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 Xanthomonas campestris PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 An NMR instrument that is manufactured by Bruker. Bruker NMR instrument Bruker NMR instrument GROUP:<http://msi-ontology.sourceforge.net> Sulfolobaceae Sulfolobaceae Leishmania infantum Leishmania infantum T cell epitope ELISA GM-CSF assay T cell epitope ELISA GM-CSF assay IEDB IEDB A T cell epitope specific cytokine production assay that measures production of GM-CSF by T cells utilizing the ELISA methodology. a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material PlanAndPlannedProcess Branch The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells specific labeling OBI branch derived specific labeling carrier role carrier role IEDB IEDB The role any object plays by being bound to or utilized as a vehicle for delivery of any object playing the role of immunogen or assay antigen. gene expression gene expression The process by which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. An assay with the objective to determine interactions between proteins, such as protein-protein binding. 20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays. protein-protein interaction detection protein-protein interaction detection factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. Philippe Rocca-Serra http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) factorial design factorial design 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. Pteridaceae Pteridaceae Clostridia Clostridia Bartonellaceae Bartonellaceae the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. PERSON:Kevin Clancy labeling labeling OBI branch derived Melanie Courtot centrifuge Eppendorf Multipurpose Centrifuge A centrifuge is an instrument, generally driven by a motor, that puts an object in rotation around a fixed axis, applying force perpendicular to the axis. The centrifuge works using the sedimentation principle, where the centripetal acceleration is used to separate substances of greater and lesser density. http://en.wikipedia.org/wiki/Centrifuge Trish Whetzel centrifuge polynomial transformation polynomial transformation Elisabetta Manduchi a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. WEB: http://mathworld.wolfram.com/Polynomial.html A reduced dimension data set is a data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. reduced dimension data set reduced dimension data set PERSON: Monnie McGee PERSON: James Malone 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. Philippe Rocca-Serra http://www.unionbio.com/products/BioSorter.html BioSorter 500 at TSRI Flow Cytometry Core Facility BioSorter500 BioSorter500 John Quinn A BioSorter500 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 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length. Thiotrichales Thiotrichales type I interferon production type I interferon production The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. Polytrichum juniperinum Polytrichum juniperinum Actinopteri Actinopteri Hordeum Hordeum Novosphingobium Novosphingobium Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. organism feature identification objective Jennifer Fostel organism feature identification objective Luminex 200 Luminex 200 John Quinn A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation http://www.luminexcorp.com/support/faqs.html Bordetella Bordetella Chlamydiaceae Chlamydiaceae Ovis Ovis Phodopus sungorus Phodopus sungorus Neolepidoptera Neolepidoptera Aquificae Aquificae A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 WEB:<http://www.chromatography-online.org/topics/vacuum.html> vacuum degasser vacuum degasser PERSON:Daniel Schober OBI branch derived transplantation transplantation a protocol application to replace an organ or tissue of an organism PlanAndPlannedProcess Branch Jessica Turner, NIF, Dirk Derom, OBI The process of measuring neural activity in the caudate nucleus measuring neural activity in the caudate nucleus Helen Parkinson measuring neural activity in the caudate nucleus An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus Biomphalaria Biomphalaria http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 GROUP:<http://msi-ontology.sourceforge.net> An NMR probe designed to allow the direct detection of acquisition nuclei. PERSON:Daniel Schober direct detection NMR probe direct detection NMR probe Pulmonata Pulmonata Picea Picea James Malone Monnie McGee A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. background corrected data visualization background corrected data visualization Streptophytina Streptophytina Coffeeae Coffeeae WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187 An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. Bruker UltraShield NMR magnet Bruker UltraShield NMR magnet PERSON:Daniel Schober For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. Bruker micro imaging probe Bruker micro imaging probe PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/probes_microimaging.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. PERSON:Daniel Schober nitrogen phosphorous detector nitrogen phosphorous detector WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 Panicoideae Panicoideae asphyxiation asphyxiation asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms. PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570- OBI branch Philippe Rocca-Serra image acquisition function image acquisition function An image acquisition function is a function to acquire an image of a material Frank Gibson Rhizobiales Rhizobiales John Quinn http://en.wikipedia.org/wiki/Flow_cytometer FACS Calibur A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. flow cytometer flow cytometer Moraxellaceae Moraxellaceae Thlaspi caerulescens Thlaspi caerulescens decapitated organism OBI Biomaterial 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 Rickettsiaceae Rickettsiaceae 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 Chlamydiae/Verrucomicrobia group Chlamydiae/Verrucomicrobia group complete linkage hierarchical clustering PERSON: Elisabetta Manduchi A complete linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. Elisabetta Manduchi complete linkage hierarchical clustering indirect detection probe indirect detection probe GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober An NMR probe designed to allow the indirect detection of acquisition nuclei. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 Chlamydomonas Chlamydomonas Philippe Rocca-Serra dissolved material entity dissolved material entity 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. organization PERSON: Philippe Rocca-Serra GROUP: OBI BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Bjoern Peters PERSON: Alan Ruttenberg PERSON: Susanna Sansone PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. organization Populus tremula Populus tremula James Malone Ryan Brinkman The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model. logit-log curve fitting logit-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively. ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 Elisabetta Manduchi Melanie Courtot A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. 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. 293-T cell culture 293-T cell culture http://www.biotech.ist.unige.it/cldb/cl5008.html IEDB IEDB Phyllobacteriaceae Phyllobacteriaceae Body substance Body substance Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. Examples: saliva, semen, cerebrospinal fluid, inhaled air, urine, feces, blood, plasma, lymph. is a material entity bearing the epitope role epitope epitope IEDB IEDB Thermoplasmataceae Thermoplasmataceae IEDB A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope. epitope specific GM-CSF release by T cells epitope specific GM-CSF release by T cells IEDB 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 Magnaporthe Magnaporthe ssRNA positive-strand viruses, no DNA stage ssRNA positive-strand viruses, no DNA stage 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 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 A data transformation is a process which produces output data from input data James Malone Helen Parkinson Philippe Rocca-Serra Melanie Courtot Branch editors The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. data processing data analysis Richard Scheuermann Ryan Brinkman data transformation Tina Hernandez-Boussard Elisabetta Manduchi data transformation antibody An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. immunoglobulin complex, circulating immunoglobulin complex, circulating tritiated thymidine tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.. PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81 DNA Subtraction OBI-Branch Philippe Rocca-Serra DNA Subtraction DNA subtraction is a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. Geospiza difficilis Geospiza difficilis Trichoderma reesei QM6a Trichoderma reesei QM6a Theria Theria differential expression analysis data transformation Melanie Courtot A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of WEB: Monnie McGee James Malone differential expression analysis data transformation Mycoplasma pneumoniae Mycoplasma pneumoniae An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster. average linkage hierarchical clustering PERSON: Elisabetta Manduchi Elisabetta Manduchi average linkage hierarchical clustering Elisabetta Manduchi PERSON: Elisabetta Manduchi An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. euclidean distance calculation euclidean distance calculation Equus subg. Equus Equus subg. Equus Salmonidae Salmonidae multispectral imaging flow cytometer multispectral imaging flow cytometer A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. http://www.amnis.com/ Melanie Courtot MIFC Streptomycetaceae Streptomycetaceae Person:Alan Ruttenberg fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation test substance role test substance role Group:OBI Candida dubliniensis Candida dubliniensis IEDB epitope specific IL-12 release by T cells epitope specific IL-12 release by T cells A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope. IEDB Cercopithecidae Cercopithecidae IEDB A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ELISPOT methodology. T cell epitope ELISPOT TNF assay T cell epitope ELISPOT TNF assay IEDB 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 Thermoproteus tenax Thermoproteus tenax expectation maximization expectation maximization James Malone PERSON: James Malone EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. Leishmania braziliensis Leishmania braziliensis Tetrapoda Tetrapoda GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 A gas chromatography device that can auto-inject a small number of samples an inlet. auto injector auto injector PERSON:Daniel Schober Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification Device_setting inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device device setting device setting PERSON: Frank Gibson Actinopterygii Actinopterygii optical filter An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. 720 LP filter, 580/30 BP filter optical filter http://en.wikipedia.org/wiki/Optical_filter John Quinn Anopheles gambiae Anopheles gambiae Methanosarcina Methanosarcina canis group canis group eurosids I eurosids I 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 Xenopus Xenopus signal amplification function Daniel Schober A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. signal amplification function Frank Gibson Bill Bug Melanie Courtot Caenorhabditis Caenorhabditis Moorella thermoacetica Moorella thermoacetica The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-6 production interleukin-6 production Pongo Pongo number of lost events electronic A number of lost events electronic is a datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. number of lost events electronic 74, 0, 14 events lost due to data acquisition electronic coincidence. person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt Regulation-assigned role is a regulatory role defined by legislation or governmental orders Jennifer Fostel regulation-assigned role regulation-assigned role Approval letter Glycine Glycine A cloning vector role is a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. cloning vector role cloning vector role 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 Zea Zea Sauropsida Sauropsida PRS to do 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 An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. OBI branch derived imaging assay imaging assay PlanAndPlannedProcess Branch Phlebobranchia Phlebobranchia Staphylococcus aureus Staphylococcus aureus Heliantheae Heliantheae Malpighiales Malpighiales IEDB T cell epitope ELISA IL-2 assay A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ELISA methodology. IEDB T cell epitope ELISA IL-2 assay Decapoda Decapoda PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 GROUP:<http://msi-ontology.sourceforge.net> A Bruker autosampler is an autosampler made by Bruker. Bruker autosampler Bruker autosampler Eurypterygii Eurypterygii Xenopus [NCBITaxon:262014] Xenopus [NCBITaxon:262014] Alcaligenaceae Alcaligenaceae Richard Scheuermann subgraph in-degree calculation PERSON: Richard Scheuermann subgraph in-degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. Helen Parkinson Benjamini and Hochberg false discovery rate correction method A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) Benjamini and Hochberg false discovery rate correction method Helen Parkinson Frank Gibson Fliter paper is a device manufacture with the intent to provide a porous unsized paper used for filtering. filter paper filter paper sep:00107 Platyhelminthes Platyhelminthes The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. hepatocyte growth factor production hepatocyte growth factor production Rubus idaeus Rubus idaeus Streptomyces coelicolor Streptomyces coelicolor recombinant plasmid A recombinant plasmid is a plasmid in which extraneous DNA has been inserted. recombinant plasmid PERSON: Bjoern Peters PERSON: Melanie Courtot GROUP: OBI Biomaterial Branch PERSON: Kevin Clancy An acyl sulfate that has formula C10H14N5O10PS. 5'-adenylyl sulfate 5'-adenylyl sulfate biological_process biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. PERSON: James Malone dimensionality reduction Melanie Courtot data projection PERSON: Melanie Courtot dimensionality reduction Elisabetta Manduchi A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. PERSON: Elisabetta Manduchi Philippe Rocca-Serra James Malone Polytrichaceae Polytrichaceae collecting specimen from organism PERSON:Bjoern Peters IEDB collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation GROUP:<http://msi-ontology.sourceforge.net> An NMR instrument that is manufactured by JEOL. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 PERSON:Daniel Schober JEOL NMR instrument JEOL NMR instrument Haemophilus Haemophilus An IFN-g ELISPOT is an assay detecting ifn-gamma production assay detecting ifn-gamma production PERSON: Bjoern Peters an assay that determines information about the production of the cytokine interferon gamma IEDB assay detecting ifn-gamma production tail probability for the proportion of false positives correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 TPPFP correction method Monnie McGee tail probability for the proportion of false positives correction method A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. Felinae Felinae GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. PERSON:Daniel Schober anion trap column anion trap column Sparus aurata Sparus aurata Jennifer Fostel pathologist role pathologist role Pathologist is a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline Lactobacillus Lactobacillus Listeria innocua Listeria innocua PERSON: Daniel Schober PERSON:Frank Gibson A glucometer measures blood glucose concentration, the glucometer has a measure function. PERSON: Melanie Courtot measure function Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. PERSON: Helen Parkinson measure function restriction enzyme Kevin Clancy, Bjoern Peters restriction enzyme A restriction enzyme is an enzyme that has a specific target cleavage sites within nucleic acids The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG T cell epitope specific proliferation assay T cell epitope specific proliferation assay IEDB IEDB Any assay that measures the proliferation of a T cell that occurs in response to TCR on that T cell binding an epitope:MHC complex. Pseudomonas putida group Pseudomonas putida group Chlorophyta Chlorophyta Thermoplasmata Thermoplasmata Caulobacter Caulobacter Cyprinus Cyprinus OBI branch derived waiting waiting not actively doing anything to a material for a duration of time. PERSON:Alan Ruttenberg Saccharomycetales Saccharomycetales Loteae Loteae Ryan Brinkman PERSON: Ryan Brinkman SVM support vector machine A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. support vector machine James Malone AB SOLiD System PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. Applied Biosystems is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation AB SOLiD System Philippe Rocca-Serra Philippe Rocca-Serra Applied Biosystems Applied Biosystems manufacturer role of applied biosystems manufacturer role of applied biosystems a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge OBI branch derived PERSON:Kevin Clancy Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change. electrophoresis electrophoresis injection into organ section injection into organ section core eudicotyledons core eudicotyledons A physical object quality which inheres in a single-bearer. quality of a single physical entity quality of a single physical entity background corrected data set background corrected data set A background corrected data set is a data set that is produced as the output of a background correction data transformation. PERSON: Melanie Courtot PERSON: James Malone Spirurida Spirurida A monadic quality of continuant inhering in an organism by virtue of its ability to undergo sexual reproduction in order to differentiate the individuals or types involved. An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. biological sex biological sex Mycobacterium Mycobacterium PERSON: Richard Scheuermann subgraph out-degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. Richard Scheuermann subgraph out-degree calculation Bruker high resolution probe http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 HR Probe PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. defprov: Bruker website Bruker high resolution probe PERSON: James Malone gas chromatography mass spectrometry gas chromatography mass spectrometry Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds. PERSON: Tina Boussard PERSON: Tina Boussard Cryptosporidium parvum Cryptosporidium parvum Saccharomyces bayanus Saccharomyces bayanus A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization clustered data visualization interleukin-14 production interleukin-14 production The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. excitation function excitation function Bill Bug Melanie Courtot Daniel Schober Frank Gibson 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. Jennifer Fostel protocol optimization protocol optimization 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 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 Enzyme-linked immunosorbent spot assay ELISPOT assay IEDB Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. ELISPOT assay ELISPOT IEDB An assay in which the number of cells producing a material in a larger cell population are stained and counted. This is done by visualizing and counting the number of spots present on a surface via an antibody specific for the produced material. Each spot represents one cell producing the material of interest. 2/26/09: RESOLVE: we need to specify the produced substance that is desired to be detected. Analyte does not work, as this is not a concentration, and this is not present at the start of the assay. Aphyllophorales Aphyllophorales This type of transformation is typically used in flow cytometry split-scale transformation A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. Joseph Spliden Ryan Brinkman split-scale transformation WEB: http://flowcyt.sourceforge.net/gating/latest.pdf Elisabetta Manduchi John Quinn A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications. FACS Scan FACS Scan http://www.brc.ubc.ca/brc/facs.html PERSON: James Malone decision tree building data transformation decision tree building data transformation James Malone A decision tree building data transformation is a data transformation that has objective decision tree induction. Andropogoneae Andropogoneae person:Melanie Courtot group:OBI plasmid plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 Schistosomatoidea Schistosomatoidea Bacillales Bacillales Oxalobacteraceae Oxalobacteraceae A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma. The principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, the rate of Factor Xa inhibition is directly proportional to the Heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the Heparin concentration. 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 spectrolyse heparin antifactor-Xa assay WEB:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). spectrolyse heparin antifactor-Xa assay Person:Alan Ruttenberg Heterobasidiomycetes Heterobasidiomycetes pa_branch (Alan, Randi, Kevin, Jay, Bjoern) recombinant vector cloning recombinant vector cloning is a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material recombinant vector cloning OBI branch derived molecular cloning Gnathostomata Gnathostomata Staphylococcus aureus subsp. aureus MSSA476 Staphylococcus aureus subsp. aureus MSSA476 clinical chemistry assay Philippe Rocca-Serra 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 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 clinical chemistry assay is 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. Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. molecular_function molecular_function PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 washing system/NMR tube washing system, XPS: device has function washing NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> Bruker AutoClean system Bruker AutoClean system phagocytophilum group phagocytophilum group Frank Gibson An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy energy supply function energy supply function Cryptosporidiidae Cryptosporidiidae boostrapping Helen Parkinson boostrapping Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. Arthropoda Arthropoda An Adapter that enabled the connection of a column to additional devices. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober column adapter column adapter http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. PERSON:Daniel Schober WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227 JEOL ECX NMR spectrometer JEOL ECX NMR spectrometer Streptococcus agalactiae Streptococcus agalactiae Note: 'cloning vector role' is really a function. Should be dealt with globally cloning plasmid cloning plasmid A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. gram gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. Geobacter metallireducens Geobacter metallireducens type III interferon production type III interferon production The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type III interferons are members of the interferon-lambda gene family. Leishmania major species complex Leishmania major species complex Bjoern Peters An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes animal care protocol animal care protocol Bjoern Peters Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. regulatory role Regulatory role is a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. OBI, CDISC regulatory role GROUP: Role branch Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 Polytrichum Polytrichum electrocution electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process. OBI branch PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376. Philippe Rocca-Serra electrocution Isoetopsida Isoetopsida An arrayer is an instrument which deposits biological material onto a substrate in a defined pattern. MO arrayer Trish Whetzel BioRobotics Microgrid II TAS, Affymetrix GMS 417 arrayer Fusobacteria Fusobacteria Tylenchina Tylenchina is the transplantation of tissue from one part of the body to another in the same individual. ) PlanAndPlannedProcess Branch autotransplantation OBI branch derived autotransplantation OBI Jennifer Fostel A regulator of chemical manufacture is a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture role of regulator of chemical manufacturer role of regulator of chemical manufacturer EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group inclusion rule PMID: 17599746-RESULTS: Fifteen trials met our inclusion criteria. The summary effect size was 0.35 (95% confidence interval 0.14, 0.56). I(2) was 0.80. inclusion rule an inclusion rule (criterion) is_ rule* in a protocol that prospective subjects must meet to be eligible for participation in a study PRS Spermatophyta Spermatophyta Saccharomycotina Saccharomycotina Drosophila Drosophila Biomphalaria glabrata Biomphalaria glabrata A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific IFN-g release by T cells epitope specific IFN-g release by T cells Yersinia pestis Yersinia pestis Methylophilales Methylophilales Caniformia Caniformia A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). Monnie McGee QPFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 quantile proportion of false positives correction method quantile proportion of false positives correction method The Supernatant Collection system is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. Daniel Schober google supernatant collection system harvesting frame supernatant collection system harvesting frame Macropodidae Macropodidae Bartonella grahamii Bartonella grahamii Lotus japonicus Lotus japonicus A person or organization that has a manufacturer role manufacturer manufacturer 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over 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 Person:Alan Ruttenberg fibroblast fibroblast A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. CD4-/CD8- T cell culture CD4-/CD8- T cell culture IEDB IEDB A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. Apis mellifera Apis mellifera Berichrom(r) Antithrombin III (A) Kit Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution Person:Alan Ruttenberg WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06 A ribosome is a protein complex protein complex protein complex Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups. A magnet which induces a certain frequency (MHz) and which has a certain bore diameter. alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. NMR magnet NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> Leymus triticoides Leymus triticoides A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. T cell T cell OBI branch derived The use of a protease to digest a protein into peptides specific enzymatic cleavage specific enzymatic cleavage a protocol application to digest the fraction of input material that is susceptible to that enzyme PERSON:Kevin Clancy Chloroflexi (class) Chloroflexi (class) IEDB T cell epitope ELISA IL-13 assay IEDB T cell epitope ELISA IL-13 assay A T cell epitope specific cytokine production assay that measures production of IL-13 by T cells utilizing the ELISA methodology. amino acids amino acids Carboxylic acids containing one or more amino groups. sodium citrate dihydrate sodium citrate dihydrate Enterococcus Enterococcus Pezizomycotina Pezizomycotina Helen Parkinson moving average Philippe Rocca-Serra PERSON: Helen Parkinson Elisabetta Manduchi A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. PERSON: Elisabetta Manduchi moving average The moving average is often used to handle data from tiling arrays. Methylobacillus Methylobacillus interleukin-20 production interleukin-20 production The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. 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 recombinant phage cloning http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 recombinant phage cloning Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. Helen Parkinson Insert selection by BamHI methyltransferase protection in P1 phage-based cloning http://www.biotech.ist.unige.it/cldb/cl3075.html IEDB L cell culture A cell line derived from mouse fibroblasts. L cell culture IEDB Penaeidae Penaeidae This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. branch derived The plan of researcher X to perform an experiment according to a protocol. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. plan plan AR, BP, JM, MC, PRS Veillonella parvula Veillonella parvula 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 glucose glucose DNA transfection DNA transfection is a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell PERSON:Kevin Clancy DNA transfection The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest OBI branch derived adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation centrifugation centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. Philippe Rocca-Serra Xanthomonadaceae Xanthomonadaceae The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. PERSON:Daniel Schober Bruker B-ACS system Bruker B-ACS system WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 Thermoanaerobacter Thermoanaerobacter PERSON:Daniel Schober y-column connector y-column connector A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 GROUP:<http://msi-ontology.sourceforge.net> 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 descriptive statistical calculation data transformation Triticum turgidum subsp. dicoccoides Triticum turgidum subsp. dicoccoides OBI-Branch enzymatic ligation An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity Philippe Rocca-Serra PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. enzymatic ligation Ehrlichia canis Ehrlichia canis average value average value An average value is a data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: Monnie McGee PERSON: James Malone Tetradontoidea Tetradontoidea Rubrivivax Rubrivivax Leishmania donovani species complex Leishmania donovani species complex ELISA Enzyme-Linked ImmunoSorbent Assay ELISA is an assay where an enzyme linked antibody is used to detect a plate bound material in a liquid (the evaluant) utilizing a chemiluminescent reaction. The detected signal is proxy for the concentration of an analyte in the evaluant. ELISA IEDB It is possible to add further restrictions, such as utilizing a plate as part of the assay. IEDB 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. Richard Scheuermann directed network graph construction directed network graph construction PERSON: Richard Scheuermann A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. ethylenediaminetetraacetic acid ethylenediaminetetraacetic acid A tetracarboxylic acid that has formula C10H16N2O8. A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> PERSON:Daniel Schober chromatography detector chromatography detector Arthropleona Arthropleona Sinorhizobium meliloti Sinorhizobium meliloti Pisum Pisum Aspergillus Aspergillus Philippe Rocca-Serra randomized group participant role randomized group participant role Strongyloides ratti Strongyloides ratti Aedes/Ochlerotatus group Aedes/Ochlerotatus group Methanosarcinaceae Methanosarcinaceae Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion Label role is a reagent role where the bearer is a material entity and which is realized in a detection of label assay need to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entity OBI label role Role Branch label role we need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1866458&amp;group_id=177891&amp;atid=886178 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 in-line filter in-line filter 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. PERSON:Daniel Schober measurement device A ruler, a microarray scanner, a Geiger counter. a processed material created to have the function to measure GROUP:OBI Philly workshop measurement device OBI HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. logarithmic voltage amplifier logarithmic voltage amplifier John Quinn bp created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. material combination material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. bp Chordata Chordata Pasteurella multocida Pasteurella multocida A T cell epitope specific cytokine production assay that measures production of IFNg by T cells utilizing the ELISA methodology. T cell epitope ELISA IFN-g assay T cell epitope ELISA IFN-g assay