.html> MAS rotor http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 a process which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. genotyping genotype profiling, SNP genotyping High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 Philippe Rocca-Serra OBI Biomaterial genotyping Rhizobium leguminosarum Rhizobium leguminosarum SomaScope Mark II Automatic Economical Josef Spidlen The SomaScope is an instrument to quantify somatic cells in milk. "http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10" SomaScope SomaScope Callitrichinae Callitrichinae Coelurosauria Coelurosauria GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 PERSON:Daniel Schober organic acid column organic acid column An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. cytokine production during immune response cytokine production during immune response The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. Xanthomonas Xanthomonas Ruminantia Ruminantia photomultiplier tube R9647 by manufactured by Hamamatsu photomultiplier tube John Quinn A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect. http://cyto.mednet.ucla.edu/Protocols/flow.htm nuclear magnetic resonance assay nuclear magnetic resonance assay A nuclear magnetic resonance assay is an assay used to identify the chemical structure of a compound or biological macromolecule. definition_source: www.nature.com/nrd/journal/v2/n5/glossary/nrd1086_glossary.html PlanAndPlannedProcess Branch OBI branch derived A quality of a nucleotide polymer that has no terminal nucleotide residues. circular circular data normalization objective PERSON: Helen Parkinson Helen Parkinson PERSON: James Malone data normalization objective PERSON: Elisabetta Manduchi A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. Elisabetta Manduchi James Malone Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. Feed role is a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 feed role OBI Jennifer Fostel feed role Schizosaccharomycetaceae Schizosaccharomycetaceae DNA sequencing by synthesis PERSON: Philippe Rocca-Serra PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25. is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. DNA sequencing by synthesis PERSON:Daniel Schober The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. GROUP:<http://msi-ontology.sourceforge.net> chart recorder chart recorder http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. Jennifer Fostel biological feature identification objective Jennifer Fostel notified body role The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB. OBI, CDISC notified body role Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive NMR probe NMR probe Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency. alt The instrument that transmits and receives radiofrequency to and from the NMR sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014 Vaccination is: an ‘administering substance in vivo’ that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intend to invoke a protective immune response. vaccination vaccination An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121 chromatography detector filter chromatography detector filter Caenorhabditis briggsae Caenorhabditis briggsae epitope specific T cell proliferation epitope specific T cell proliferation IEDB A biological process where T cells proliferate resulting from the recognition of a T cell epitope. IEDB Kinetoplastida Kinetoplastida PlanAndPlannedProcess Branch sample preparation for assay study Nutrigenomics 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. Agrotis ipsilon Agrotis ipsilon are we happy calling collection of urine a material separation? is a portion of urine collected from an organism urine specimen urine specimen This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active Triticum aestivum Triticum aestivum feature extraction objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. feature extraction objective James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction Elisabetta Manduchi Taeniopygia guttata Taeniopygia guttata Trish Whetzel hybridization station MO An instrument which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. Labnet Problot12 hybridization station http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 FPD WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. flame photometric detector PERSON:Daniel Schober flame photometric detector pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.. OBI pellet role centrifuge pellet role Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet GROUP: Role branch centrifuge pellet role interleukin-18 production interleukin-18 production The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. canonical variate analysis canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. CVA WEB: http://en.wikipedia.org/wiki/Canonical_analysis Tina Hernandez-Boussard canonical variate analysis Inert pill shaped like aspirin tablet Jennifer Fostel blinded medication role blinded medication role similarity calculation similarity calculation Elisabetta Manduchi A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. PERSON: Elisabetta Manduchi GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 tecmag NMR instrument tecmag NMR instrument PERSON:Daniel Schober An NMR instrument that is manufactured by tecmag. Deinococcus-Thermus Deinococcus-Thermus Trypanosoma Trypanosoma Pleuronichthys Pleuronichthys OBI branch derived genetic transformation genetic transformation the introduction. alteration or integration of genetic material into a cell or organism PERSON:Kevin Clancy The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 Aculeata Aculeata Paracoccidioides brasiliensis Paracoccidioides brasiliensis Glycine max Glycine max 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 Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and quantitative subgraph degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. PERSON: Richard Scheuermann Richard Scheuermann quantitative subgraph degree calculation Deltaproteobacteria Deltaproteobacteria Euryarchaeota Euryarchaeota Populus tomentosa Populus tomentosa CyFlow Space CyFlow Space http://www.partec.de/products/cyflowspace.html John Quinn A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research. CyFlow Space at TSRI Flow Cytometry Core Facility Trifolium Trifolium Corticiaceae Corticiaceae IEDB IEDB PBMC cell culture PBMC cell culture A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types). Melanie Courtot http://en.wikipedia.org/wiki/Ionization The ion source in amass spectrometer Daniel Schober ionization function An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. ionization function Bill Bug Frank Gibson MO heating block heating block An instrument used to heat and/or maintain material at a set temperature. Daniel Schober A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay PERSON: Helen Parkinson A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient to be treated with active ingredient role to be treated with active ingredient role Person:Alan Ruttenberg Role of a patient in a group treated with an active substance in a clinical trial Anaplasma Anaplasma Bos Bos Penaeus monodon Penaeus monodon A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience. adaptive immune effector function adaptive immune effector function IEDB IEDB Felis catus Felis catus Betulaceae Betulaceae A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> PERSON:Daniel Schober chromatofocusing column chromatofocusing column Euacanthomorpha Euacanthomorpha light emission function Daniel Schober Frank Gibson Bill Bug A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Melanie Courtot light emission function Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 Jennifer Fostel regulator role OBI regulator role Regulator role is a regulatory role involved with making and/or enforcing relevant legislation and governmental orders a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors transcription factor binding site identification 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 PERSON: Bjoern Peters a cell derived from a multicellular organism that has the potential to replicate indefinitely a single Hela cell immortal cell immortal cell GROUP: OBI Biomaterial Branch PPPB branch material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. material separation objective PPPB branch is an objective to transform a material entity into spatially separated components. Phaseoleae Phaseoleae PERSON: Frank Gibson PERSON: Daniel Schober PERSON: Melanie Courtot Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. consume data function consume data function is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. library construction PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. Philippe Rocca-Serra library preparation library preparation An NMR instrument that is manufactured by Varian. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234 Varian NMR instrument Varian NMR instrument target of material addition 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. A cell culture into which a mixture of peptides is being added. IEDB A material entity into which another is being added in a material combinatino process target of material addition Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. person:Chris Stoeckert group:OBI gene list gene list A gene list is a report of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. Xanthomonas campestris